Commit message (Collapse) | Author | Age | Files | Lines | |
---|---|---|---|---|---|
* | sci-biology/MolBioLib: yet another package with bundled samtools, bamtools etc. | Martin Mokrejš | 2016-04-01 | 3 | -0/+44 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/roche454ace2caf: Drop keywords, Bump to EAPI=6 | Marius Brehler | 2016-04-01 | 1 | -3/+3 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/gap2caf: Drop keywords | Marius Brehler | 2016-04-01 | 1 | -2/+2 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/staden: Drop keywords since keywords were droped for staden_doc | Marius Brehler | 2016-04-01 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/staden: Fix copyright and dependcies | Marius Brehler | 2016-04-01 | 2 | -4/+4 |
| | | | | | Package-Manager: portage-2.2.26 RepoMan-Options: --force | ||||
* | sci-biology/bamtools: version bump; still suffers gentoo bug #550144 | Martin Mokrejš | 2016-04-01 | 3 | -0/+55 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/reapr: quick and dirty Debian patches do not help me with ↵ | Martin Mokrejš | 2016-04-01 | 3 | -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 package | Martin Mokrejš | 2016-03-31 | 3 | -0/+46 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/cross_genome: polish ebuild syntax | Martin Mokrejš | 2016-03-30 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/CONTIGuator: version bump; added KEYWORDS because DEPENDencies ↵ | Martin Mokrejš | 2016-03-30 | 3 | -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 Mokrejš | 2016-03-30 | 3 | -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 Mokrejš | 2016-03-30 | 3 | -0/+43 |
| | | | | | | runtime; added new version Package-Manager: portage-2.2.28 | ||||
* | sci-biology/reapr: new package with bundled samtools, bamtools, tabix ↵ | Martin Mokrejš | 2016-03-30 | 3 | -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 Mokrejš | 2016-03-30 | 3 | -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 tisean | Martin Mokrejš | 2016-03-30 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/TransDecoder: version bump | Martin Mokrejš | 2016-03-30 | 3 | -0/+106 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | fixing /# : $/# $/ | Martin Mokrejš | 2016-03-30 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | fixing /# : $/# $/ | Martin Mokrejš | 2016-03-30 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | fixing /# : $/# $/ | Martin Mokrejš | 2016-03-30 | 3 | -0/+38 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/perga: added some LICENSE, fix CFLAGS | Martin Mokrejš | 2016-03-30 | 2 | -0/+48 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/artemis: install docs, cleanup ebuild and bring it in sync with ↵ | Martin Mokrejš | 2016-03-30 | 2 | -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 Mokrejš | 2016-03-30 | 1 | -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 Mokrejš | 2016-03-30 | 2 | -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 binaries | Martin Mokrejš | 2016-03-30 | 3 | -0/+66 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/scaffold_builder: clarify description | Martin Mokrejš | 2016-03-30 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.28 | ||||
* | sci-biology/staden_doc: removing KEYWORDS as upstream just fixed generation ↵ | Martin Mokrejš | 2016-03-29 | 1 | -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-tk | Justin Lecher | 2016-03-29 | 1 | -1/+1 |
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> | ||||
* | sci-biology/manatee-igs: Fix typo in deps | Justin Lecher | 2016-03-29 | 1 | -3/+3 |
| | | | | | | * Bump to EAPI=6 Signed-off-by: Justin Lecher <jlec@gentoo.org> | ||||
* | sci-biology/ONTO-PERL: Fix typo in deps | Justin Lecher | 2016-03-29 | 1 | -3/+3 |
| | | | | | | * Bump to EAPI=6 Signed-off-by: Justin Lecher <jlec@gentoo.org> | ||||
* | sci-biology/staden: add a note about some tutorial available | Martin Mokrejš | 2016-03-25 | 2 | -0/+8 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/staden: io_lib/bam.h appeared first in io_lib-1.13.8 | Martin Mokrejš | 2016-03-25 | 2 | -2/+3 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/staden: rename patch files; remove unnecessary patch | Martin Mokrejš | 2016-03-25 | 4 | -17/+0 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/fgap: fix typo in a package name | Martin Mokrejš | 2016-03-25 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/consed: fix ebuild not to create /etc/consedrc/ but to create a ↵ | Martin Mokrejš | 2016-03-24 | 1 | -2/+1 |
| | | | | | | file /etc/consedrc instead Package-Manager: portage-2.2.26 | ||||
* | sci-biology/amos: document 'Could not open file ↵ | Martin Mokrejš | 2016-03-23 | 2 | -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 Mokrejš | 2016-03-23 | 3 | -18/+11 |
| | | | | | | for a separate package Package-Manager: portage-2.2.26 | ||||
* | sci-biology/staden_doc: new package | Martin Mokrejš | 2016-03-23 | 3 | -0/+57 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/fgap: new package which needs either octave or matlab runtime | Martin Mokrejš | 2016-03-23 | 3 | -0/+39 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/consed-29: add also DEPEND on >=samtools-0.1.18 | Martin Mokrejš | 2016-03-20 | 1 | -0/+1 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/consed: fix the autogenerated /etc/env.d/ file and make sure the ↵ | Martin Mokrejš | 2016-03-18 | 1 | -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 DESCRIPTION | Martin Mokrejš | 2016-03-17 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/cutadapt: version bump and remove old ones; update HOMEPAGE | Martin Mokrejš | 2016-03-15 | 5 | -41/+3 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/cd-hit: add a local copy of the wiki manual | Martin Mokrejš | 2016-03-15 | 3 | -4/+215 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/cd-hit: update digest of the fetched HTML manual | Martin Mokrejš | 2016-03-15 | 1 | -1/+1 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/cd-hit: version bump; new SRC_URI; merge with ↵ | Martin Mokrejš | 2016-03-15 | 4 | -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 download | Martin Mokrejš | 2016-03-15 | 2 | -3/+3 |
| | | | | Package-Manager: portage-2.2.26 | ||||
* | sci-biology/scbi_mapreduce: version bump; do not die on missing README.rdoc ↵ | Martin Mokrejš | 2016-03-14 | 2 | -2/+2 |
| | | | | | | and History.txt Package-Manager: portage-2.2.26 | ||||
* | sci-biology/cg-cat: working ebuild, still could provide shellscript callers ↵ | Martin Mokrejš | 2016-03-14 | 1 | -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 Mokrejš | 2016-03-13 | 1 | -4/+8 |
| | | | | | | HOMEPAGE Package-Manager: portage-2.2.26 | ||||
* | sci-biology/full_lengther_next: version bump | Martin Mokrejš | 2016-03-13 | 2 | -1/+1 |
| | | | | Package-Manager: portage-2.2.26 |