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-rw-r--r--sci-biology/SPAdes/Manifest8
-rw-r--r--sci-biology/SPAdes/SPAdes-3.15.5.ebuild (renamed from sci-biology/SPAdes/SPAdes-3.15.3.ebuild)10
-rw-r--r--sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch49
-rw-r--r--sci-biology/SPAdes/metadata.xml11
-rw-r--r--sci-biology/afni/Manifest7
-rw-r--r--sci-biology/afni/afni-20.1.16.ebuild73
-rw-r--r--sci-biology/afni/afni-20.3.03.ebuild73
-rw-r--r--sci-biology/afni/afni-22.0.21.ebuild75
-rw-r--r--sci-biology/afni/afni-24.0.04-r1.ebuild110
-rw-r--r--sci-biology/afni/afni-24.0.08-r1.ebuild114
-rw-r--r--sci-biology/afni/files/afni-20.1.16-python.patch11
-rw-r--r--sci-biology/afni/files/afni-24.0.04-whirlgif.patch39
-rw-r--r--sci-biology/afni/metadata.xml3
-rw-r--r--sci-biology/ants/files/ants-2.4.1-fix-compile.patch13
-rw-r--r--sci-biology/behaviopy/Manifest1
-rw-r--r--sci-biology/behaviopy/behaviopy-0.2.ebuild42
-rw-r--r--sci-biology/behaviopy/metadata.xml26
-rw-r--r--sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch30
-rw-r--r--sci-biology/clview/Manifest2
-rw-r--r--sci-biology/clview/clview-0.1.ebuild108
-rw-r--r--sci-biology/clview/metadata.xml15
-rw-r--r--sci-biology/deeptools/deeptools-3.5.0.ebuild5
-rw-r--r--sci-biology/deeptools/deeptools-3.5.1.ebuild5
-rw-r--r--sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild5
-rw-r--r--sci-biology/fastp/Manifest1
-rw-r--r--sci-biology/fastp/fastp-0.23.4.ebuild20
-rw-r--r--sci-biology/fastp/metadata.xml11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch12
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch21
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch10
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-setup.patch198
-rw-r--r--sci-biology/fsl/fsl-6.0.4.ebuild4
-rw-r--r--sci-biology/gffcompare/files/Makefile.patch79
-rw-r--r--sci-biology/imagej/Manifest5
-rw-r--r--sci-biology/imagej/imagej-1.53t.ebuild122
-rw-r--r--sci-biology/imagej/imagej-1.54h-r1.ebuild (renamed from sci-biology/imagej/imagej-1.54f.ebuild)4
-rw-r--r--sci-biology/imagej/imagej-9999.ebuild4
-rw-r--r--sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild2
-rw-r--r--sci-biology/libBigWig/Manifest1
-rw-r--r--sci-biology/libBigWig/libBigWig-0.4.7.ebuild31
-rw-r--r--sci-biology/multiqc/Manifest1
-rw-r--r--sci-biology/multiqc/metadata.xml12
-rw-r--r--sci-biology/multiqc/multiqc-1.19.ebuild40
-rw-r--r--sci-biology/neuroconv/Manifest2
-rw-r--r--sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild (renamed from sci-biology/neuroconv/neuroconv-0.2.4.ebuild)12
-rw-r--r--sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch39
-rw-r--r--sci-biology/nitime/Manifest1
-rw-r--r--sci-biology/nitime/metadata.xml6
-rw-r--r--sci-biology/nitime/nitime-0.10.2.ebuild33
-rw-r--r--sci-biology/nitime/nitime-9999.ebuild10
-rw-r--r--sci-biology/samri/samri-0.5.3.ebuild2
-rw-r--r--sci-biology/samri/samri-0.5.4.ebuild2
-rw-r--r--sci-biology/samri/samri-9999.ebuild2
-rw-r--r--sci-biology/sra-tools/files/libs_sra_Makefile.patch77
-rw-r--r--sci-biology/sra-tools/files/sra_sdk-destdir.patch76
-rw-r--r--sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch12
56 files changed, 525 insertions, 1162 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/afni/Manifest b/sci-biology/afni/Manifest
index e8caa43d1..d1e783ff1 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,3 +1,4 @@
-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-24.0.04.gh.tar.gz 52888143 BLAKE2B db414b9ac9489aaab824e6f99cae54a1982e600d3b6d93a01cf3f175220ab76923a53ce6da647e4d8be87d3b50699c1b9603f8f0de43d812d34ceb1a65bde19d SHA512 aff673b63453a18c1f687775a6316614ee7495ff583e86c341aa0eed40d5f99b15cb599dea79baf05f8f8b77fea292436e3adc51b906dc13589968a8bdffa3d8
+DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6
+DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2
+DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5
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/${CONFLICT}" || die
- done
-}
diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild
new file mode 100644
index 000000000..557fbd579
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -0,0 +1,110 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${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
+ "
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-libs/glib:2
+ dev-libs/libf2c
+ dev-libs/expat
+ dev-build/ninja
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ 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="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+src_prepare() {
+ tar xf "${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}/${P}-whirlgif.patch"
+ fi
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(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
+}
diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild
new file mode 100644
index 000000000..20293877f
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2021 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 cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+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
+ "
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-libs/glib:2
+ dev-libs/libf2c
+ dev-libs/expat
+ dev-build/ninja
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ 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="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+ #tar xf "${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
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(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
+}
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/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/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/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/fastp/metadata.xml b/sci-biology/fastp/metadata.xml
new file mode 100644
index 000000000..d51d87c5a
--- /dev/null
+++ b/sci-biology/fastp/metadata.xml
@@ -0,0 +1,11 @@
+<?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">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/imagej/Manifest b/sci-biology/imagej/Manifest
index bd58b4117..4c5068f0a 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-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615
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-1.54h-r1.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-1.54f.ebuild
+++ b/sci-biology/imagej/imagej-1.54h-r1.ebuild
@@ -6,7 +6,7 @@ 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"
@@ -59,7 +59,7 @@ src_prepare() {
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..0252d6613 100644
--- a/sci-biology/imagej/imagej-9999.ebuild
+++ b/sci-biology/imagej/imagej-9999.ebuild
@@ -6,7 +6,7 @@ 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"
@@ -59,7 +59,7 @@ src_prepare() {
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="${ED}"
+}
diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest
new file mode 100644
index 000000000..3585038a3
--- /dev/null
+++ b/sci-biology/multiqc/Manifest
@@ -0,0 +1 @@
+DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354
diff --git a/sci-biology/multiqc/metadata.xml b/sci-biology/multiqc/metadata.xml
new file mode 100644
index 000000000..09bd2b6e6
--- /dev/null
+++ b/sci-biology/multiqc/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">ewels/MultiQC</remote-id>
+ <remote-id type="pypi">multiqc</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild
new file mode 100644
index 000000000..187f06c22
--- /dev/null
+++ b/sci-biology/multiqc/multiqc-1.19.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+
+inherit pypi distutils-r1
+
+DESCRIPTION="Aggregate bioinformatics results across many samples into a single report"
+HOMEPAGE="https://multiqc.info/"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+
+RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/coloredlogs[${PYTHON_USEDEP}]
+ dev-python/future[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/lzstring[${PYTHON_USEDEP}]
+ dev-python/markdown[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/rich[${PYTHON_USEDEP}]
+ dev-python/rich-click[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/spectra[${PYTHON_USEDEP}]
+ dev-python/importlib-metadata[$PYTHON_USEDEP]
+ dev-python/humanize[$PYTHON_USEDEP]
+ dev-python/pyaml-env[$PYTHON_USEDEP]"
+
+# pypi tarball does not include tests
+RESTRICT="test"
+#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/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[${PYTHON_USEDEP}]
@@ -35,7 +33,3 @@ RDEPEND="
distutils_enable_tests pytest
distutils_enable_sphinx doc
-
-python_test() {
- virtx pytest -v || die
-}
diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild
index d6ffd5f1f..f632f83a8 100644
--- a/sci-biology/samri/samri-0.5.3.ebuild
+++ b/sci-biology/samri/samri-0.5.3.ebuild
@@ -48,7 +48,7 @@ RDEPEND="
>=sci-libs/nipy-0.4.1[${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 \