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* sci-biology/embassy-emnu: Patch out -L/usr/lib for LLDDavid Seifert2020-11-021-22/+23
| | | | | | Closes: https://bugs.gentoo.org/731750 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/clustalw-mpi: Port to EAPI 7David Seifert2020-11-014-18/+32
| | | | | | | | | | * Rename USE flags to avoid underscore * Fix building against GCC 10 / -fno-common Closes: https://bugs.gentoo.org/695122 Closes: https://bugs.gentoo.org/706960 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/lagan: Port to EAPI 7David Seifert2020-11-0112-664/+550
| | | | | | | | | | | | | * Fix building against GCC 10 / -fno-common * Fix building against C99 / -O0 * Fix broken build system * Import patches from Debian Closes: https://bugs.gentoo.org/685736 Closes: https://bugs.gentoo.org/688700 Closes: https://bugs.gentoo.org/707404 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/seaview: Remove old 4.5.4David Seifert2020-11-012-77/+0
| | | | | | Closes: https://bugs.gentoo.org/588506 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/seaview: Port to EAPI 7David Seifert2020-11-013-12/+203
| | | | | | | | | | * Fix building against GCC 10 / -fno-common * Fix building against Clang Closes: https://bugs.gentoo.org/707842 Closes: https://bugs.gentoo.org/741198 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/newick-utils: Port to EAPI 7David Seifert2020-11-015-24/+245
| | | | | | | | | | | | * Don't build static libraries by default * Fix GCC 10 / -fno-common * Disable automagic guile and lua Closes: https://bugs.gentoo.org/708534 Closes: https://bugs.gentoo.org/712312 Closes: https://bugs.gentoo.org/727986 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Patch out -L/usr/lib for LLDDavid Seifert2020-11-011-17/+17
| | | | | | Closes: https://bugs.gentoo.org/731858 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Fix -fno-commonDavid Seifert2020-11-012-2/+632
| | | | | | Closes: https://bugs.gentoo.org/706414 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gmap: Remove old 2015.12.31.5David Seifert2020-11-012-21/+0
| | | | | | Closes: https://bugs.gentoo.org/708626 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gmap: Version bump to 2020.10.27David Seifert2020-11-013-0/+40
| | | | | | Bug: https://bugs.gentoo.org/708626 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/paml: Remove old 4.4c-r1David Seifert2020-11-012-48/+0
| | | | | | Closes: https://bugs.gentoo.org/706708 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/paml: Version bump to 4.9jDavid Seifert2020-11-014-0/+100
| | | | | | Bug: https://bugs.gentoo.org/706708 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/dialign-tx: Fix -fno-commonDavid Seifert2020-11-013-6/+49
| | | | | | | Closes: https://bugs.gentoo.org/707008 Closes: https://bugs.gentoo.org/727966 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/profphd: Port to EAPI 7David Seifert2020-10-272-17/+24
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/profphd: Remove old 1.0.39David Seifert2020-10-272-38/+0
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/muscle: Port to EAPI 7David Seifert2020-10-272-12/+9
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/unafold: Port to EAPI 7David Seifert2020-10-272-8/+22
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/phylip: Remove oldDavid Seifert2020-10-274-162/+0
| | | | | | | Closes: https://bugs.gentoo.org/707150 Closes: https://bugs.gentoo.org/727982 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/phylip: Version bump to 3.698David Seifert2020-10-274-0/+397
| | | | | | | Bug: https://bugs.gentoo.org/707150 Bug: https://bugs.gentoo.org/727982 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/amos: Remove last-rited pkgMichał Górny2020-10-097-357/+0
| | | | | Closes: https://bugs.gentoo.org/735448 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/embassy-meme: Remove last-rited pkgMichał Górny2020-10-094-129/+0
| | | | | Closes: https://bugs.gentoo.org/735446 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/meme: Remove last-rited pkgMichał Górny2020-10-096-901/+0
| | | | | Closes: https://bugs.gentoo.org/735446 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/shrimp: Remove last-rited pkgMichał Górny2020-10-093-91/+0
| | | | | Closes: https://bugs.gentoo.org/735440 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/vienna-rna: Remove last-rited pkgMichał Górny2020-10-096-193/+0
| | | | | Closes: https://bugs.gentoo.org/735438 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bwa: Remove old 0.7.16aDavid Seifert2020-09-264-71/+0
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bwa: Bump version to 0.7.17David Seifert2020-09-264-0/+93
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/seaview: drop old EAPI=5Aaron Bauman2020-09-242-77/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/seqan: remove unused fileMichael Mair-Keimberger2020-09-181-10/+0
| | | | | | | Closes: https://github.com/gentoo/gentoo/pull/17590 Package-Manager: Portage-3.0.6, Repoman-3.0.1 Signed-off-by: Michael Mair-Keimberger <m.mairkeimberger@gmail.com> Signed-off-by: David Seifert <soap@gentoo.org>
* Move {sci-libs → dev-python}/scipyMichał Górny2020-09-181-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: [QA] Remove redundant <longdescription/>sMichał Górny2020-09-142-6/+0
| | | | | | Signed-off-by: Michał Górny <mgorny@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/17540 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/embassy: Remove embassy-memeMichał Górny2020-09-091-2/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/seqan: Eradicate doc (python2)Michał Górny2020-09-092-34/+16
| | | | | Closes: https://bugs.gentoo.org/735442 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/seqan: Remove old (drop to ~arch)Michał Górny2020-09-096-243/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bowtie: Remove oldMichał Górny2020-09-0910-718/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/libgtextutils: update maintainer email since current is not ↵Agostino Sarubbo2020-09-081-1/+1
| | | | | | | subscribed to bugzilla Package-Manager: Portage-2.3.103, Repoman-2.3.23 Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/biopython: Inherit optfeature.eclassDavid Seifert2020-09-071-1/+1
| | | | | Package-Manager: Portage-3.0.5, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopython: Remove old 1.73David Seifert2020-08-222-58/+0
| | | | | Package-Manager: Portage-3.0.4, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopython: Version bump to 1.77David Seifert2020-08-222-0/+63
| | | | | Package-Manager: Portage-3.0.4, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopandas: Remove old 0.2.1David Seifert2020-08-172-44/+0
| | | | | | Closes: https://bugs.gentoo.org/718470 Package-Manager: Portage-3.0.3, Repoman-3.0.0 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopandas: Version bump to 0.2.7David Seifert2020-08-172-0/+41
| | | | | | Bug: https://bugs.gentoo.org/718470 Package-Manager: Portage-3.0.3, Repoman-3.0.0 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Add missing ${PYTHON_DEPS} to BDEPENDDavid Seifert2020-08-161-1/+3
| | | | | Package-Manager: Portage-3.0.2, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Remove oldDavid Seifert2020-08-162-46/+0
| | | | | | Closes: https://bugs.gentoo.org/718468 Package-Manager: Portage-3.0.2, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Version bump to 2.29.2David Seifert2020-08-165-0/+185
| | | | | | Bug: https://bugs.gentoo.org/718468 Package-Manager: Portage-3.0.2, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: Remove oldDavid Seifert2020-08-034-525/+0
| | | | | | Closes: https://bugs.gentoo.org/728018 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: Remove oldDavid Seifert2020-08-037-148/+0
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: Remove oldDavid Seifert2020-08-033-111/+0
| | | | | | | | Closes: https://bugs.gentoo.org/645060 Closes: https://bugs.gentoo.org/646986 Closes: https://bugs.gentoo.org/718472 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: [QA] Fix UnnecessarySlashStripDavid Seifert2020-08-031-5/+5
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: Remove ancient py2 varfilter.py scriptDavid Seifert2020-08-031-23/+13
| | | | | | Closes: https://bugs.gentoo.org/735444 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: Remove oldDavid Seifert2020-08-032-32/+0
| | | | | | | | | * Remove the package.mask entry again Closes: https://bugs.gentoo.org/696484 Closes: https://bugs.gentoo.org/718466 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: Sync live ebuildDavid Seifert2020-08-031-6/+8
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>