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* sci-biology/MolBioLib: yet another package with bundled samtools, bamtools etc.Martin Mokrejš2016-04-013-0/+44
| | | | Package-Manager: portage-2.2.28
* sci-biology/roche454ace2caf: Drop keywords, Bump to EAPI=6Marius Brehler2016-04-011-3/+3
| | | | Package-Manager: portage-2.2.26
* sci-biology/gap2caf: Drop keywordsMarius Brehler2016-04-011-2/+2
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* sci-biology/staden: Drop keywords since keywords were droped for staden_docMarius Brehler2016-04-011-1/+1
| | | | Package-Manager: portage-2.2.26
* sci-biology/staden: Fix copyright and dependciesMarius Brehler2016-04-012-4/+4
| | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --force
* sci-biology/bamtools: version bump; still suffers gentoo bug #550144Martin Mokrejš2016-04-013-0/+55
| | | | Package-Manager: portage-2.2.28
* sci-biology/reapr: quick and dirty Debian patches do not help me with ↵Martin Mokrejš2016-04-013-3/+277
| | | | | | sci-biology/bamtools-2.3.0 installed site-wide; the bundled bamtools do not start to compile and tehrefore reapr linking steps fail while using using system-wide incompatible version Package-Manager: portage-2.2.28
* sci-biology/karect: new packageMartin Mokrejš2016-03-313-0/+46
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* sci-biology/cross_genome: polish ebuild syntaxMartin Mokrejš2016-03-301-1/+1
| | | | Package-Manager: portage-2.2.28
* sci-biology/CONTIGuator: version bump; added KEYWORDS because DEPENDencies ↵Martin Mokrejš2016-03-303-17/+32
| | | | | | are in the tree now Package-Manager: portage-2.2.28
* sci-biology/arachne: new package; does not compile (upstream contacted) and ↵Martin Mokrejš2016-03-303-0/+54
| | | | | | the LICENSE is not exactly MIT? Package-Manager: portage-2.2.28
* sci-biology/cap3-bin: fix version number to match version generated at ↵Martin Mokrejš2016-03-303-0/+43
| | | | | | runtime; added new version Package-Manager: portage-2.2.28
* sci-biology/reapr: new package with bundled samtools, bamtools, tabix ↵Martin Mokrejš2016-03-303-0/+70
| | | | | | (nowadays part of samtools) and other binaries; does not link probably due to a clash of symbols with my system-wide installed -lbamtools Package-Manager: portage-2.2.28
* sci-biology/exomiser-bin: improve ebuild, fix LICENSE, a 19GB files should ↵Martin Mokrejš2016-03-303-24/+34
| | | | | | be fetched manually but the ebuild should get access to it, unpack it and install as the files make grounding for a usable workspace Package-Manager: portage-2.2.28
* sci-biology/DisEMBL: added DEPENDency on tiseanMartin Mokrejš2016-03-301-1/+1
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* sci-biology/TransDecoder: version bumpMartin Mokrejš2016-03-303-0/+106
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* fixing /# : $/# $/Martin Mokrejš2016-03-301-1/+1
| | | | Package-Manager: portage-2.2.28
* fixing /# : $/# $/Martin Mokrejš2016-03-301-1/+1
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* fixing /# : $/# $/Martin Mokrejš2016-03-303-0/+38
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* sci-biology/perga: added some LICENSE, fix CFLAGSMartin Mokrejš2016-03-302-0/+48
| | | | Package-Manager: portage-2.2.28
* sci-biology/artemis: install docs, cleanup ebuild and bring it in sync with ↵Martin Mokrejš2016-03-302-6/+16
| | | | | | sci-biology/act-bin and sci-biology/artemis-9999 Package-Manager: portage-2.2.28
* sci-biology/artemis-bin: install docs, cleanup ebuild and bring it in sync ↵Martin Mokrejš2016-03-301-1/+1
| | | | | | with sci-biology/act-bin and sci-biology/artemis-9999 Package-Manager: portage-2.2.28
* sci-biology/artemis-bin: install docs, cleanup ebuild and bring it in sync ↵Martin Mokrejš2016-03-302-6/+25
| | | | | | with sci-biology/act-bin and sci-biology/artemis-9999 Package-Manager: portage-2.2.28
* sci-biology/act-bin: new java package with upstream binariesMartin Mokrejš2016-03-303-0/+66
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* sci-biology/scaffold_builder: clarify descriptionMartin Mokrejš2016-03-301-1/+1
| | | | Package-Manager: portage-2.2.28
* sci-biology/staden_doc: removing KEYWORDS as upstream just fixed generation ↵Martin Mokrejš2016-03-291-1/+1
| | | | | | of the manual pages, currently available code does not work Package-Manager: portage-2.2.28
* sci-biology/perlprimer: Follow pkgmove of perl-tkJustin Lecher2016-03-291-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/manatee-igs: Fix typo in depsJustin Lecher2016-03-291-3/+3
| | | | | | * Bump to EAPI=6 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/ONTO-PERL: Fix typo in depsJustin Lecher2016-03-291-3/+3
| | | | | | * Bump to EAPI=6 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/staden: add a note about some tutorial availableMartin Mokrejš2016-03-252-0/+8
| | | | Package-Manager: portage-2.2.26
* sci-biology/staden: io_lib/bam.h appeared first in io_lib-1.13.8Martin Mokrejš2016-03-252-2/+3
| | | | Package-Manager: portage-2.2.26
* sci-biology/staden: rename patch files; remove unnecessary patchMartin Mokrejš2016-03-254-17/+0
| | | | Package-Manager: portage-2.2.26
* sci-biology/fgap: fix typo in a package nameMartin Mokrejš2016-03-251-1/+1
| | | | Package-Manager: portage-2.2.26
* sci-biology/consed: fix ebuild not to create /etc/consedrc/ but to create a ↵Martin Mokrejš2016-03-241-2/+1
| | | | | | file /etc/consedrc instead Package-Manager: portage-2.2.26
* sci-biology/amos: document 'Could not open file ↵Martin Mokrejš2016-03-232-2/+17
| | | | | | LIBGUESTFS_PATH=/usr/share/guestfs/appliance' error to be solved; add support for a system-wide config file via AMOSCONF env variable Package-Manager: portage-2.2.26
* sci-biology/staden: version bump; remove unused USE=curl, introduce USE=doc ↵Martin Mokrejš2016-03-233-18/+11
| | | | | | for a separate package Package-Manager: portage-2.2.26
* sci-biology/staden_doc: new packageMartin Mokrejš2016-03-233-0/+57
| | | | Package-Manager: portage-2.2.26
* sci-biology/fgap: new package which needs either octave or matlab runtimeMartin Mokrejš2016-03-233-0/+39
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* sci-biology/consed-29: add also DEPEND on >=samtools-0.1.18Martin Mokrejš2016-03-201-0/+1
| | | | Package-Manager: portage-2.2.26
* sci-biology/consed: fix the autogenerated /etc/env.d/ file and make sure the ↵Martin Mokrejš2016-03-181-4/+4
| | | | | | EPREFIX is expanded in it (should be also fixed in consed-27 in the main gentoo repo), check yourself 'printenv | grep CONSED' and do not forger env-update && . /etc/profile before re-testing; the first part of the patch now properly edits the variable in perl-based scripts/*; however, I am still getting some issue with 'consed -ace 454Contigs.ace.1 -fixContigEnds' giving me:\nabout to run: /usr/bin/fixContigEnd.perl right_contig00004|m.2.ref_160318.171619.fasta right_contig00004|m.2.ref_160318.171619.fixConsensusEndAceFile.fof\nUse of uninitialized value [1] in string eq at /usr/bin/fixContigEnd.perl line 21.\nsh: m.2.ref_160318.171619.fasta: command not found\nsh: m.2.ref_160318.171619.fixConsensusEndAceFile.fof: command not found\n Package-Manager: portage-2.2.26
* sci-biology/scythe: improve DESCRIPTIONMartin Mokrejš2016-03-171-1/+1
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* sci-biology/cutadapt: version bump and remove old ones; update HOMEPAGEMartin Mokrejš2016-03-155-41/+3
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* sci-biology/cd-hit: add a local copy of the wiki manualMartin Mokrejš2016-03-153-4/+215
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* sci-biology/cd-hit: update digest of the fetched HTML manualMartin Mokrejš2016-03-151-1/+1
| | | | Package-Manager: portage-2.2.26
* sci-biology/cd-hit: version bump; new SRC_URI; merge with ↵Martin Mokrejš2016-03-154-70/+133
| | | | | | sci-biology/cd-hit-auxtools Package-Manager: portage-2.2.26
* sci-biology/trimmomatic: version bump; no 0.35 PDF manual exists for downloadMartin Mokrejš2016-03-152-3/+3
| | | | Package-Manager: portage-2.2.26
* sci-biology/scbi_mapreduce: version bump; do not die on missing README.rdoc ↵Martin Mokrejš2016-03-142-2/+2
| | | | | | and History.txt Package-Manager: portage-2.2.26
* sci-biology/cg-cat: working ebuild, still could provide shellscript callers ↵Martin Mokrejš2016-03-141-9/+26
| | | | | | to call the java .jar file and add -d64 on amd64 hosts Package-Manager: portage-2.2.26
* sci-biology/full_lengther_next: added more DEPENDencies, added more relevant ↵Martin Mokrejš2016-03-131-4/+8
| | | | | | HOMEPAGE Package-Manager: portage-2.2.26
* sci-biology/full_lengther_next: version bumpMartin Mokrejš2016-03-132-1/+1
| | | | Package-Manager: portage-2.2.26