diff options
Diffstat (limited to 'sci-biology')
86 files changed, 832 insertions, 1494 deletions
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest index 57f4fc569..cf724a82a 100644 --- a/sci-biology/SPAdes/Manifest +++ b/sci-biology/SPAdes/Manifest @@ -1,4 +1,4 @@ -DIST SPAdes-3.15.3.tar.gz 13687286 BLAKE2B d1c2204889ecd4e95306f10ca1bc4c1243369737822ba882ed141aa203005ce5240698b421e6f9c867684567abe971afb7562b837ad5464cfd91ce572d5e7af4 SHA512 e1b454c03f1edc857b552ebca9b5f4cd842d8e23caebdf11bb0cd05cb16a45e45421a03c67a5ecb04ea6dba0f30ec2652f0bf07afded39e823563518dc8080f4 -DIST SPAdes-3.15.3_manual.html 80507 BLAKE2B 14510ed5ff2ee1b7a6643f7e39761479180a022c6bae7b1bfac7a07fdf8d5f7889e619fc8bbd6c8354aa7b775241a34b0ab14aa6bf92c0b5af2d0e1588d5c4a7 SHA512 73538e487da7056b42715ec46dacd41e8abef0e268d3a4fe2997b49d208db402367913f3a86acd9643c8ff6a9cadd6d1ff109a2bc511ffb63de059633fe3255b -DIST SPAdes-3.15.3_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8 -DIST SPAdes-3.15.3_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd +DIST SPAdes-3.15.5.tar.gz 13692466 BLAKE2B c4fe59e6b253c91a6e409cf3c2e5a8181f3c0e93892e3b87f603aa75a6d025d5f1466a87ada5c86d6602f74de9048639e9b057d2abfbe449265f9c1796c608d1 SHA512 98b17f1ab0019a45e6abaf1bc7128a5edb5102120d50a47ddfbd5e30fc7130c7895a096cef16ba8e40be71c8a1f0feff38da54f02f9d2e62bd39d2d91a54f9bd +DIST SPAdes-3.15.5_manual.html 91156 BLAKE2B e5776ec98e972f52eb630cb2048f8cd12318f0cfc020ce464bbe72e14f3716b72199d5ea34f219351d79b3fd0f4201c99f68ca487edde0d258d8794aea1f4675 SHA512 b21cc705a1f3a224dad882fce26e15dfd6d249c46627172189b285584a11d2846d0fa3c4b5aa01ca6436a494cec552122cffd4b79f6cc31446a03d610486dfaa +DIST SPAdes-3.15.5_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8 +DIST SPAdes-3.15.5_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild index 002004bca..026dd0476 100644 --- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..12} ) inherit python-single-r1 DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" @@ -27,7 +27,13 @@ DEPEND=" ${PYTHON_DEPS} " RDEPEND="${DEPEND}" -BDEPEND="dev-util/cmake" +BDEPEND="dev-build/cmake" + +# Remove for next release: +# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831 +PATCHES=( + "${FILESDIR}/${P}-gcc13.patch" +) src_install(){ einstalldocs diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch new file mode 100644 index 000000000..3dd3f8c02 --- /dev/null +++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch @@ -0,0 +1,49 @@ +From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001 +From: Bo YU <tsu.yubo@gmail.com> +Date: Wed, 19 Jul 2023 18:42:04 +0800 +Subject: [PATCH] fix build issues due to gcc-13 + +Signed-off-by: Bo YU <tsu.yubo@gmail.com> +--- + ext/include/llvm/Support/Signals.h | 1 + + src/common/pipeline/library_data.hpp | 1 + + src/common/sequence/nucl.hpp | 2 ++ + 3 files changed, 4 insertions(+) + +diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h +index e0a18e72f..148216b8f 100644 +--- a/ext/include/llvm/Support/Signals.h ++++ b/ext/include/llvm/Support/Signals.h +@@ -14,6 +14,7 @@ + #ifndef LLVM_SUPPORT_SIGNALS_H + #define LLVM_SUPPORT_SIGNALS_H + ++#include <cstdint> + #include <string> + + namespace llvm { +diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp +index 3cbaf0adb..1ffaa7b37 100644 +--- a/src/common/pipeline/library_data.hpp ++++ b/src/common/pipeline/library_data.hpp +@@ -8,6 +8,7 @@ + + #include <map> + #include <string> ++#include <cstdint> + + // Forward decls for LLVM YAML API + namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } } +diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp +index 9c7d6de13..e10e7f583 100755 +--- a/src/common/sequence/nucl.hpp ++++ b/src/common/sequence/nucl.hpp +@@ -8,6 +8,8 @@ + #ifndef NUCL_HPP_ + #define NUCL_HPP_ + ++#include <cstdint> ++ + #include "utils/verify.hpp" + + /** diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml index 0845ad7a4..5f573393e 100644 --- a/sci-biology/SPAdes/metadata.xml +++ b/sci-biology/SPAdes/metadata.xml @@ -10,8 +10,11 @@ <name>Gentoo Biology Project</name> </maintainer> <longdescription> -truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. -hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. -dipspades is assembly module for highly polymorphic diploid genomes -</longdescription> + truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. + hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. + dipspades is assembly module for highly polymorphic diploid genomes + </longdescription> + <upstream> + <remote-id type="github">ablab/spades</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild index 49f2b6d9f..096349f5a 100644 --- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild +++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild @@ -16,7 +16,7 @@ KEYWORDS="~amd64" RDEPEND=" >=sci-biology/bioperl-1.4 >=sci-biology/velvet-0.7.5.1 - dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh + dev-lang/perl[perl_features_ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh src_install(){ dobin VelvetOptimiser.pl diff --git a/sci-biology/afni-datasets/Manifest b/sci-biology/afni-datasets/Manifest new file mode 100644 index 000000000..99d2de1a8 --- /dev/null +++ b/sci-biology/afni-datasets/Manifest @@ -0,0 +1 @@ +DIST afni-datasets-20240503.tar.gz 57863597 BLAKE2B 07508c1d7b7d162a8116887ead440e3dd728ec53c19eb5b6c6662dfcc7c51ed13b1e9fdce2289410c1225010329b6ab3f9917d45f48a906571ba9c83747470f4 SHA512 5636ab403335c0ed8b34c00d89b38344654cda783fd928af632dd72f7cb51803b35caa60bc0561b8a1684870670d2977f3471ef6083676db33f172b41adb47f5 diff --git a/sci-biology/afni-datasets/afni-datasets-20240503.ebuild b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild new file mode 100644 index 000000000..4d554a633 --- /dev/null +++ b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_P="afni_atlases_dist_2024_0503" + +DESCRIPTION="Datasets for using and testing sci-biology/afni" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI="https://afni.nimh.nih.gov/pub/dist/atlases/${MY_P}.tgz -> ${P}.tar.gz" + +S="${WORKDIR}/${MY_P}" +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_install() { + insinto /usr/share/${PN} + doins -r * +} diff --git a/sci-biology/afni-datasets/metadata.xml b/sci-biology/afni-datasets/metadata.xml new file mode 100644 index 000000000..cb6710311 --- /dev/null +++ b/sci-biology/afni-datasets/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest index e8caa43d1..cc0d96468 100644 --- a/sci-biology/afni/Manifest +++ b/sci-biology/afni/Manifest @@ -1,3 +1,6 @@ -DIST afni-20.1.16.tar.gz 43355499 BLAKE2B ad7750e64dd9f4c2ca7e5c67bd99faeb8595a41d8a16192e77202f3d307e912083affc11dcbb5da3530079b9e3cf3c2b6b470050f57d5d7af2bb35cc2322772f SHA512 e6fdb8baea6165865bae5bb186375bd65e862564c48470523a8fe026a12f00715fd21bd852bd77c4077ea444a97642c4c3d2ca8060640ba5ddd57bd7883901a6 -DIST afni-20.3.03.tar.gz 43263734 BLAKE2B 7fdaf3de874edff9b32950a2724ba8b4cbcdda538b09effb12658a042326d5c8badf48f1a4dfb4555eb069347099cf3cdb08c4fe1a12999e6eca3ca6f8dca639 SHA512 3c5007f59d6c46093d38f9419c72aa36fb5701314690811f757d9568561b386cf3cd602ddf910ae08fd071ea7ae1e51f5762081217f7a29b23e32f1490f5db65 -DIST afni-22.0.21.tar.gz 43934548 BLAKE2B 3efd5b7fcbbb7b98000e8de51c363ec936a691fcbd505871ff406824ba6ecd5fef358102f6dd2e4d0991b0a40589db6416c1ef14966138c5c36499d7efa3b089 SHA512 1c741e36227075bd8b4f9983510eef95528084cbc4971f9d6d028726ffc2bb211da7a74df98991538d8f6caed041633fdceb0c4366e04d6594faa0160a0e6d2b +DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6 +DIST afni-24.1.15.gh.tar.gz 53136605 BLAKE2B aab19b572b3d3f32e4d91414c127a8ef5cfd5cef04cb55836060298340c3d0e6cf0ec2f5f324590ce432e920842358007858a278198b37b47e6eeb8f318855b3 SHA512 ca8e3d26a32feea0118e4219c5915f8541bf5194f0db8e4b51637fb79a08c15d1772bc75499b71a47af5cac831bbd484efb3fce848d499f51ef002f9f52a6e10 +DIST afni-24.1.16.gh.tar.gz 53139168 BLAKE2B dff31b9b6e89cd2c62e2ab8cb1b7d1ed28e7bc3bbeb586ae7218ccc276237b0632d06c65928469560684871b8fd25dc382e5bdffcc4c5181c5b9855565398df8 SHA512 c507bc8d3bbad8b61daef3321e48bd88c2f020c940c61a7c3ff4dafe1d2823dad5c87b96080716ab6c59d5312b7fa33c8289426f3fcc4938d3ef049df54134b3 +DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2 +DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5 +DIST nifti-f24bec503f1a5d501c0413c1bb8aa3d6e04aebda.tar.gz 451555 BLAKE2B d83e8e265d996bb041fa7c712e4f67f6ab3c4e7e7b9713f5d5a0e045b11c2c5c34a193a0d6f69594d37ff1ac09bb295f9be6b04a7a29711cfad8d27167c15058 SHA512 8a4707edfd11112bdb0c359223bb39c6e1d9281234759ebf65bffe34b52a0530053b2e9368c36a77b788194113db5ac66ddf44204036983fffda3d81699e1d5b diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild deleted file mode 100644 index e3e16f834..000000000 --- a/sci-biology/afni/afni-20.1.16.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - eapply "${FILESDIR}/${P}-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild deleted file mode 100644 index 1d9043ebb..000000000 --- a/sci-biology/afni/afni-20.3.03.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild deleted file mode 100644 index 149deede8..000000000 --- a/sci-biology/afni/afni-22.0.21.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/${PN}-AFNI_${PV}/src" - -LICENSE="GPL-3+" -SLOT="0" -# SUMA error: https://ppb.chymera.eu/4223de.log -KEYWORDS="" - -RDEPEND=" - dev-libs/libf2c - dev-libs/expat - media-libs/freeglut - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif -" - -DEPEND="${RDEPEND} - app-shells/tcsh -" - -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count) - -src_prepare() { - # more easily applied here than via PATCHES at phase end. - eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + || die - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" || die - done -} diff --git a/sci-biology/afni/afni-24.0.08-r3.ebuild b/sci-biology/afni/afni-24.0.08-r3.ebuild new file mode 100644 index 000000000..12d6c8f87 --- /dev/null +++ b/sci-biology/afni/afni-24.0.08-r3.ebuild @@ -0,0 +1,125 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +S="${WORKDIR}/afni-AFNI_${PV}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-build/ninja + dev-libs/expat + dev-libs/glib:2 + dev-libs/libf2c + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-biology/afni-datasets + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm + + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die +src_prepare() { + tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die + tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die + cmake_src_prepare + default + } + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" + fi + # Fix AFNI version, no better way seemed to work + sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake + export CFLAGS="-pthread ${CFLAGS}" + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode + doenvd "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-biology/afni/afni-24.1.15.ebuild b/sci-biology/afni/afni-24.1.15.ebuild new file mode 100644 index 000000000..12d6c8f87 --- /dev/null +++ b/sci-biology/afni/afni-24.1.15.ebuild @@ -0,0 +1,125 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +S="${WORKDIR}/afni-AFNI_${PV}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-build/ninja + dev-libs/expat + dev-libs/glib:2 + dev-libs/libf2c + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-biology/afni-datasets + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm + + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die +src_prepare() { + tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die + tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die + cmake_src_prepare + default + } + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" + fi + # Fix AFNI version, no better way seemed to work + sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake + export CFLAGS="-pthread ${CFLAGS}" + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode + doenvd "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-biology/afni/afni-24.1.16.ebuild b/sci-biology/afni/afni-24.1.16.ebuild new file mode 100644 index 000000000..0759d30a0 --- /dev/null +++ b/sci-biology/afni/afni-24.1.16.ebuild @@ -0,0 +1,127 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="f24bec503f1a5d501c0413c1bb8aa3d6e04aebda" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +S="${WORKDIR}/afni-AFNI_${PV}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-build/ninja + dev-libs/expat + dev-libs/glib:2 + dev-libs/libf2c + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-biology/afni-datasets + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm + +PATCHES=("${FILESDIR}/afni-24.1.16-niftiio.patch") + + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die +src_prepare() { + # We need a name without the hash to reference in patches + mv "${WORKDIR}/nifti_clib-${NIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github" + mv "${WORKDIR}/gifti_clib-${GIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github" + cmake_src_prepare +} + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" + fi + # Fix AFNI version, no better way seemed to work + sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake + export CFLAGS="-pthread ${CFLAGS}" + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode + doenvd "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni new file mode 100644 index 000000000..dbf463f47 --- /dev/null +++ b/sci-biology/afni/files/97afni @@ -0,0 +1 @@ +export AFNI_ATLAS_PATH=/usr/share/afni-datasets diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch deleted file mode 100644 index 8c3e859f5..000000000 --- a/sci-biology/afni/files/afni-20.1.16-python.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400 -+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400 -@@ -11,8 +11,6 @@ - - # ------------------------------ - # python from C --IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7 --LDPYTHON = -lpython2.7 - - # ---------------------------------------------------------------------- - # X configuration diff --git a/sci-biology/afni/files/afni-24.0.04-whirlgif.patch b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch new file mode 100644 index 000000000..a357799e6 --- /dev/null +++ b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch @@ -0,0 +1,39 @@ +diff --git a/packaging/installation_components.txt b/packaging/installation_components.txt +index 127193338..ba8825a7b 100644 +--- a/packaging/installation_components.txt ++++ b/packaging/installation_components.txt +@@ -347,7 +347,6 @@ uniq_images, corebinaries + unu, corebinaries + waver, corebinaries + whereami, corebinaries +-whirlgif, corebinaries + 3dMax, tcsh + 3dPAR2AFNI.pl, tcsh + @1dDiffMag, tcsh +diff --git a/src/CMakeLists_binaries.txt b/src/CMakeLists_binaries.txt +index d53368390..8c8e9e1fb 100644 +--- a/src/CMakeLists_binaries.txt ++++ b/src/CMakeLists_binaries.txt +@@ -209,7 +209,6 @@ foreach( + uniq_images + unu + whereami +- whirlgif + ) + + add_afni_executable(${target} ${target}.c) +diff --git a/src/Makefile.INCLUDE b/src/Makefile.INCLUDE +index f44103def..7ac08a87d 100644 +--- a/src/Makefile.INCLUDE ++++ b/src/Makefile.INCLUDE +@@ -3495,11 +3495,6 @@ help_format:help_format.o + ibinom:ibinom.o + $(CC) -o ibinom ibinom.o $(LFLAGS) $(LLIBS) + +-## GIF animation +- +-whirlgif:whirlgif.h whirlgif.c +- $(CC) -o whirlgif whirlgif.c $(INFLAGS) $(LFLAGS) $(LLIBS) +- + extor.o:extor.c + $(CCFAST) -c extor.c $(INFLAGS) diff --git a/sci-biology/afni/files/afni-24.1.16-niftiio.patch b/sci-biology/afni/files/afni-24.1.16-niftiio.patch new file mode 100644 index 000000000..a4eb35435 --- /dev/null +++ b/sci-biology/afni/files/afni-24.1.16-niftiio.patch @@ -0,0 +1,27 @@ +From 05dbcd2659fa6177b221a2686300036e4ae435d6 Mon Sep 17 00:00:00 2001 +From: Yaroslav Halchenko <debian@onerussian.com> +Date: Mon, 3 Jun 2024 19:28:21 -0400 +Subject: [PATCH] Announce niftiio as PRIVATE for linking to prevent + propagating linking against it + +I am just a messanger from the cmake-wise @leej3 at +https://github.com/afni/afni/issues/639#issuecomment-2145703256 + +Supposedly closes #639 +--- + src/nifti/nifticdf/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/nifti/nifticdf/CMakeLists.txt b/src/nifti/nifticdf/CMakeLists.txt +index 473be7e3be..01b18a14d8 100644 +--- a/nifti_clib_from_github/nifticdf/CMakeLists.txt ++++ b/nifti_clib_from_github/nifticdf/CMakeLists.txt +@@ -8,7 +8,7 @@ set_target_properties( + "${CMAKE_CURRENT_LIST_DIR}/nifticdf.h" + ) + target_compile_options(${NIFTI_CDFLIB_NAME} PRIVATE "-D__COMPILE_UNUSED_FUNCTIONS__") +-target_link_libraries(${NIFTI_CDFLIB_NAME} PUBLIC ${NIFTI_PACKAGE_PREFIX}niftiio) ++target_link_libraries(${NIFTI_CDFLIB_NAME} PRIVATE ${NIFTI_PACKAGE_PREFIX}niftiio) + get_lib_version_vars("nifticdf_version.h" NIFTICDF_VERSION NIFTICDF_MAJOR_VERSION) + if(BUILD_SHARED_LIBS) + set_target_properties(${NIFTI_CDFLIB_NAME} diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml index cbb8a4299..39ec69d08 100644 --- a/sci-biology/afni/metadata.xml +++ b/sci-biology/afni/metadata.xml @@ -13,6 +13,9 @@ Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity. </longdescription> + <use> + <flag name="whirlgif">Build optional whirlgif binary</flag> + </use> <upstream> <remote-id type="github">afni/afni</remote-id> </upstream> diff --git a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch deleted file mode 100644 index bd7eecbcf..000000000 --- a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx -index d1e7586..048d934 100644 ---- a/Examples/PrintHeader.cxx -+++ b/Examples/PrintHeader.cxx -@@ -281,7 +281,7 @@ PrintHeader(int argc, char * argv[]) - // Get the metadata as a generic object - string key = itMeta->first, v_string; - itk::SpatialOrientation::ValidCoordinateOrientationFlags v_oflags = -- itk::SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_INVALID; -+ itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_INVALID; - - if (itk::ExposeMetaData<string>(mdd, key, v_string)) - { diff --git a/sci-biology/behaviopy/Manifest b/sci-biology/behaviopy/Manifest deleted file mode 100644 index 916b93320..000000000 --- a/sci-biology/behaviopy/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST behaviopy-0.2.tar.gz 36812 BLAKE2B 099f245027ddbbd38478bc48df1746e25e5a2b8d32a381f3352cb4c1339f9aa7a101ff0a3b797bceb543db1656044470911dd2e3addd44f5d2cd8d661e20a0cf SHA512 b7939ac3dcbbc445b5459a2bb96e413ca71e720c14e441d3d9864422be13c6b78178c5a1006f851d141c70a3f1ab9635ea636841610e0f210ca3f35a0f12f9bc diff --git a/sci-biology/behaviopy/behaviopy-0.2.ebuild b/sci-biology/behaviopy/behaviopy-0.2.ebuild deleted file mode 100644 index dc875e7a5..000000000 --- a/sci-biology/behaviopy/behaviopy-0.2.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_10 ) - -inherit distutils-r1 - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://github.com/TheChymera/behaviopy" -SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="evaluation" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/seaborn[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -python_prepare_all() { - if ! use evaluation; then - rm behaviopy/evaluation.py || die - fi - distutils-r1_python_prepare_all -} - -python_test() { - cd behaviopy/examples || die - echo "backend : Agg" > matplotlibrc || die - for i in *py; do - echo "Executing $i" - ${EPYTHON} $i || die - done -} diff --git a/sci-biology/behaviopy/metadata.xml b/sci-biology/behaviopy/metadata.xml deleted file mode 100644 index a33886a68..000000000 --- a/sci-biology/behaviopy/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - BehavioPy is a Python toolkit providing evaluation (e.g. event - tracking) and plotting functions for behavioural data. Manual event - tracking is done via a simple and configurable PsychoPy-based - interface. Plotting functions are designed to work with preformatted - data in CSV format (e.g. as exported by pandas), and use Seaborn and - custom BehavioPy styles for maximum beautification. - </longdescription> - <upstream> - <remote-id type="github">TheChymera/behaviopy</remote-id> - </upstream> - <use> - <flag name="evaluation">Installs evaluation submodule.</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest index 90147dff7..69572ef1e 100644 --- a/sci-biology/bx-python/Manifest +++ b/sci-biology/bx-python/Manifest @@ -1,2 +1 @@ -DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea -DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc +DIST bx-python-0.12.0.gh.tar.gz 1660806 BLAKE2B 0eddb9b9a93520319d275001067a3518015483605cf4d096729ec92e14c0eb35f2ceb34db964216dd3c6687351a7415c46061960b1f66a7564c90efeba3a587b SHA512 821b33841dd2935485669f6c112277d404475b1cd778deb3eaa1194f3b21594335a219d9345e279e7afc3adb1e347e71e60f0029712fc58e95d1e70f9e8fbb55 diff --git a/sci-biology/bx-python/bx-python-0.12.0.ebuild b/sci-biology/bx-python/bx-python-0.12.0.ebuild new file mode 100644 index 000000000..1a00b0395 --- /dev/null +++ b/sci-biology/bx-python/bx-python-0.12.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 + +DESCRIPTION="Library for rapid implementation of genome scale analyses" +HOMEPAGE="https://github.com/bxlab/bx-python" +SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# doctests have external deps +PATCHES=( + "${FILESDIR}/no-doctest.patch" +) + +distutils_enable_tests pytest + +# https://github.com/bxlab/bx-python/issues/101 +EPYTEST_DESELECT=( + lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo + lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer +) + +python_test() { + cd "${BUILD_DIR}/build" || die + ln -s "${S}/pytest.ini" . || die + ln -s "${S}/test_data" . || die + epytest +} diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild deleted file mode 100644 index 6cffba1be..000000000 --- a/sci-biology/bx-python/bx-python-0.8.9.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild deleted file mode 100644 index 6cffba1be..000000000 --- a/sci-biology/bx-python/bx-python-0.9.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild deleted file mode 100644 index b29975b58..000000000 --- a/sci-biology/bx-python/bx-python-9999.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 git-r3 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -EGIT_REPO_URI="https://github.com/bxlab/bx-python" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/files/no-doctest.patch b/sci-biology/bx-python/files/no-doctest.patch new file mode 100644 index 000000000..d0c2b2e62 --- /dev/null +++ b/sci-biology/bx-python/files/no-doctest.patch @@ -0,0 +1,9 @@ +diff --git a/pytest.ini b/pytest.ini +index e77e08f..4184247 100644 +--- a/pytest.ini ++++ b/pytest.ini +@@ -1,4 +1,3 @@ + [pytest] +-addopts = --doctest-cython --doctest-modules + python_files = *_tests.py + testpaths = lib script_tests/ diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index f1fc4360e..2ead27d78 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -5,10 +5,6 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> <upstream> <remote-id type="github">bxlab/bx-python</remote-id> <remote-id type="pypi">bx-python</remote-id> diff --git a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch deleted file mode 100644 index 69f3a963e..000000000 --- a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- X11/gui.c 2007-05-05 00:21:30.000000000 -0500 -+++ X11/gui.c-new 2007-08-09 04:25:53.000000000 -0500 -@@ -1786,15 +1786,15 @@ - { int item_no = (int) client_data; - switch (item_no) - { case CMD_HELP_HTMLHELP: -- { system("netscape "PREFIX"/cluster/html/index.html &"); -+ { system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &"); - break; - } - case CMD_HELP_MANUAL: -- { system("acroread "PREFIX"/cluster/doc/cluster3.pdf &"); -+ { system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &"); - break; - } - case CMD_HELP_DOWNLOAD: -- { system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); -+ { system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); - break; - } - case CMD_HELP_FILEFORMAT: -@@ -1852,7 +1852,7 @@ - XtManageChild(widget); - free(helptext); - n = 0; -- pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0); -+ pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0); - XtSetArg(args[n], XmNx, 10); n++; - XtSetArg(args[n], XmNy, 410); n++; - XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++; diff --git a/sci-biology/clview/Manifest b/sci-biology/clview/Manifest deleted file mode 100644 index 271e4eb76..000000000 --- a/sci-biology/clview/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST clview_linux_i386.tar.gz 1050318 BLAKE2B c5c52662df29a0f70a5355c0f2f563e8fef0ec473a707aed0c51d79bd1f1d7e9555139a21bb0c83c509fbac549d8c532d2af8d9ecb9af77b329be581f255493f SHA512 2fbd5ed5ef7bb96a715537a1b1d8f0957e5733d2603aacc5a0dba5a5002a27483ca57dd53780204a98d5ce05ac1090e3d04a3b2784cec021f0afc545e98b35b1 -DIST clview_src.tar.gz 62178 BLAKE2B b116a03c6ddba0caf77168fdd9e39bb86f4b1eccc0535dcd9f81a1e7c2a9b81c1219a4786ae37944abeb4913633acd9cf6b94824adba9851359a955440d9f21f SHA512 24c115b76041981d6dba731180485108d92cccc4719fe6982a135d73c3d18deed2e89ebb6d7daeb8d79941084ec912be2c3333369ec0bf403f96a156932909b9 diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild deleted file mode 100644 index 2f200426d..000000000 --- a/sci-biology/clview/clview-0.1.ebuild +++ /dev/null @@ -1,108 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="clview is an assembly .ace file viewer from TIGR Gene Indices project tools" -HOMEPAGE="https://sourceforge.net/projects/clview" -SRC_URI=" - https://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_src.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_linux_i386.tar.gz" - -# the ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/tgi_cpp_library.tar.gz -# contain maybe an older but definitely larger set of .cpp files compared to clview/gcl/ -# contents. clview compiles against both versions with same warning messages from g++. -# -# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/gclib/ -# total 188 -# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Dec 2 22:23 . -# drwx------ 5 mmokrejs portage 4096 Dec 2 22:23 .. -# -rw-r--r-- 1 mmokrejs mmokrejs 11632 Sep 17 2008 AceParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 906 Sep 14 2008 AceParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32276 Dec 2 22:23 AceParser.o -# -rw-r--r-- 1 mmokrejs mmokrejs 11012 Jan 22 2009 GBase.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 9200 Dec 16 2008 GBase.h -# -rw-r--r-- 1 mmokrejs mmokrejs 8844 Dec 2 22:23 GBase.o -# -rw-r--r-- 1 mmokrejs mmokrejs 16813 Jul 29 2008 GHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 16516 Sep 10 2008 GList.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 11221 Jan 22 2009 LayoutParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6246 Sep 14 2008 LayoutParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32956 Dec 2 22:23 LayoutParser.o -# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/tgi_cl/gcl/ -# total 268 -# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Nov 18 2008 . -# drwxr-xr-x 3 mmokrejs mmokrejs 4096 Oct 18 2006 .. -# -rw-r--r-- 1 mmokrejs mmokrejs 9515 Nov 7 2005 AceParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 886 Nov 7 2005 AceParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 10768 Nov 7 2005 BitHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 7250 Nov 7 2005 GArgs.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 2507 Nov 7 2005 GArgs.h -# -rw-r--r-- 1 mmokrejs mmokrejs 10156 Nov 18 2008 GBase.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 8142 Nov 18 2008 GBase.h -# -rw-r--r-- 1 mmokrejs mmokrejs 14742 Nov 7 2005 GCdbYank.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 1831 Nov 7 2005 GCdbYank.h -# -rw-r--r-- 1 mmokrejs mmokrejs 16723 Nov 7 2005 GFastaFile.h -# -rw-r--r-- 1 mmokrejs mmokrejs 16245 Nov 7 2005 GHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 15561 Nov 7 2005 GList.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 28 Nov 7 2005 GReadBuf.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 4022 Nov 7 2005 GReadBuf.h -# -rw-r--r-- 1 mmokrejs mmokrejs 48 Nov 7 2005 GShMem.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 4012 Nov 7 2005 GShMem.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32875 Nov 7 2005 GString.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 8453 Nov 7 2005 GString.h -# -rw-r--r-- 1 mmokrejs mmokrejs 11157 Nov 7 2005 LayoutParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6063 Nov 7 2005 LayoutParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 20253 Nov 7 2005 gcdb.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6941 Nov 7 2005 gcdb.h -# -rw-r--r-- 1 mmokrejs mmokrejs 8998 Nov 7 2005 gcompress.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 3670 Nov 7 2005 gcompress.h -# - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND="=x11-libs/fox-1.6*" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_unpack() { - unpack clview_src.tar.gz -} - -src_prepare() { - default - # FIXME: we have to run `/usr/bin/fox-config --cflags' to yield - # `-I/usr/include/fox-1.6' - # similarly `fox-config --libs' to yield e.g. - # `-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11 - # -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz -lbz2 -lm - # -lcups -lnsl -lGLU -lGL' - FOXVERSION=`WANT_FOX="1.6" fox-config --version` - FOXPREFIX=`WANT_FOX="1.6" fox-config --prefix` - FOXINCPATH=`WANT_FOX="1.6" fox-config --cflags` - FOXLIBS=`WANT_FOX="1.6" fox-config --libs` - einfo "Discovered path to fox ${FOXVERSION} files: ${FOXINCPATH}\n${FOXLIBS}" - - sed -i "s#FOXPREFIX = /mylocal/geo#FOXPREFIX = ${FOXPREFIX}#" clview/Makefile || die "Failed to hack FOXPREFIX in clview/Makefile" - sed -i "s#FOXINCDIR := .*#FOXINCDIR := ${FOXINCPATH}#" clview/Makefile || die "Failed to hack FOXINCDIR in clview/Makefile" - sed -i "s#-I\${FOXINCDIR}#\${FOXINCDIR}#" clview/Makefile || die "Failed to revert the extra -I we introduced on a previous line to clview/Makefile" - sed -i "s#FOXLIBDIR := .*#FOXLIBDIR := ${FOXPREFIX}/lib#" clview/Makefile || die "Failed to hack FOXLIBDIR in clview/Makefile" - sed -i "s#LOADLIBS :=.*#LOADLIBS := ${FOXLIBS}#" clview/Makefile || die "Failed to hack LOADLIBS in clview/Makefile" - sed -i "s#-I-#-I #" clview/Makefile || die - - # see tgi_cl/gcl/ - sed -i "s#TGICLASSDIR := /tucan/geo/src/tgi_cl#TGICLASSDIR := ../gcl#" clview/Makefile || die -} - -src_compile(){ - cd "${S}"/clview || die - default -} - -src_install() { - # install at least the binaries for clview when we cannot compile it - dobin clview/clview -} diff --git a/sci-biology/clview/metadata.xml b/sci-biology/clview/metadata.xml deleted file mode 100644 index 7adf609cd..000000000 --- a/sci-biology/clview/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">clview</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild index 49bf65452..56c76a408 100644 --- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild @@ -7,7 +7,7 @@ inherit toolchain-funcs DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage" HOMEPAGE="https://codonw.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz +SRC_URI="https://downloads.sourceforge.net/${PN}/CodonWSourceCode_${PV//./_}.tar.gz https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf" LICENSE="GPL-2" diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.0.ebuild index a76bf6690..7c2eaa739 100644 --- a/sci-biology/deeptools/deeptools-3.5.0.ebuild +++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -13,7 +14,7 @@ SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" # TODO: fix this RESTRICT="test" diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild index a76bf6690..7c2eaa739 100644 --- a/sci-biology/deeptools/deeptools-3.5.1.ebuild +++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -13,7 +14,7 @@ SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" # TODO: fix this RESTRICT="test" diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild index 86304f4f3..8ddd4007e 100644 --- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild +++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild @@ -6,7 +6,7 @@ EAPI=8 inherit check-reqs DESCRIPTION="BIDS data files released with the DRLFOM publication" -HOMEPAGE="http://chymera.eu/docs/focus/open-science/" +HOMEPAGE="https://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3598424/files/${P}.tar.xz " @@ -15,9 +15,6 @@ LICENSE="CC-BY-SA-4.0" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -RDEPEND="" -DEPEND="" - pkg_pretend() { CHECKREQS_DISK_BUILD="21G" check-reqs_pkg_pretend diff --git a/sci-biology/fastp/Manifest b/sci-biology/fastp/Manifest new file mode 100644 index 000000000..c158050fa --- /dev/null +++ b/sci-biology/fastp/Manifest @@ -0,0 +1 @@ +DIST fastp-0.23.4.tar.gz 164071 BLAKE2B 58745d494b83bbf9ae34593159228dbef5c854ab856af91fea8770fef171ed7b3053a4cac8c31053af3dcd91d4298fddb7594670a32963f53f75bd5fa1ec3a68 SHA512 2c929e974708f8cd2d8cab95d59c0a5fd01bea912f6ba5d08841fd929f0f5019ef89e506c771057bd02b879836ae30564b8417271866b6bbcb4917fbeb387e76 diff --git a/sci-biology/fastp/fastp-0.23.4.ebuild b/sci-biology/fastp/fastp-0.23.4.ebuild new file mode 100644 index 000000000..70d5ce330 --- /dev/null +++ b/sci-biology/fastp/fastp-0.23.4.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2023 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="An ultra-fast all-in-one FASTQ preprocessor" +HOMEPAGE="https://github.com/OpenGene/fastp" +SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64" + +LICENSE="MIT" +SLOT="0" + +DEPEND="app-arch/libdeflate + dev-libs/isa-l" + +src_install() { + dodir /usr/bin + emake PREFIX="${ED}"/usr install +} diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/fastp/metadata.xml index b80afba97..d51d87c5a 100644 --- a/sci-biology/pybedtools/metadata.xml +++ b/sci-biology/fastp/metadata.xml @@ -5,11 +5,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> <upstream> - <remote-id type="github">daler/pybedtools</remote-id> + <remote-id type="github">OpenGene/fastp</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch deleted file mode 100644 index a3872acf0..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk ---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400 -+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400 -@@ -141,7 +141,7 @@ - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) - #$(info $$CUDAVER is [${CUDAVER}]) --CUDA_INSTALLATION = /opt/cuda-${CUDAVER} -+CUDA_INSTALLATION = /opt/cuda - GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) - LIB_CUDA = ${CUDA_INSTALLATION}/lib64 - INC_CUDA = ${CUDA_INSTALLATION}/include diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch deleted file mode 100644 index 40409ec08..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile ---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400 -+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400 -@@ -29,6 +29,8 @@ - TMPCXXFLAGS_2= - TMPNAME_1= - TMPNAME_2= -+cuda=1 -+cpu=1 - - ifndef cuda - ifndef cpu #Default single cpu, no threading -@@ -74,7 +75,7 @@ - ifdef NVCC11 - NVCC=${NVCC11} - endif --NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 -+NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@ - ifeq ($(CLOBBER_CLANG),1) - NVCCFLAGS+= -DCLOBBER_CLANG - endif diff --git a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch deleted file mode 100644 index 9ddb11a2b..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400 -+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400 -@@ -75,6 +75,7 @@ - #include <iostream> - #include <fstream> - #include <sstream> -+#include <stdexcept> - #include "NewNifti/NewNifti.h" - #include "newmatio.h" - #include "newimage.h" diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch deleted file mode 100644 index 39737fd85..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch +++ /dev/null @@ -1,198 +0,0 @@ -From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001 -From: François Bissey <frp.bissey@gmail.com> -Date: Mon, 20 Jan 2020 11:54:37 +1300 -Subject: [PATCH] Adjust the build system so it doesnt build packages - externally provided by portage. Make the compilation flags more generic and - easily adjustable. Make the build system stop at the first fault. - ---- - build | 6 +++--- - config/buildSettings.mk | 20 ++++++++++---------- - config/common/buildproj | 8 +++++--- - config/common/vars.mk | 10 +++++----- - extras/build | 8 ++++---- - src/mist-clean/Makefile | 2 +- - 6 files changed, 28 insertions(+), 26 deletions(-) - -diff --git a/build b/build -index 05dac06c..d90e407b 100755 ---- a/build -+++ b/build -@@ -3,7 +3,7 @@ - if [ $# -ge 1 ] ; then - PROJECTS="$@"; - else -- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ -+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ - meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \ - DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \ - asl_mfree \ -@@ -80,8 +80,8 @@ xtract"; - done - fi - --echo "Building projects - see build.log file for progress..." --./config/common/buildproj $PROJECTS > ./build.log 2>&1 -+echo "Building projects" -+./config/common/buildproj $PROJECTS - finalStatus=$? - if [ $finalStatus -eq 0 ]; then - echo "Build completed successfully."; -diff --git a/config/buildSettings.mk b/config/buildSettings.mk -index b2e1f150..04532fc2 100644 ---- a/config/buildSettings.mk -+++ b/config/buildSettings.mk -@@ -18,7 +18,7 @@ MV = /bin/mv - CHMOD = /bin/chmod - MKDIR = /bin/mkdir - INSTALL = install -p --TCLSH = ${FSLDIR}/bin/fsltclsh -+TCLSH = tclsh - DEPENDFLAGS = -MM - MACHDBGFLAGS = -g - ##################################################################### -@@ -124,19 +124,19 @@ endif # if Darwin - ##################################################################### - ifeq ($(SYSTYPE), Linux) - ############### System Vars ##################################### --CC = gcc --CXX = c++ --CXX11 = c++ -+CC = @@GENTOO_CC@@ -+CXX = @@GENTOO_CXX@@ -+CXX11 = @@GENTOO_CXX@@ - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static --ARCHFLAGS = -m64 --ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib' -+ARCHFLAGS = -+ARCHLDFLAGS = - PARALLELFLAGS = -fopenmp --OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS = - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn - ANSI_FLAGS = ${GNU_ANSI_FLAGS} --RANLIB = echo -+RANLIB = @@GENTOO_RANLIB@@ - FSLML = ${FSLDIR}/bin/fslml - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) -@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include - NVCC = ${CUDA_INSTALLATION}/bin/nvcc - ############### External Libs ##################################### - # ZLIB library --LIB_ZLIB = /lib64 --INC_ZLIB = /usr/include -+#LIB_ZLIB = /lib64 -+#INC_ZLIB = /usr/include - # QT library - QTDIR = /usr/lib/qt3 - LIB_QT = ${QTDIR}/lib -diff --git a/config/common/buildproj b/config/common/buildproj -index 2f0f2b8f..48624a1f 100755 ---- a/config/common/buildproj -+++ b/config/common/buildproj -@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then - fi - PROJECTS="$@" ; export PROJECTS ; - --FSLDIR=`pwd` -+#FSLDIR=`pwd` - FSLDEVDIR=${FSLDIR} - FSLCONFDIR=${FSLDIR}/config --FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` -+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` - FSLMASTERBUILD=1 - export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD - -@@ -67,7 +67,7 @@ for projname in $PROJECTS; do - if [ -x ./fslconfig ] ; then - . ./fslconfig ; - fi -- if ${MAKE} -k ${MAKEOPTIONS} ; then -+ if ${MAKE} ${MAKEOPTIONS} ; then - if ${MAKE} ${MAKEOPTIONS} install ; then - installok=true; - # Clean up after ourselves -@@ -82,6 +82,7 @@ for projname in $PROJECTS; do - if [ $installok = false ] ; then - echo " " - echo "ERROR::Could not install $projname successfully" ; -+ exit 1 - fi - else - echo " " -@@ -90,6 +91,7 @@ for projname in $PROJECTS; do - echo " " - echo " " - errorprojs="$errorprojs $projname" ; export errorprojs ; -+ exit 1 - fi - fi - done -diff --git a/config/common/vars.mk b/config/common/vars.mk -index b027b010..aeeae67c 100755 ---- a/config/common/vars.mk -+++ b/config/common/vars.mk -@@ -24,15 +24,15 @@ USRINCFLAGS = - USRCFLAGS = - USRCXXFLAGS = - --LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} -+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS} - --AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} -+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS} - - CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+ ${AccumulatedIncFlags} ${USERCFLAGS} - --CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -+ ${AccumulatedIncFlags} ${USERCXXFLAGS} - - HFILES = *.h - AFILES = *.a -diff --git a/extras/build b/extras/build -index 59e7a2ed..0d68232e 100755 ---- a/extras/build -+++ b/extras/build -@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then - BUILDICONV=1 - fi - fi --PROJECTS="tcl tk" -+#PROJECTS="tcl tk" - if [ ${BUILDZLIB} -eq 1 ]; then - PROJECTS="${PROJECTS} zlib" - fi --PROJECTS="${PROJECTS} libpng" -+#PROJECTS="${PROJECTS} libpng" - if [ ${BUILDICONV} -eq 1 ]; then - PROJECTS="${PROJECTS} libiconv" - fi --PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" --PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat" -+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran" -+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat" - for projname in $PROJECTS; do - if [ -d $FSLESRCDIR/$projname ] ; then - buildIt $FSLESRCDIR $projname 1 -diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile -index 20402cca..6918bee4 100755 ---- a/src/mist-clean/Makefile -+++ b/src/mist-clean/Makefile -@@ -52,6 +52,6 @@ installpython: - cp -r python/* ${DESTDIR}/python/mist - - clean: -- rm -f ${OBJS} mist/mist.o mist/mist -+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion." - - .PHONY: all clean installdata --- -2.24.1 - diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild index cd91cf192..6e5d6e779 100644 --- a/sci-biology/fsl/fsl-6.0.4.ebuild +++ b/sci-biology/fsl/fsl-6.0.4.ebuild @@ -151,8 +151,8 @@ src_compile() { # define the default build system to match upstream official standard # -> individual projects may overwrite the '-std=' flag - export ANSI_CFLAGS="-std=c99" - export ANSI_CXXFLAGS="-std=c++98" + export ANSI_CFLAGS="-std=c11" + export ANSI_CXXFLAGS="-std=c++11" export USERLDFLAGS="${LDFLAGS}" export USERCFLAGS="${CFLAGS}" diff --git a/sci-biology/gffcompare/files/Makefile.patch b/sci-biology/gffcompare/files/Makefile.patch deleted file mode 100644 index afb52b2e1..000000000 --- a/sci-biology/gffcompare/files/Makefile.patch +++ /dev/null @@ -1,79 +0,0 @@ ---- gffcompare-0.10.5/Makefile 2018-06-26 09:24:06.058542487 +0200 -+++ gffcompare-0.10.5/Makefile 2018-06-26 09:28:08.045119603 +0200 -@@ -16,7 +16,7 @@ - endif - - # CVS checked in --CC := g++ -+CXX ?= g++ - BASEFLAGS = -Wall -Wextra ${INCDIRS} $(MARCH) \ - -fno-exceptions -fno-rtti -D_REENTRANT - -@@ -24,7 +24,8 @@ - - ifneq (,$(filter %release %static, $(MAKECMDGOALS))) - # -- release build -- CFLAGS = -O3 -DNDEBUG $(BASEFLAGS) -+ CXXFLAGS ?= -O3 -g -+ CXXFLAGS += -DNDEBUG $(BASEFLAGS) - LDFLAGS = - LIBS = - ifneq (,$(findstring static,$(MAKECMDGOALS))) -@@ -37,16 +38,16 @@ - ifeq "$(GCCVER49)" "0" - $(error gcc version 4.9 or greater is required for this build target) - endif -- CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address -+ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address - GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5) - ifeq "$(GCCVER5)" "1" -- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr -- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size -- #CFLAGS += -fcheck-pointer-bounds -mmpx -+ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr -+ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size -+ #CXXFLAGS += -fcheck-pointer-bounds -mmpx - endif -- CFLAGS += $(BASEFLAGS) -- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS) -- LDFLAGS := -g -+ CXXFLAGS += $(BASEFLAGS) -+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector -+ LDFLAGS ?= -g - #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS) - LIBS := -lasan -lubsan -ldl $(LIBS) - else -@@ -55,26 +56,26 @@ - # GMEMTRACE=1 - #endif - #--- just plain debug build --- -- CFLAGS = -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -- LDFLAGS = -g -+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -+ LDFLAGS += -g - LIBS = - endif - endif - - %.o : %.c -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cc -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.C -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cpp -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cxx -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - # C/C++ linker - diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest index e8b006cbf..ca30cec83 100644 --- a/sci-biology/gffutils/Manifest +++ b/sci-biology/gffutils/Manifest @@ -1 +1 @@ -DIST gffutils-0.11.1.tar.gz 1646787 BLAKE2B 96e573cf366844c8a348aff062362aeaea1a46360c74ae75a2d8d730d37cd69f0e6c658d1d0f348ca8f8e8c49d9a7c923c52619341e8d2dabd92a329fb43b677 SHA512 1844e9d7626a800549def2ba09b4d97e60c8a1a0fce2da60d7841cf4c4347da50aea850e8c1a67b07de08d4e6cf737b0d5c2bf8eb5fc87900427866282e82bdb +DIST gffutils-0.13.gh.tar.gz 1644910 BLAKE2B c8c4bc5d8a51e2e63d359bed8953730dc2d64ab04a96021fbaa891443f77c259886bcb81bab59eff622f23aeaed77c30bd1635b03761607ec562fa52d92ebea7 SHA512 617f84aeaa4d16b140083012c6b3656d5ea44a9a0619f8516e51379f92e9be85dff42e31c9ac2c3a77d7e3715f43c0106cd534317cc6ff4b6257fce56a1b635f diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild deleted file mode 100644 index 8ee8fd4b5..000000000 --- a/sci-biology/gffutils/gffutils-0.11.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) - -inherit distutils-r1 - -DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" -SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -# Nose tests no longer supported, migration on next release -#RESTRICT="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/argh[${PYTHON_USEDEP}] - dev-python/argcomplete[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - sci-biology/pybedtools[${PYTHON_USEDEP}] - sci-biology/pyfaidx[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -python_prepare_all() { - if use test; then - sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py || die - fi - distutils-r1_python_prepare_all -} - -python_test() { - distutils_install_for_testing - nosetests -v -x --with-doctest -a '!slow' || die -} diff --git a/sci-biology/gffutils/gffutils-0.13.ebuild b/sci-biology/gffutils/gffutils-0.13.ebuild new file mode 100644 index 000000000..fbd90b6d9 --- /dev/null +++ b/sci-biology/gffutils/gffutils-0.13.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="GFF and GTF file manipulation and interconversion" +HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" +SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/argh[${PYTHON_USEDEP}] + dev-python/argcomplete[${PYTHON_USEDEP}] + dev-python/pyfaidx[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +# https://github.com/daler/gffutils/issues/233 + cli not installed yet +EPYTEST_DESELECT=( + gffutils/test/test_biopython_integration.py::test_roundtrip + gffutils/test/test_cli.py::test_issue_224 +) + +distutils_enable_tests pytest diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml index c9fe23ced..dc2c60220 100644 --- a/sci-biology/gffutils/metadata.xml +++ b/sci-biology/gffutils/metadata.xml @@ -5,10 +5,6 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> <upstream> <remote-id type="github">daler/gffutils</remote-id> </upstream> diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest index bd58b4117..c8a1eba20 100644 --- a/sci-biology/imagej/Manifest +++ b/sci-biology/imagej/Manifest @@ -1,4 +1,3 @@ -DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3 -DIST ij153.zip 6503763 BLAKE2B 7b3b30b55fe844e110f3e85eab7790376fc2d62300312c0b9037726758fcbfd5c4a6072842aa09e6ed08a2d593c2b1966d985de5972d801cf01638b41134325e SHA512 788003b35f7c3dd6f9bcda298637a3de78d745de8dd685cf88d8cc6ae22e142b07620c1e47a182d1e87178d68d591e381813f40cedc59f08d21af317065d7de0 -DIST ij153t-src.zip 1549329 BLAKE2B 7e43b759b96c8683be2175348a88080cdd4f038153a937717ebb0f480f9c8fb83d15184f8bf25060dc395ac3b13fd57f905621e680e481ad7dfdc090bbefb323 SHA512 861ecba6a20835566ec4038ffa30211308d37c41cecdfb97ea33d963c0ac2f1dbec0679c014335f89df24317334aeb30350dd09ee5f0fa33990f5355dd2fd06f -DIST imagej-1.54f.gh.tar.gz 5768851 BLAKE2B a3c04ec949937e01ccf9b2a3a8432206c30833fc1f26a8ff0f487dece26c35a315b3c72cf88fec63ba090c5da6db51795c471b85d43f017f676c9f557f802cfc SHA512 a46deeec0e43c56598a0950393e6d72f866c9026434fb87fd5e4a604efcd13f3e50332b3893ba9cf443dd73fdfab9ddbcbf90604d7acfba7d1a1b72d7d1c916b +DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9 +DIST imagej-1.54i.gh.tar.gz 5826446 BLAKE2B 05a21929a29e7c4109a91714d0d4d2763f9fe5d83500d334a717d7050765d50c08119b8a7bb54b9290ccf4f82a75cfb392fdf2ee269ee0b05e0f7447aa7c2d1b SHA512 13a0ec252328f972570ccbd85881b64cff25b03f92eb5f68bb6b1b00d7530ba31cd2ff617c462aa428158027f042ea1d18682f3e0deb4d0728ae56965ed5f8e8 +DIST imagej.png 14480 BLAKE2B a507afad5be462cf7a6e693b7930e40abc10877d137d1adeea7938c2b95fecef1b73eb401dc32670ccee6d83a5ecdfc4b6487ed908820bfaa09bec39400cd576 SHA512 87a2bbc17353488a17adb446f2199fb75292ba3bdf00cb97c0508107ee56c12f282bebd8d6618bf6e12ebbcfca7a12bf24057803aeb570edefa992d975b386f5 diff --git a/sci-biology/imagej/imagej-1.53t.ebuild b/sci-biology/imagej/imagej-1.53t.ebuild deleted file mode 100644 index 952eff08b..000000000 --- a/sci-biology/imagej/imagej-1.53t.ebuild +++ /dev/null @@ -1,122 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit java-pkg-2 java-ant-2 desktop - -MY_PN="ij" -MY_PV=${PV//.} -IJ_PV=${MY_PV::-1} - -DESCRIPTION="Image Processing and Analysis in Java" -HOMEPAGE="https://imagej.nih.gov/ij/" - -SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip - https://imagej.nih.gov/ij/images/ImageJ.png - plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" -# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins -# plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )" - -LICENSE="public-domain" # http://imagej.net/disclaimer.html -SLOT="0" - -KEYWORDS="~amd64" - -IUSE="doc plugins debug" - -RDEPEND=" - >=virtual/jre-1.7:* - dev-java/java-config -" -DEPEND="${RDEPEND} - >=virtual/jdk-1.7:* -" -BDEPEND=" - dev-java/ant-core - app-arch/unzip -" - -S="${WORKDIR}/source" -IJ_S=${WORKDIR}/ImageJ - -src_prepare() { - cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die - - if ! use debug ; then - sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die - fi - default -} - -src_compile() { - local antflags="build" - use doc && antflags="${antflags} javadocs" - - ant ${antflags} || die "ant build failed" - - # Max memory usage depends on available memory and CPU type - MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) - IJ_MAX_MEM=$(expr ${MEM} / 1024) - if use x86 && $IJ_MAX_MEM -gt 2048 ; then - IJ_MAX_MEM=2048 - fi - # build finished, generate startup wrapper - cat <<EOF > "${T}/${PN}" -#!${EPREFIX}/bin/bash -IJ_LIB=${EPREFIX}/usr/share/${PN}/lib -if !([ "\${IJ_HOME}" ]) ; then - IJ_HOME=\${HOME}/.imagej -fi -if [ -d \${IJ_HOME}/plugins ] ; then - IJ_PLG=\${IJ_HOME} -else - IJ_PLG=${EPREFIX}/usr/share/${PN}/lib -fi -if !([ "\$IJ_MEM" ]) ; then - IJ_MEM=${IJ_MAX_MEM} -fi -if !([ "\$IJ_CP" ]) ; then - IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar -else - IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP} -fi -\$(java-config --java) \\ - -Xmx\${IJ_MEM}m -Dswing.aatext=true \\ - -Dawt.useSystemAAFontSettings=on\\ - -cp \${IJ_CP} \\ - -Duser.home=\${IJ_HOME} \\ - -Dplugins.dir=\${IJ_PLG} \\ - ij.ImageJ "\$@" -EOF -} - -src_install() { - java-pkg_dojar *.jar - dobin "${T}/${PN}" - - if use plugins ; then - cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/ - cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/ - fi - - use doc && java-pkg_dohtml -r "${WORKDIR}"/api - - insinto /usr/share/pixmaps - doins "${WORKDIR}/${PN}".png - make_desktop_entry "${PN}" ImageJ "${PN}" Graphics -} - -pkg_postinst() { - einfo "" - einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt," - einfo "by setting the environmental variable, \$IJ_HOME." - einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt." - einfo "" - einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM," - einfo "and the class path by setting the environmental variable, \$IJ_CP." - einfo "" - einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html" - einfo "and add *.class files to \$IJ_HOME/plugins folder" - einfo "" -} diff --git a/sci-biology/imagej/imagej-1.54f.ebuild b/sci-biology/imagej/imagej-1.54i-r1.ebuild index 33a10b0e4..f95167bcd 100644 --- a/sci-biology/imagej/imagej-1.54f.ebuild +++ b/sci-biology/imagej/imagej-1.54i-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -6,17 +6,17 @@ EAPI=8 inherit java-pkg-2 java-ant-2 desktop MY_PN="ij" -IJ_PV="153" #plugins not currently available under 154 +IJ_PV="154" #plugins now available for 154 DESCRIPTION="Image Processing and Analysis in Java" HOMEPAGE=" - https://imagej.nih.gov/ij/ + https://imagej.net/software/imagej/ https://github.com/imagej " SRC_URI=" - https://imagej.nih.gov/ij/images/ImageJ.png + https://imagej.net/media/icons/imagej.png plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" # plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins @@ -50,16 +50,15 @@ DEPEND=" " BDEPEND=" - dev-java/ant-core app-arch/unzip " src_prepare() { - cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die if [[ ${PV} == 9999 ]]; then if use plugins ; then - unpack "${MY_PN}${IJ_PV}.zip" + unpack "${MY_PN}${IJ_PV}.zip" fi fi diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild index 33a10b0e4..f95167bcd 100644 --- a/sci-biology/imagej/imagej-9999.ebuild +++ b/sci-biology/imagej/imagej-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -6,17 +6,17 @@ EAPI=8 inherit java-pkg-2 java-ant-2 desktop MY_PN="ij" -IJ_PV="153" #plugins not currently available under 154 +IJ_PV="154" #plugins now available for 154 DESCRIPTION="Image Processing and Analysis in Java" HOMEPAGE=" - https://imagej.nih.gov/ij/ + https://imagej.net/software/imagej/ https://github.com/imagej " SRC_URI=" - https://imagej.nih.gov/ij/images/ImageJ.png + https://imagej.net/media/icons/imagej.png plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" # plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins @@ -50,16 +50,15 @@ DEPEND=" " BDEPEND=" - dev-java/ant-core app-arch/unzip " src_prepare() { - cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die if [[ ${PV} == 9999 ]]; then if use plugins ; then - unpack "${MY_PN}${IJ_PV}.zip" + unpack "${MY_PN}${IJ_PV}.zip" fi fi diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild index 3faf27a11..021929bad 100644 --- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild +++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit check-reqs DESCRIPTION="BIDS data files released with the IRSABI publication" -HOMEPAGE="http://chymera.eu/docs/focus/open-science/" +HOMEPAGE="https://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3601531/files/${P}.tar.xz " diff --git a/sci-biology/libBigWig/Manifest b/sci-biology/libBigWig/Manifest index 4a1880c5f..249395f6f 100644 --- a/sci-biology/libBigWig/Manifest +++ b/sci-biology/libBigWig/Manifest @@ -1 +1,2 @@ DIST libBigWig-0.4.4.tar.gz 272926 BLAKE2B ffde5fced9991b28cf1fdb8b296a88744d949ea6f044d3bc6f5bbcb3405bc8a08906d94a614d489758fbfc625361b910bbbdcf9ea721fa22dee0edf2f286fc08 SHA512 85e0b60e4ce541eb1328528d834f54ea827cc79b5890093688661dfc9bc72e417c8d293cfe5b93987973b4584b042f10a6edd77adca6ea6b1e57ed3741edba71 +DIST libBigWig-0.4.7.tar.gz 302341 BLAKE2B 667aff6153dc11a3491362e19673b64ff72a0779f5c722508d21f2af8ce4c5e9fb410c9685fc2ecfc3a1fade85454f40ada8d2969948eb1d3336b13ed3a816be SHA512 52f1b7c8e21e16238b3bb07baef6aa3611797b1b5ff44d912c874f8f4527c516a0676877fad21c103b8b25a733e84bef48530f28dc224a79d43f7764eae7ed40 diff --git a/sci-biology/libBigWig/libBigWig-0.4.7.ebuild b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild new file mode 100644 index 000000000..7dc83ceed --- /dev/null +++ b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)" +HOMEPAGE="https://github.com/dpryan79/libBigWig" + +if [[ ${PV} == 9999 ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/dpryan79/libBigWig" +else + SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" + +DEPEND="net-misc/curl" +RDEPEND="${DEPEND}" + +src_prepare(){ + default + sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die + sed -e "s:/lib:/$(get_libdir):" -i Makefile || die +} + +src_install(){ + emake install DESTDIR="${ED}" +} diff --git a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild index 5d89c0822..42fc0b62d 100644 --- a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild +++ b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild @@ -7,7 +7,7 @@ inherit flag-o-matic toolchain-funcs DESCRIPTION="Micro Read Fast Alignment Search Tool" HOMEPAGE="http://mrfast.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest new file mode 100644 index 000000000..cf36e2eb5 --- /dev/null +++ b/sci-biology/multiqc/Manifest @@ -0,0 +1 @@ +DIST multiqc-1.23.gh.tar.gz 5639815 BLAKE2B 1cd02d82d5a1856470777cdd5db48fbf2d86a37e713fa32118edb608703c9fbf1d23af6254a0ed15c47f2c073999a58c53a5a67c6df9a6bfc61cb773fc857bae SHA512 f7d910122ec34373dfa2d60dd7436ec66494980daf7e46729fbae90481bcceb1318c5dbafc64725dca2079deb5fe66834371813aa4dda7e9bf676dff5a043995 diff --git a/sci-biology/multiqc/metadata.xml b/sci-biology/multiqc/metadata.xml new file mode 100644 index 000000000..09bd2b6e6 --- /dev/null +++ b/sci-biology/multiqc/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">ewels/MultiQC</remote-id> + <remote-id type="pypi">multiqc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/multiqc/multiqc-1.23.ebuild b/sci-biology/multiqc/multiqc-1.23.ebuild new file mode 100644 index 000000000..bf45065aa --- /dev/null +++ b/sci-biology/multiqc/multiqc-1.23.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 + +DESCRIPTION="Aggregate bioinformatics results across many samples into a single report" +HOMEPAGE="https://multiqc.info/" +SRC_URI="https://github.com/MultiQC/MultiQC/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}"/MultiQC-${PV} + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/click[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + dev-python/importlib-metadata[${PYTHON_USEDEP}] + >=dev-python/jinja-3.0.0[${PYTHON_USEDEP}] + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + >=dev-python/pillow-10[${PYTHON_USEDEP}] + >=dev-python/plotly-5.18[${PYTHON_USEDEP}] + >=dev-python/pyyaml-4[${PYTHON_USEDEP}] + dev-python/pyaml-env[${PYTHON_USEDEP}] + >=dev-python/rich-10[${PYTHON_USEDEP}] + dev-python/rich-click[${PYTHON_USEDEP}] + dev-python/coloredlogs[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + >=dev-python/spectra-0.0.10[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.7.1[${PYTHON_USEDEP}] + dev-python/typeguard[${PYTHON_USEDEP}]" +# dev-python/kaleido[${PYTHON_USEDEP}] # tested and is optional + +RESTRICT="test" # no items collected +#distutils_enable_tests pytest diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest index 54770b3ae..35c461b92 100644 --- a/sci-biology/neuroconv/Manifest +++ b/sci-biology/neuroconv/Manifest @@ -1 +1 @@ -DIST neuroconv-0.2.4.gh.tar.gz 757136 BLAKE2B a3a21b3a00667bde4461d91ade514891c8710f309413b100e1cccfd2684dfcbf9b21feaf4f58b3c5ff845aa08e69bf47467b411926eeb7d3b2862753302b1d9b SHA512 293038feae2704442b81ba0f012d775ba96d7bdffb6aaacaaebd09ca2f8b39e91ef4ea69c972abf060f0f9ab8cb76fedb77dda67455fa992edd52f0e6e504b0d +DIST neuroconv-0.4.8.gh.tar.gz 1020546 BLAKE2B 880d7c4bdce3faf3bc969c9a0fd4206e1fd9d57254e40aa1181cf2d8f48abd72491b8b66d8ccc1988a623f8b2a8be160f2575f59ea69080a8bb6ed501c389881 SHA512 d06a625823a71f21a5eac957e452ab80b6fb847fc5f8c8e68fb6c46360402c4bc338f7fc611537272e72c0b72555a2951c346d38aa89c8ac8b209921ea7af72d diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild index c554ce791..b21c2fd8e 100644 --- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild +++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild @@ -17,17 +17,21 @@ KEYWORDS="~amd64" IUSE="+ecephys +icephys +ophys" RDEPEND=" + dev-python/docstring-parser[${PYTHON_USEDEP}] dev-python/h5py[${PYTHON_USEDEP}] + dev-python/hdmf-zarr[${PYTHON_USEDEP}] dev-python/hdmf[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] + dev-python/parse[${PYTHON_USEDEP}] dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] dev-python/pynwb[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] dev-python/tqdm[${PYTHON_USEDEP}] - dev-vcs/dandi-cli[${PYTHON_USEDEP}] ecephys? ( dev-python/spikeinterface[${PYTHON_USEDEP}] ) @@ -46,6 +50,12 @@ BDEPEND=" distutils_enable_tests pytest +# Reported upstream: +# https://github.com/catalystneuro/neuroconv/issues/785 +EPYTEST_DESELECT=( + tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface +) + python_test() { # Additional tests require complex data getting infrastructure, ophys tests still have issues: # https://github.com/catalystneuro/neuroconv/issues/305 diff --git a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch b/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch deleted file mode 100644 index e229d25fb..000000000 --- a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch +++ /dev/null @@ -1,39 +0,0 @@ ---- a/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:07.700111595 +0200 -+++ b/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:29.453556439 +0200 -@@ -219,36 +219,6 @@ - assert_raises(ValueError, masker.fit_transform, data_img) - - --def test_joblib_cache(): -- from sklearn.externals.joblib import hash, Memory -- mask = np.zeros((40, 40, 40)) -- mask[20, 20, 20] = 1 -- mask_img = Nifti1Image(mask, np.eye(4)) -- -- with testing.write_tmp_imgs(mask_img, create_files=True) as filename: -- masker = NiftiMasker(mask_img=filename) -- masker.fit() -- mask_hash = hash(masker.mask_img_) -- masker.mask_img_.get_data() -- assert_true(mask_hash == hash(masker.mask_img_)) -- -- # Test a tricky issue with memmapped joblib.memory that makes -- # imgs return by inverse_transform impossible to save -- cachedir = mkdtemp() -- try: -- masker.memory = Memory(cachedir=cachedir, mmap_mode='r', -- verbose=0) -- X = masker.transform(mask_img) -- # inverse_transform a first time, so that the result is cached -- out_img = masker.inverse_transform(X) -- out_img = masker.inverse_transform(X) -- out_img.to_filename(os.path.join(cachedir, 'test.nii')) -- finally: -- # enables to delete "filename" on windows -- del masker -- shutil.rmtree(cachedir, ignore_errors=True) -- -- - def test_mask_init_errors(): - # Errors that are caught in init - mask = NiftiMasker(mask_strategy='oops') diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild index 3064c0ba5..92c788f28 100644 --- a/sci-biology/nilearn/nilearn-0.8.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild @@ -27,7 +27,7 @@ BDEPEND=" RDEPEND=" >=dev-python/joblib-0.12[${PYTHON_USEDEP}] >=dev-python/numpy-1.16[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}] + >=dev-python/scikit-learn-0.21[${PYTHON_USEDEP}] >=dev-python/scipy-1.2[${PYTHON_USEDEP}] >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}] >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}] diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild index 425e79444..4dbe5101e 100644 --- a/sci-biology/nilearn/nilearn-0.9.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild @@ -25,7 +25,7 @@ RDEPEND=" >=dev-python/requests-2[${PYTHON_USEDEP}] >=dev-python/scipy-1.5[${PYTHON_USEDEP}] >=sci-libs/nibabel-3[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}] + >=dev-python/scikit-learn-0.22[${PYTHON_USEDEP}] " PATCHES=( "${FILESDIR}/${P}-tests.patch" ) diff --git a/sci-biology/nitime/Manifest b/sci-biology/nitime/Manifest index 2ba87b1bb..4a9a85cc0 100644 --- a/sci-biology/nitime/Manifest +++ b/sci-biology/nitime/Manifest @@ -1 +1,2 @@ +DIST nitime-0.10.2.tar.gz 6231004 BLAKE2B 2214eb4fcb29567ebb4e819451bf7401ae6b467c0a2d196904c08bc44343e5c1ea840770f72d37df5e6642df455d895bfc9453b9389d8ef96cc88f3abc0d586e SHA512 c8c687f6c5e189e48bbe5cba4bbe3f19f34e6d087b43e3b0aa42d587f46081d3727867dbe07fa6d945381119086e12c98cdf12798055529a484152a4c04eae21 DIST nitime-0.9.tar.gz 6222979 BLAKE2B 45dbf34fd89b805f97ae5d4f88264f47ff88fa1f89b7ef05527477270bfa588a79fd1b356b2e7206919ed675936207accc02ad5b9a4be27e916a1dcf0561147e SHA512 cd8af7c3463143ac1765c472c1274915adfaf85508c334008c703ef72961e0a5e9ccbbd9321aaf62f7a58d9534934386baf1c7269a1d8f2d41b678707cd69406 diff --git a/sci-biology/nitime/metadata.xml b/sci-biology/nitime/metadata.xml index 041507ac7..606822ddb 100644 --- a/sci-biology/nitime/metadata.xml +++ b/sci-biology/nitime/metadata.xml @@ -10,9 +10,9 @@ <name>Gentoo Science Project</name> </maintainer> <longdescription lang="en"> -Nitime is a library for time-series analysis of data from neuroscience experiments -in both the time and spectral domains. -</longdescription> + Nitime is a library for time-series analysis of data from neuroscience experiments + in both the time and spectral domains. + </longdescription> <upstream> <remote-id type="github">nipy/nitime</remote-id> <remote-id type="pypi">nitime</remote-id> diff --git a/sci-biology/nitime/nitime-0.10.2.ebuild b/sci-biology/nitime/nitime-0.10.2.ebuild new file mode 100644 index 000000000..7e47d7288 --- /dev/null +++ b/sci-biology/nitime/nitime-0.10.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Time-series analysis of neuroscience data" +HOMEPAGE="http://nipy.org/nitime/index.html" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="${COMMON_DEPEND} + dev-python/cython[${PYTHON_USEDEP}] + " +RDEPEND=" + ${COMMON_DEPEND} + dev-python/networkx[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + " + +distutils_enable_tests pytest +distutils_enable_sphinx doc diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild index f297c85f0..ee81c01dc 100644 --- a/sci-biology/nitime/nitime-9999.ebuild +++ b/sci-biology/nitime/nitime-9999.ebuild @@ -3,9 +3,10 @@ EAPI=8 +DISTUTILS_USE_PEP517=setuptools PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 git-r3 virtualx +inherit distutils-r1 git-r3 DESCRIPTION="Time-series analysis of neuroscience data" HOMEPAGE="http://nipy.org/nitime/index.html" @@ -16,9 +17,6 @@ LICENSE="BSD" SLOT="0" KEYWORDS="" -# import file mismatch: -RESTRICT="test" - COMMON_DEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] @@ -35,7 +33,3 @@ RDEPEND=" distutils_enable_tests pytest distutils_enable_sphinx doc - -python_test() { - virtx pytest -v || die -} diff --git a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild index bae672851..bc15bb8f4 100644 --- a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild +++ b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild @@ -5,7 +5,7 @@ EAPI=7 DESCRIPTION="Primers design for standard PCR, bisulphite PCR and Real-time PCR" HOMEPAGE="http://perlprimer.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.bz2" LICENSE="GPL-2" SLOT="0" diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest deleted file mode 100644 index a952ac4b8..000000000 --- a/sci-biology/pybedtools/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe -DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18 diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild deleted file mode 100644 index bc02bda6f..000000000 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools - -inherit distutils-r1 - -DESCRIPTION="Use BED and GFF files from python using BEDtools" -HOMEPAGE="https://daler.github.io/pybedtools" -SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-biology/bedtools - sci-biology/pysam[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] -" - -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" - -# TODO: fix docs building -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -# even if pybedtools is installed -#distutils_enable_sphinx docs/source -distutils_enable_tests pytest - -python_test() { - # Requires network - local EPYTEST_DESELECT=( - test/test_helpers.py::test_chromsizes - ) - cd "${T}" || die - epytest --pyargs pybedtools -} diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild deleted file mode 100644 index bc02bda6f..000000000 --- a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools - -inherit distutils-r1 - -DESCRIPTION="Use BED and GFF files from python using BEDtools" -HOMEPAGE="https://daler.github.io/pybedtools" -SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-biology/bedtools - sci-biology/pysam[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] -" - -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" - -# TODO: fix docs building -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -# even if pybedtools is installed -#distutils_enable_sphinx docs/source -distutils_enable_tests pytest - -python_test() { - # Requires network - local EPYTEST_DESELECT=( - test/test_helpers.py::test_chromsizes - ) - cd "${T}" || die - epytest --pyargs pybedtools -} diff --git a/sci-biology/pyfaidx/Manifest b/sci-biology/pyfaidx/Manifest deleted file mode 100644 index 0bb3b35f4..000000000 --- a/sci-biology/pyfaidx/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST pyfaidx-0.5.9.2.tar.gz 93438 BLAKE2B 3d3d225907f8bd04fdf4b20d608d02cd0e5a723f2a73df24b732992f139102e2a9042c37c5a73f762256fd007dd7e14bace910c0961e60870926c2ce1dca3ac3 SHA512 57b94421d6858fa2bd7b867b386d47d53d3afd75878b08e6e32fb7d8f4942f2a051e0123e6c4b4395abe656d639fa4f47afadbd8c4b2cbc001c5113cbbf96af4 -DIST pyfaidx-0.7.2.1.tar.gz 102951 BLAKE2B d8c76bb9f817a7f4a0f3aa58ef20344c1d5aa5e99a181f1171145264baab4603d772d7c37f8286654442ee0f6bf3b62f8d94d6e0495a65f54495e084403c0b92 SHA512 20833c2e11f942aa69b524170a0203ca4d035d058d1d8029c2fab50c4b60a4e947cbbdc0dc954e4ecdefbf07d095f861a86dbebdfdac4bdbecf65a691226e25c diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml deleted file mode 100644 index 47cc39d79..000000000 --- a/sci-biology/pyfaidx/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mschu.dev@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">pyfaidx</remote-id> - <remote-id type="github">mdshw5/pyfaidx</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild deleted file mode 100644 index bec223f6c..000000000 --- a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Efficient pythonic random access to fasta subsequences" -HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx" -SRC_URI="https://github.com/mdshw5/pyfaidx/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -REPEND="dev-python/six[${PYTHON_USEDEP}]" - -#distutils_enable_tests nose diff --git a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild deleted file mode 100644 index 14f557869..000000000 --- a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools - -inherit distutils-r1 pypi - -DESCRIPTION="Efficient pythonic random access to fasta subsequences" -HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -# Test issues reported upstream: -# https://github.com/mdshw5/pyfaidx/issues/208 -RESTRICT="test" - -REPEND="dev-python/six[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild index d6ffd5f1f..f632f83a8 100644 --- a/sci-biology/samri/samri-0.5.3.ebuild +++ b/sci-biology/samri/samri-0.5.3.ebuild @@ -48,7 +48,7 @@ RDEPEND=" >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild index d6ffd5f1f..f632f83a8 100644 --- a/sci-biology/samri/samri-0.5.4.ebuild +++ b/sci-biology/samri/samri-0.5.4.ebuild @@ -48,7 +48,7 @@ RDEPEND=" >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild index d6ffd5f1f..f632f83a8 100644 --- a/sci-biology/samri/samri-9999.ebuild +++ b/sci-biology/samri/samri-9999.ebuild @@ -48,7 +48,7 @@ RDEPEND=" >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] diff --git a/sci-biology/sra-tools/files/libs_sra_Makefile.patch b/sci-biology/sra-tools/files/libs_sra_Makefile.patch deleted file mode 100644 index 44acc42b0..000000000 --- a/sci-biology/sra-tools/files/libs_sra_Makefile.patch +++ /dev/null @@ -1,77 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100 -@@ -100,7 +100,7 @@ - $(addsuffix .$(LOBX),$(SRAPATH_SRC)) - - $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ) -- $(LD) --slib -o $@ $^ -+ $(LD) --slib -o $(DESTDIR)$@ $^ - - libsrapath.vers.h: - @ true -@@ -138,10 +138,10 @@ - -dklib - - $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB) - - SRASCHEMA_SRC = \ - sraschema-stub -@@ -168,10 +168,10 @@ - $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC)) - - $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) - - libsraschema_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ) -@@ -205,10 +205,10 @@ - -dklib - - $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - libsradb_tag: $(SRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ) -@@ -236,10 +236,10 @@ - -dklib - - $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - libwsradb_tag: $(WSRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ) -@@ -266,10 +266,10 @@ - -dklib - - $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - libsrareader_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ) diff --git a/sci-biology/sra-tools/files/sra_sdk-destdir.patch b/sci-biology/sra-tools/files/sra_sdk-destdir.patch deleted file mode 100644 index bf66c6e46..000000000 --- a/sci-biology/sra-tools/files/sra_sdk-destdir.patch +++ /dev/null @@ -1,76 +0,0 @@ -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env 2011-08-31 21:46:21.000000000 +0200 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env 2012-02-06 02:02:38.000000000 +0100 -@@ -141,7 +141,7 @@ - - # create all required output directories - makedirs: -- @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR) -+ @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR) - - ifeq (win,$(OS)) - -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2012-02-06 02:23:07.000000000 +0100 -@@ -38,10 +38,10 @@ - # versioned output - if [ "$VERS" = "" ] - then -- DLIB_CMD="$DLIB_CMD -o $TARG" -- EXE_CMD="$EXE_CMD -o $TARG" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG" -+ EXE_CMD="$EXE_CMD -o $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -- EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -+ EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS" - fi -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2012-02-06 02:34:46.000000000 +0100 -@@ -52,12 +52,12 @@ - - set-vers $(echo $VERS | tr '.' ' ') - --cd "$OUTDIR" || exit 5 -+cd $DESTDIR$OUTDIR || exit 5 - - # create link - create-link () - { -- rm -f "$2" -+ rm -f $DESTDIR"$2" - local CMD="ln -s $1 $2" - echo $CMD - $CMD ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:16.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:29.000000000 +0100 -@@ -77,7 +77,7 @@ - CMD="$CMD $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" -+ CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS" - fi - - # tack on object files ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori 2012-02-06 04:24:39.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc 2012-02-06 04:22:57.000000000 +0100 -@@ -36,12 +36,12 @@ - LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - # tool options - WARN = -Wall -Wno-variadic-macros # -Wconversion diff --git a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch deleted file mode 100644 index 738d67cbd..000000000 --- a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100 -@@ -89,7 +89,7 @@ - $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg - - $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg -- cp $^ $@ -+ cp $^ $(DESTDIR)$@ - - VDB_COPY_SRC = \ - num-gen \ |