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* 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>
* sci-biology/bowtie: Respect CXXJustin Lecher2015-10-142-1/+2
| | | | | Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bowtie: bring back stable bowtie-0.12.8Ted Tanberry2015-10-143-0/+90
| | | | | bowtie-0.12.8 is the only stable variant and removing it breaks the stable depgraph.
* sci-biology/bowtie-2.2.6: Enable 'tbb' USE flag by defaultTed Tanberry2015-10-141-1/+1
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* sci-biology/bowtie-1.1.2: Enable 'tbb' USE flag by defaultTed Tanberry2015-10-141-1/+1
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* sci-biology/bowtie: remove REQUIRED_USETed Tanberry2015-10-141-1/+7
| | | | | | When SSE2 support is not explicitly enabled, the user is informed by erroring out instead of portage recommending enabling cpu flags.
* sci-biology/bowtie: include descriptive header in patchTed Tanberry2015-10-141-0/+4
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* sci-biology/bowtie: do not remove -Wall from CXXFLAGSTed Tanberry2015-10-141-3/+0
| | | | Retain -Wall in CXXFLAGS in bowtie-1.1.2
* sci-biology/bowtie: Add bowtie2 in SLOT=2Ted Tanberry2015-10-141-0/+54
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* sci-biology/bowtie: version bump, SLOT major versionTed Tanberry2015-10-147-133/+79
| | | | | | sci-biology/bowtie is now SLOTed, in order to allow for a parallel installation with bowtie2. In addition, the latest bowtie now supports dev-cpp/tbb with 'tbb' USE flag.
* fix various encoding corruptionMike Frysinger2015-10-102-2/+2
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* Add missing remote-id type=sourceforgeJustin Lecher2015-10-0119-19/+76
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: amd64/ppc/x86 stable, (ALLARCHES policy) wrt bug #561946Agostino Sarubbo2015-10-011-1/+1
| | | | Package-Manager: portage-2.2.20.1
* sci-biology/rebase: Version BumpJustin Lecher2015-10-012-0/+47
| | | | | Package-Manager: portage-2.2.22 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Cleaned oldJustin Lecher2015-10-012-47/+0
| | | | | Package-Manager: portage-2.2.22 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/beast-mcmc: Updated dev-java/jdom slot from 1.0 -> 0 for v1William L. Thomson Jr2015-09-294-89/+6
| | | | Also removed old version.
* sci-biology/mothur: Drop oldJustin Lecher2015-09-252-34/+0
| | | | | Package-Manager: portage-2.2.21 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/uchime: x86 stable wrt bug #556066Agostino Sarubbo2015-09-251-1/+1
| | | | | Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="x86"