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* 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>
* sci-biology/muscle: drop unused flag-o-matic from 5.1.0Sam James2024-03-201-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/muscle: add 5.1.0Eli Schwartz2024-03-203-0/+83
| | | | | | | | | | | | | | | Major new release, major new build system that is majorly broken. <3 scientific code. This package has not been updated since before the import of gentoo into git, so I shall simply assume this major version is safe. From the homepage, it is a "major rewrite", "based on new algorithms", which is "much more accurate, is often faster, and scales to much larger datasets". I think that's another way of saying "same old program but with fixes". Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/muscle: mark as LTO-unsafe, strict-aliasing unsafeEli Schwartz2024-03-201-2/+10
| | | | | | Closes: https://bugs.gentoo.org/862276 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/glimmerhmm: update EAPI 7 -> 8Sam James2024-03-121-3/+2
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/glimmerhmm: fix SRC_URISam James2024-03-121-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/glimmerhmm: add 3.0.4Eli Schwartz2024-03-123-0/+202
| | | | | | | This is the 2015 release so about time we packaged it, I suppose. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/glimmerhmm: patch sources to fix LTOEli Schwartz2024-03-122-1/+29
| | | | | | | | | Upstream last released in 2015. I don't have high hopes for a change but I sent an email to the contact address. ;) Closes: https://bugs.gentoo.org/862270 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/abyss: mark as LTO-unsafeEli Schwartz2024-03-081-1/+6
| | | | | | Closes: https://bugs.gentoo.org/862252 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/abyss: remove useless sedEli Schwartz2024-03-081-2/+1
| | | | | | | | It seds out something that hasn't existed since 2012: https://github.com/bcgsc/abyss/commit/ded065d3b257e72ceb70ad3f6dd399019b00b46e Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/bwa: mark as LTO-unsafeEli Schwartz2024-02-291-2/+7
| | | | | | Closes: https://bugs.gentoo.org/862255 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/exonerate: mark LTO-unsafeEli Schwartz2024-02-291-2/+7
| | | | | | Closes: https://bugs.gentoo.org/862264 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* Move {sys-devel → dev-build}/consMichał Górny2024-01-171-2/+3
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* Move {sys-devel → dev-build}/autoconf-archiveMichał Górny2024-01-151-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/biopython: sys-devel/flex -> app-alternatives/lexSam James2024-01-081-2/+2
| | | | | | | | | | All of these will be using app-alternatives/lex anyway as they're not unsetting YACC or LEX, so make the dep reflect reality. (Included both YACC and LEX out of conservatism.) Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/pilercr: Stabilize 1.0-r3 amd64, #920144Arthur Zamarin2023-12-161-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-biology/tree-puzzle: fix configure checks for modern cSam James2023-12-022-0/+21
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/treeviewx: add 0.5.1.20100823_p4Pacho Ramos2023-11-242-0/+53
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/stride: stabilize 20060723 for amd64Pacho Ramos2023-10-191-1/+1
| | | | | | | As current stable cannot be installed and, at the end, it is the same code from updated sources Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/stride: add 20060723Pacho Ramos2023-10-192-0/+37
| | | | | | | Update upstream sources location and rebase our patch Closes: https://bugs.gentoo.org/912948 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/express: treecleanFlorian Schmaus2023-10-025-121/+0
| | | | | Closes: https://bugs.gentoo.org/912828 Signed-off-by: Florian Schmaus <flow@gentoo.org>