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* Set appropriate maintainer types in metadata.xml (GLEP 67)Michał Górny2016-01-24151-161/+161
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* Replace all herds with appropriate projects (GLEP 67)Michał Górny2016-01-24150-153/+612
| | | | | Replace all uses of herd with appropriate project maintainers, or no maintainers in case of herds requested to be disbanded.
* Unify quoting in metadata.xml files for machine processingMichał Górny2016-01-2421-22/+21
| | | | | | | Force unified quoting in all metadata.xml files since lxml does not preserve original use of single and double quotes. Ensuring unified quoting before the process allows distinguishing the GLEP 67-related metadata.xml changes from unrelated quoting changes.
* sci-biology/iedera: Remove hardcoded {C,CXX,LD}FLAGS from configure.acDavid Seifert2016-01-212-4/+24
| | | | Package-Manager: portage-2.2.27
* sci-biology/gmap: Version bump to 2015.12.31.5David Seifert2016-01-212-0/+22
| | | | | | | | Gentoo-Bug: 521640 * Remove use of 'einstall' * EAPI=6 Package-Manager: portage-2.2.27
* Fix typo repo wideJustin Lecher2016-01-211-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/iedera: Version bump to 1.05David Seifert2016-01-212-0/+23
| | | | | | | | Gentoo-Bug: 521642 * Remove use of 'einstall' * EAPI=6 Package-Manager: portage-2.2.26
* sci-biology/newick-utils: Version bump to 1.6David Seifert2016-01-212-0/+22
| | | | | | | | Gentoo-Bug: 521644 * Remove use of 'einstall' * EAPI=6 Package-Manager: portage-2.2.26
* sci-biology/vaal: Place blockers on sci-biology/allpaths{,lg}David Seifert2016-01-171-4/+10
| | | | | | Gentoo-Bug: 572128 Package-Manager: portage-2.2.26
* sci-biology/allpathslg: Add blocking packages to RDEPEND tooDavid Seifert2016-01-171-6/+10
| | | | Package-Manager: portage-2.2.26
* Drop myself as maintainerJustin Lecher2016-01-093-10/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Update remote-ids in metadata.xmlJustin Lecher2016-01-071-1/+2
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Drop oldJustin Lecher2016-01-032-47/+0
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: amd64/ppc/x86 stable, (ALLARCHES policy) wrt bug #570636Agostino Sarubbo2016-01-021-1/+1
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/rebase: Drop oldJustin Lecher2016-01-022-47/+0
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2016-01-022-0/+47
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/dialign-tx: fixes GCC-5 inline semantics and -Wformat= warnings, ↵Ted Tanberry2015-12-312-1/+132
| | | | | | #570252 Package-Manager: portage-2.2.26
* sci-biology/allpathslg: Block sci-biology/vaal as it is nicluded in this releaseJustin Lecher2015-12-291-1/+1
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=570070 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/vaal: Remove old patchesTed Tanberry2015-12-275-286/+0
| | | | Package-Manager: portage-2.2.26
* sci-biology/vaal: Gentoo-Bug: 568438, fix global namespace std:: clash.Ted Tanberry2015-12-272-0/+953
| | | | Package-Manager: portage-2.2.26
* sci-biology/embassy-vienna: Add explicit -std=gnu89 to CFLAGSTed Tanberry2015-12-261-1/+6
| | | | Package-Manager: portage-2.2.26
* sci-biology/bowtie: Chop DESCRIPTION to 80 charsJustin Lecher2015-12-261-1/+1
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bowtie: Drop oldJustin Lecher2015-12-263-90/+0
| | | | | | | | obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bowtie: x86 stable wrt bug #569706Agostino Sarubbo2015-12-251-1/+1
| | | | | | Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bowtie: x86 stable wrt bug #569708Agostino Sarubbo2015-12-251-1/+1
| | | | | | Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bowtie: amd64 stable wrt bug #569706Agostino Sarubbo2015-12-251-1/+1
| | | | | | Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bowtie: amd64 stable wrt bug #569708Agostino Sarubbo2015-12-251-1/+1
| | | | | | Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bfast: Fix inliningJustin Lecher2015-12-251-2/+4
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=569656 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/mcl: Version bump, fix bug 569040 and QA issues.Ted Tanberry2015-12-253-0/+64
| | | | Package-Manager: portage-2.2.26
* sci-biology/rmblast: Fix bug 569622.Ted Tanberry2015-12-251-0/+1
| | | | Package-Manager: portage-2.2.26
* sci-biology/t-coffee: Import fix for CVE-2015-8621Justin Lecher2015-12-253-0/+63
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=569650 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/allpathslg: Drop oldJustin Lecher2015-12-233-92/+0
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/allpathslg: default_src_configure doesn't support myeconfargsJustin Lecher2015-12-231-4/+2
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/allpathslg: Version bump and fix bug 568440.Ted Tanberry2015-12-234-0/+1832
| | | | Package-Manager: portage-2.2.26
* sci-biology/bamtools: Add missing die and drop old patchJustin Lecher2015-12-132-33/+3
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bamtools: Unbundle dev-libs/jsoncppJustin Lecher2015-12-131-9/+24
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=568090 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-emnu: Fix call to eclass functionJustin Lecher2015-12-072-2/+2
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=567630 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/phylip: Fix install path for libsJustin Lecher2015-12-071-0/+1
| | | | | Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/biopandas: New package, ebuild written by meJustin Lecher2015-11-243-0/+56
| | | | | Package-Manager: portage-2.2.25 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-mse: Move use_enable call to local scopeJustin Lecher2015-11-232-2/+6
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=566546 Package-Manager: portage-2.2.25 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-emnu: Move use_enable call to local scopeJustin Lecher2015-11-232-3/+7
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=566546 Package-Manager: portage-2.2.25 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/seaview: Version BumpJustin Lecher2015-11-202-0/+78
| | | | | | | | | fixes compilation problems with newer fltk Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=556750 Package-Manager: portage-2.2.25 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2015-10-302-0/+47
| | | | | Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/biopython: Version BumpJustin Lecher2015-10-262-0/+57
| | | | | Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/treeviewx: Import debian patchset for wxgtk-3.0 supportJustin Lecher2015-10-258-73/+250
| | | | | | | Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=563970 Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop deprecated usage of parallel python eclass functionsJustin Lecher2015-10-221-1/+1
| | | | | | | | Python eclasses dropped parallel execution support some while ago. python_parallel_foreach_impl was an alias for python_foreach_impl for some time already. Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/tophat: correct dependency on sci-biology/seqanSergey Popov2015-10-192-2/+2
| | | | | | Gentoo-Bug: 546816 Package-Manager: portage-2.2.20
* sci-biology/seqan: drop SSE instruction check in pkg_pretend(), which ↵Sergey Popov2015-10-191-12/+3
| | | | | | sometimes fails on correct situations, add -msse4.1 unconditionally Package-Manager: portage-2.2.20
* sci-biology/seqan: correct dependency on sci-biology/samtoolsSergey Popov2015-10-191-1/+9
| | | | | | | | | Seqan 1.3.1 does not compile with samtools greater than 0.1.19 Also it does not compile with GCC 4.9 or higher, so restrict this too Gentoo-Bug: 514250 Package-Manager: portage-2.2.20
* Update remote-idsJustin Lecher2015-10-161-1/+4
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>