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* sci-biology/amap: drop 2.2-r5Volkmar W. Pogatzki2024-09-011-59/+0
| | | | | Signed-off-by: Volkmar W. Pogatzki <gentoo@pogatzki.net> Signed-off-by: Miroslav Šulc <fordfrog@gentoo.org>
* sci-biology/amap: build with java-pkg-simple, add apidocsVolkmar W. Pogatzki2024-08-271-0/+55
| | | | | | Signed-off-by: Volkmar W. Pogatzki <gentoo@pogatzki.net> Closes: https://github.com/gentoo/gentoo/pull/37468/commits/0b394429f6c5387f57fbc675683e003eaff25337 Signed-off-by: Miroslav Šulc <fordfrog@gentoo.org>
* sci-biology/fasta: add 36.3.8iEli Schwartz2024-08-222-0/+82
| | | | | | | | | | A 2022 release, how modern. :D Ignore the part where the tag name contains the date "2020". It obsoletes the patch as well, which seems good. However it does NOT fix the LTO issue. Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-biology/fasta: mark as LTO-unsafeEli Schwartz2024-08-221-0/+5
| | | | | Closes: https://bugs.gentoo.org/862267 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-biology/fasta: remove tcsh as a test dependency, drop IUSEEli Schwartz2024-08-221-5/+2
| | | | | | | | | | | | | | | | | | | | | This has been present since the initial import into cvs: https://gitweb.gentoo.org/archive/repo/gentoo-2.git/commit/?id=fe5d632c39746b7b396434277896dd0e58e15567 It does not seem to have made any sense at the time -- the compile phase required running `emake -f ../make/Makefile***` because upstream was one of those projects that apparently liked having code separate from ways to build the code (???) and no src_test was defined at all. So having a test dependency made no real sense as tests were never run!!! There is an actual test phase today. It manually runs an sh script, and tcsh still isn't involved anywhere. There are two entirely separate tcsh scripts in the upstream codebase, though. Regardless, having this test dependency is nonsensical. So is having IUSE=test and a matching RESTRICT. None of this gets us *anything*. Therefore, drop it. Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-biology/bowtie: enable py3.12Pacho Ramos2024-07-301-1/+1
| | | | | Closes: https://bugs.gentoo.org/929753 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/treeviewx: drop 0.5.1-r3Pacho Ramos2024-07-0510-367/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/biopython: enable py3.12Alexey Shvetsov2024-06-051-1/+1
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-biology/ucsc-genome-browser: BDEPEND on cpioSam James2024-06-021-1/+4
| | | | | Closes: https://bugs.gentoo.org/688748 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/ucsc-genome-browser: EAPI 8Sam James2024-06-021-14/+12
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/ucsc-genome-browser: fix USE=-serverSam James2024-06-021-1/+7
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/ucsc-genome-browser: workaround modern C issuesSam James2024-06-021-1/+3
| | | | | | | | | Build with -std=gnu89 as it has many issues. Closes: https://bugs.gentoo.org/831491 Closes: https://bugs.gentoo.org/919200 Closes: https://bugs.gentoo.org/921261 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/pysam: drop 0.21.0David Seifert2024-05-243-97/+0
| | | | | | | Closes: https://bugs.gentoo.org/923243 Closes: https://bugs.gentoo.org/927872 Closes: https://bugs.gentoo.org/929754 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: add 0.22.1David Seifert2024-05-242-0/+69
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: add 1.20David Seifert2024-05-242-0/+43
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add 1.20David Seifert2024-05-242-0/+48
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: drop 1.17David Seifert2024-05-242-48/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: drop 1.17David Seifert2024-05-242-43/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/raxml: drop 7.2.6David Seifert2024-05-243-67/+0
| | | | | | Closes: https://bugs.gentoo.org/822408 Closes: https://bugs.gentoo.org/831489 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/raxml: add 8.2.13David Seifert2024-05-244-4/+83
| | | | | | Bug: https://bugs.gentoo.org/822408 Bug: https://bugs.gentoo.org/831489 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/hmmer: Add missing include into configureNHOrus2024-05-092-1/+20
| | | | | | | | | | | There are no autotools source files, so we can't just autoreconf the problem out of existence [sam: Revbump.] Closes: https://bugs.gentoo.org/900551 Signed-off-by: NHOrus <jy6x2b32pie9@yahoo.com> Closes: https://github.com/gentoo/gentoo/pull/36599 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/paml: restore ~x86Sam James2024-05-081-1/+1
| | | | | | Unclear why it was dropped. Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/paml: respect CC, CPPFLAGS, LDFLAGSSam James2024-05-082-4/+64
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/paml: add 4.10.7NHOrus2024-05-083-0/+41
| | | | | | | | | | Project source is now hosted on github. Closes: https://bugs.gentoo.org/831488 Closes: https://bugs.gentoo.org/919885 Signed-off-by: NHOrus <jy6x2b32pie9@yahoo.com> Closes: https://github.com/gentoo/gentoo/pull/36048 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/velvet: fixup whitespace & openmp checkSam James2024-05-081-9/+18
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/velvet: scrub patch, add bug refSam James2024-05-081-2/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/velvet: Fix incompatible pointer types in 1.2.10NHOrus2024-05-082-2/+38
| | | | | | | | | | | | * C99 porting. Split multi-assignments of NULLs into multiple lines * Also added dependencies on OpenMP if USE=openmp is enabled [sam: Formatting tweaks to commit msg.] Closes: https://bugs.gentoo.org/919223 Signed-off-by: NHOrus <jy6x2b32pie9@yahoo.com> Closes: https://github.com/gentoo/gentoo/pull/35993 Signed-off-by: Sam James <sam@gentoo.org>
* */*: inline mirror://sourceforgeLucio Sauer2024-04-3010-21/+21
| | | | | | | bump copyright of touched ebuilds to 2024 Signed-off-by: Lucio Sauer <watermanpaint@posteo.net> Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/maq: Fix assignment to incompatible pointer typeBrahmajit Das2024-04-272-2/+26
| | | | | | | Closes: https://github.com/gentoo/gentoo/pull/36459 Closes: https://bugs.gentoo.org/921137 Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/maqview: Fix passing of incompatible pointer typeBrahmajit Das2024-04-272-2/+15
| | | | | | | Closes: https://github.com/gentoo/gentoo/pull/36460 Closes: https://bugs.gentoo.org/930767 Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: treecleanArthur Zamarin2024-04-274-145/+0
| | | | | | Closes: https://bugs.gentoo.org/910015 Bug: https://bugs.gentoo.org/923242 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-biology/bedtools/files: add upstream PR referenceDavid Seifert2024-04-252-0/+4
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: add 2.31.1David Seifert2024-04-255-0/+352
| | | | | | | Bug: https://bugs.gentoo.org/881783 Bug: https://bugs.gentoo.org/907971 Bug: https://bugs.gentoo.org/929751 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/treeviewx: Stabilize 0.5.1.20100823_p4 amd64, #930203Sam James2024-04-181-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/treeviewx: add github upstream metadataPacho Ramos2024-04-181-0/+3
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/treeviewx: Update icon cachePacho Ramos2024-04-181-2/+2
| | | | | Closes: https://bugs.gentoo.org/924697 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/newick-utils: update EAPI 7 -> 8Eli Schwartz2024-04-111-1/+1
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/newick-utils: update HOMEPAGE, SRC_URI to archive.orgEli Schwartz2024-04-111-2/+2
| | | | | | | | The whole thing is a redirect now to a website with no real info, that points to a github repo without even any tags. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/newick-utils: mark as LTO-unsafeEli Schwartz2024-04-111-2/+7
| | | | | | Closes: https://bugs.gentoo.org/862279 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/kallisto: update EAPI 7 -> 8Eli Schwartz2024-04-071-1/+1
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/kallisto: port to catch2 version 3Eli Schwartz2024-04-073-9/+13
| | | | | | | | | Which is the current default distributed version. Nicer than requiring people to downgrade to an old version. Closes: https://bugs.gentoo.org/877887 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/emboss: avoid file collision with dev-texlive/texlive-latexextraDavid Seifert2024-03-301-0/+3
| | | | | Closes: https://bugs.gentoo.org/927976 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopandas: Remove last-rited pkgMichał Górny2024-03-293-45/+0
| | | | | Closes: https://bugs.gentoo.org/878721 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bcftools: add 1.19David Seifert2024-03-262-0/+43
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add 1.19.2David Seifert2024-03-262-0/+48
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mothur: uncomment patch...Sam James2024-03-221-1/+1
| | | | | Closes: https://bugs.gentoo.org/927495 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/mothur: add 1.48.0Sam James2024-03-224-0/+139
| | | | | | | | Filter LTO too, and no-SA. Not reported upstream as it has a lot of open bugs already and seems low activity. Closes: https://bugs.gentoo.org/862273 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/qrna: add 2.0.4Eli Schwartz2024-03-213-0/+443
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is the 2006 edition of the software. It has a bunch of useful fixes: - it fixes Modern C porting issues - it fixes LTO errors - it incorporates the glibc-2.10 patch just by upgrading! It's about time we upgrade, since it is 18 years later. Along the way we fix up the ebuild a bit: - bump to EAPI 8 - acquire an actual SRC_URI, not just the gentoo mirror - update the homepage along with the SRC_URI. The original homepage is dead, and the domain redirects to a new domain (whence comes the new distfile). It has some shortcomings too: - the distfile comes with free .svn directories, which have to be pruned. - the distfile comes without the 80mb demos To solve this, we use the old distfile (which I think only exists on Gentoo's mirror network) and gate it behind a USE=examples flag, in case anyone needs them. Closes: https://bugs.gentoo.org/862285 Closes: https://bugs.gentoo.org/884283 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/t-coffee: mark as LTO-unsafe, strict-aliasing unsafeEli Schwartz2024-03-201-1/+9
| | | | | | Closes: https://bugs.gentoo.org/862327 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/muscle: fix variable orderSam James2024-03-201-2/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>