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* 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"
* sci-biology/mothur: x86 stable wrt bug #556066Agostino Sarubbo2015-09-251-1/+1
| | | | | Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="x86"
* sci-biology/samtools: amd64 stable wrt bug #525630Agostino Sarubbo2015-09-241-1/+1
| | | | | Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="amd64"
* Update hashes in ManifestJustin Lecher2015-09-2342-63/+63
| | | | | | Add missing SHA512 and WHIRLPOOL hashes Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/flower: remove package masked in bug #553636.Michael Orlitzky2015-09-214-87/+0
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* sci-biology/rebase: amd64/ppc/x86 stable, (ALLARCHES policy) wrt bug #559222Agostino Sarubbo2015-09-191-1/+1
| | | | Package-Manager: portage-2.2.20.1
* ADd missing remote-id entriesJustin Lecher2015-09-071-0/+3
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bedtools: Fixing HOMEPAGE move due to code.google.com shutdownTobias Klausmann2015-09-012-2/+2
| | | | Package-Manager: portage-2.2.20.1
* sci-biology/beast-mcmc: Fixing HOMEPAGE move due to code.google.com shutdownTobias Klausmann2015-09-013-3/+3
| | | | Package-Manager: portage-2.2.20.1
* sci-biology/rebase: Version BumpJustin Lecher2015-08-312-0/+47
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/emboss: Drop oldJustin Lecher2015-08-273-232/+0
| | | | | | | | | | | | | | | | | obsolets multiple bugs Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=542274 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=534418 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521604 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=514014 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=493724 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=406279 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=393311 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=382321 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=378443 Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/clustal-omega: Drop oldJustin Lecher2015-08-272-39/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-cbstools: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-domalign: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-domainatrix: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-domsearch: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-emnu: Drop oldJustin Lecher2015-08-272-21/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-esim4: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-hmmer: Drop oldJustin Lecher2015-08-272-23/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-iprscan: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-memenew: Drop obsoleteJustin Lecher2015-08-273-26/+0
| | | | | | Gentoo-Bugs: https://bugs.gentoo.org/556932 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-mira: Drop obsoleteJustin Lecher2015-08-273-20/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-mse: Drop oldJustin Lecher2015-08-272-21/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-phylipnew: Drop oldJustin Lecher2015-08-272-16/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-signature: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-structure: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/embassy-topo: Drop oldJustin Lecher2015-08-272-15/+0
| | | | | Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>