diff options
Diffstat (limited to 'sci-biology')
14 files changed, 96 insertions, 103 deletions
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 9cbcbdd02db5..67e4996d956c 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,2 +1,2 @@ -DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502 SHA512 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68 DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B 43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f SHA512 a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746 +DIST bcftools-1.20.tar.bz2 7883049 BLAKE2B 36bfd82c9500f384b75ef93242a5879123f7fd63c893c95a1ce5efbfa9396f2c1fd75025ea2dd48d37e7dc93426ffaffbb2f3c6bdf64128fbdd3af2a2f760b17 SHA512 c77294923a6bb5cb97a2c4947e79aa215612a62f71ba0e4dde627cd3d97ee9a28a3682e8ab2f3bedd0e75e2bb9800915d9430f9504f09ead4492d3583553db2a diff --git a/sci-biology/bcftools/bcftools-1.17.ebuild b/sci-biology/bcftools/bcftools-1.20.ebuild index 6adee705bb46..27d474fe35f9 100644 --- a/sci-biology/bcftools/bcftools-1.17.ebuild +++ b/sci-biology/bcftools/bcftools-1.20.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) inherit python-single-r1 diff --git a/sci-biology/biopython/biopython-1.81-r1.ebuild b/sci-biology/biopython/biopython-1.81-r1.ebuild index f4fd86ba3ffb..96d83b74b492 100644 --- a/sci-biology/biopython/biopython-1.81-r1.ebuild +++ b/sci-biology/biopython/biopython-1.81-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) DISTUTILS_USE_PEP517="setuptools" DISTUTILS_EXT=1 diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 2bc79f89f441..2859d25293fc 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1 @@ -DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7 +DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350 diff --git a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch deleted file mode 100644 index 303a4fb0dcdc..000000000000 --- a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch +++ /dev/null @@ -1,24 +0,0 @@ -From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001 -From: John Marshall <jmarshall@hey.com> -Date: Sat, 8 Apr 2023 11:00:46 +1200 -Subject: [PATCH] Remove incorrect type annotation - -The annotation already in pysam/libcbcf.pyi is correct. -Fixes #1179 as reopened on April 6th. ---- - pysam/libcbcf.pyx | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx -index 8c088af2..8ecfe5f3 100644 ---- a/pysam/libcbcf.pyx -+++ b/pysam/libcbcf.pyx -@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object): - return bcf_format_get_alleles(self) - - @alleles.setter -- def alleles(self, value: tuple): -+ def alleles(self, value): - # Sets the genotype, supply a tuple of alleles to set. - # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord - # The genotype is reset when an empty tuple, None or (None,) is supplied diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.22.1.ebuild index 77292ed29613..9070476873e1 100644 --- a/sci-biology/pysam/pysam-0.21.0.ebuild +++ b/sci-biology/pysam/pysam-0.22.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) inherit distutils-r1 @@ -17,30 +17,26 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="=sci-libs/htslib-1.17*:=" +RDEPEND="=sci-libs/htslib-1.20*:=" DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] dev-python/setuptools[${PYTHON_USEDEP}]" BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] test? ( - =sci-biology/bcftools-1.17* - =sci-biology/samtools-1.17* + =sci-biology/bcftools-1.20* + =sci-biology/samtools-1.20* )" distutils_enable_tests pytest DISTUTILS_IN_SOURCE_BUILD=1 -PATCHES=( - # backport - # https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9 - "${FILESDIR}"/${P}-cython-3.patch -) - EPYTEST_DESELECT=( # only work with bundled htslib 'tests/tabix_test.py::TestRemoteFileHTTP' 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' + + 'tests/AlignedSegment_test.py::TestBaseModifications' ) python_prepare_all() { diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest index 8b5ec91eee6e..56416ac10d7f 100644 --- a/sci-biology/raxml/Manifest +++ b/sci-biology/raxml/Manifest @@ -1 +1 @@ -DIST RAxML-7.2.6.tar.bz2 202803 BLAKE2B 579676ff9fad1563eabb9507015acff010977a89ae087df9b828b80bc9352ed44c98faeaf4c8d884ffa14176bfa28772dc9872ad8b5d401aff8b834c728e5f65 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 +DIST raxml-8.2.13.tar.gz 10201721 BLAKE2B ee48dc599947619d12a54cafef1eee554abc0df30a31ba2fdb501b228dadec9f137acff8f472047f4686304f74d27893696c95ff808baa128c2c3d83539366a1 SHA512 c99dc3f8c8798cda38c644501f474c0261e72c1f3b64d594d5006fa03e8d8c4da3bdf20b8e3c6c9f669c9509d5af27a0c286a2570a54c8ff7df7cd63c1f78885 diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch deleted file mode 100644 index 6b82ed65b770..000000000000 --- a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch +++ /dev/null @@ -1,29 +0,0 @@ - Makefile.gcc | 6 +++--- - 1 files changed, 3 insertions(+), 3 deletions(-) - -diff --git a/Makefile.gcc b/Makefile.gcc -index 716b6c6..f0c1de2 100644 ---- a/Makefile.gcc -+++ b/Makefile.gcc -@@ -1,10 +1,10 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> - --CC = gcc -+CC ?= gcc - - --CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse -+CPPFLAGS += -D_GNU_SOURCE - - - -@@ -19,7 +19,7 @@ all : raxmlHPC - GLOBAL_DEPS = axml.h globalVariables.h - - raxmlHPC : $(objs) -- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) -+ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) $(LIBS) - - classify.o : classify.c $(GLOBAL_DEPS) - evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/files/raxml-8.2.13-makefile.patch b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch new file mode 100644 index 000000000000..d774b1fb824d --- /dev/null +++ b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch @@ -0,0 +1,37 @@ +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,7 +1,6 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> + +-CC = gcc + + ARCH := $(shell uname -m) + ifeq ($(ARCH), x86_64) +@@ -10,7 +9,7 @@ + ARCH_CFLAGS= + endif + +-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast ++CFLAGS += -D_GNU_SOURCE #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + + LIBRARIES = -lm + +@@ -23,7 +22,7 @@ + GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h + + raxmlHPC : $(objs) +- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) + + rmqs.o : rmqs.c $(GLOBAL_DEPS) + classify.o : classify.c $(GLOBAL_DEPS) +@@ -51,8 +50,6 @@ + + + +-eigen.o : eigen.c $(GLOBAL_DEPS) +- $(CC) -c -o eigen.o eigen.c + clean : + $(RM) *.o raxmlHPC + diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml index ccdff086e20b..dd68d972db31 100644 --- a/sci-biology/raxml/metadata.xml +++ b/sci-biology/raxml/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">stamatak/standard-RAxML</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild index adb044426381..859016195389 100644 --- a/sci-biology/raxml/raxml-7.2.6.ebuild +++ b/sci-biology/raxml/raxml-8.2.13.ebuild @@ -1,29 +1,30 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit flag-o-matic toolchain-funcs DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" -HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" -SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" -S="${WORKDIR}/RAxML-${PV}" +HOMEPAGE="https://github.com/stamatak/standard-RAxML" +SRC_URI="https://github.com/stamatak/standard-RAxML/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/standard-RAxML-${PV}" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="cpu_flags_x86_sse3 +threads" -REQUIRED_USE="cpu_flags_x86_sse3" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) src_configure() { - use cpu_flags_x86_sse3 && append-cppflags -D__SIM_SSE3 - use threads && \ - append-cppflags -D_USE_PTHREADS && \ - append-libs -pthread + use cpu_flags_x86_sse3 && + append-cppflags -D__SIM_SSE3 && + append-cflags -msse3 + use threads && + append-cppflags -D_USE_PTHREADS && + append-cflags -pthread tc-export CC } diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 09cffe1bb5b0..c3163dc68eeb 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,2 +1,2 @@ -DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3 DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f +DIST samtools-1.20.tar.bz2 9179938 BLAKE2B b534e659899a822e191c779a6ce9247854036da3435a0b63748783edc96d610ff0f02f73bbb5c1eab3ff86dbcca331113f3312a7c3376141ef89b6a8684446e4 SHA512 8526286243d057758cb846311d0a8c728026d31438e87fcc03e0df576f33bcc6da0e18bce141dbdc438a116341c94aa92701cdf10ba6b1301eadedbb34120822 diff --git a/sci-biology/samtools/samtools-1.17.ebuild b/sci-biology/samtools/samtools-1.20.ebuild index e105621c7865..42879b0f8698 100644 --- a/sci-biology/samtools/samtools-1.17.ebuild +++ b/sci-biology/samtools/samtools-1.20.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 diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild index f0bb0676ae85..ef96f491fb51 100644 --- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild @@ -1,32 +1,40 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 +WEBAPP_MANUAL_SLOT="yes" +# TODO: use WEBAPP_OPTIONAL? inherit toolchain-funcs flag-o-matic webapp DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath" HOMEPAGE="http://genome.ucsc.edu/" SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip" +S="${WORKDIR}/kent" LICENSE="blat" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="+mysql +server static-libs" - REQUIRED_USE="server? ( mysql )" -WEBAPP_MANUAL_SLOT="yes" - +# TODO: test with other webservers RDEPEND=" - dev-libs/openssl:0= - media-libs/libpng:0= + dev-libs/openssl:= + media-libs/libpng:= !<sci-biology/ucsc-genome-browser-223 - mysql? ( dev-db/mysql-connector-c:0= ) - server? ( virtual/httpd-cgi )" # TODO: test with other webservers -DEPEND="${RDEPEND} app-arch/unzip" - -S="${WORKDIR}/kent" + mysql? ( dev-db/mysql-connector-c:= ) + server? ( virtual/httpd-cgi ) +" +DEPEND="${RDEPEND}" +BDEPEND=" + app-alternatives/cpio + app-arch/unzip +" + +pkg_setup() { + use server && webapp_pkg_setup +} src_prepare() { default @@ -35,6 +43,8 @@ src_prepare() { # bug #708064 append-flags -fcommon + # bug #831491, bug #919200, bug #921261 + append-flags -std=gnu89 sed \ -e 's/-Werror//' \ @@ -64,10 +74,9 @@ src_compile() { export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none" - # TODO: Change ${EPREFIX} to ${ESYSROOT} in EAPI 7 - # (and ideally use pkg-config here) - use mysql && export MYSQLLIBS="-L${EPREFIX%/}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ - MYSQLINC="${EPREFIX%/}/usr/include/mysql" + # TODO: use pkg-config here + use mysql && export MYSQLLIBS="-L${ESYSROOT}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ + MYSQLINC="${ESYSROOT}/usr/include/mysql" use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \ CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin" |