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* sci-biology/cluster: Correct masking, #419999Justin Lecher2012-06-093-2/+7
| | | | (Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/cluster: Rename cluster to cluster3, #419999Justin Lecher2012-06-072-0/+61
| | | | (Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)
* improved die() message to inform user that gcc-4.5.3 does not work while ↵Martin Mokrejs2012-06-012-1/+6
| | | | | | gcc-4.3.6 does (Portage version: 2.1.10.63/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/cluster: Version Bump, Move to EAPI=4Justin Lecher2012-05-245-65/+62
| | | | (Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/mira: Add missing eutils.eclass, bump to EAPI=4, remove usage of ↵Justin Lecher2012-05-226-188/+22
| | | | | | base.eclass; drop old (Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/gbrowse: Add missing eutils.eclass, bump to EAPI=4, remove ↵Justin Lecher2012-05-224-25/+35
| | | | | | unnecessary bits (Portage version: 2.2.0_alpha107/git/Linux x86_64, RepoMan options: --force, unsigned Manifest commit)
* sci-biology/est2uni: Bump to EAPI=4, remove unnecessary bitsJustin Lecher2012-05-223-41/+47
| | | | (Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/emboss: Add missing eutils.eclassJustin Lecher2012-05-222-3/+6
| | | | (Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/amos: Bump to EAPI=4, remove unnecessary bitsJustin Lecher2012-05-222-16/+19
| | | | (Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
* in main treeAndrey Kislyuk2012-04-154-40/+0
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* fix manifestAndrey Kislyuk2012-03-221-1/+3
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* New package, ebuild written by meAndrey Kislyuk2012-03-224-0/+53
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* This version and newer is in the treeJustin Lecher2012-03-215-391/+0
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* sci-biology/mosaik: masking mosaik-2.1.33 mosaik-9999Martin Mokrejs2012-03-163-2/+9
| | | | (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/sra_sdk-2.1.9: added missing insintoMartin Mokrejs2012-03-152-0/+5
| | | | (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/sra_sdk-2.1.9: use EAPI=4 hoping it will handle symlinks in bin/ ↵Martin Mokrejs2012-03-152-4/+23
| | | | | | and lib/ directories properly (but it does not, bug #408199 (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/mosaik: version bump for 2.1.33 and GIT HEAD, neither compiles ↵Martin Mokrejs2012-03-153-14/+71
| | | | | | so far; upstream re-contacted (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* version bump, added the pdf documentation to SRC_URI, the compile process ↵Martin Mokrejs2012-03-155-0/+107
| | | | | | leaks through many 'Fastq.cpp:224: error: conditional expression between distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266, Fasta.cpp:268, but the package itself installs and executes at least (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/cutadapt: new packageMartin Mokrejs2012-03-034-0/+41
| | | | (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/phylobayes: new package, no explicit LICENSE statedMartin Mokrejs2012-03-022-0/+11
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* sci-biology/phylobayes: new package, no explicit LICENSE statedMartin Mokrejs2012-03-022-0/+47
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* sci-biology/cufflinks: new packageMartin Mokrejs2012-03-024-0/+40
| | | | (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* updated ManifestMartin Mokrejs2012-02-291-3/+3
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* sci-biology/sra_sdk-2.1.9: remove trailing whitespaceMartin Mokrejs2012-02-281-1/+1
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* sci-biology/sra_sdk-2.1.9: almost working ebuildMartin Mokrejs2012-02-284-27/+120
| | | | (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/gbrowse-2.48: added dependency on <=sci-biology/primer3-2, per ↵Martin Mokrejs2012-02-284-1/+210
| | | | | | http://generic-model-organism-system-database.450254.n5.nabble.com/PrimerDesigner-working-in-2-40-tp4724773p5479669.html (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/artemis: adjust ebuild based on upstream providing a MakefileMartin Mokrejs2012-02-082-2/+5
| | | | (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/artemis: adjust ebuild based on upstream providing a MakefileMartin Mokrejs2012-02-082-2/+10
| | | | (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/apollo: new packageMartin Mokrejs2012-02-082-1/+11
| | | | (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/tablet-bin: adjust PATH to point to the installation placeMartin Mokrejs2012-02-072-0/+7
| | | | (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* adjust PATH to point to the installation place, few comment lines changesMartin Mokrejs2012-02-072-3/+12
| | | | (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/tablet-bin-1.11.11.01: make use of the TMPDIR variableMartin Mokrejs2012-02-073-5/+9
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* added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS ↵Martin Mokrejs2012-02-072-7/+10
| | | | | | DENIED messages quiet, bugs #402507 (learned from bug #387227) (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS ↵Martin Mokrejs2012-02-072-1/+18
| | | | | | DENIED messages quiet, bugs #402507 (learned from bug #387227) (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/OBO-Edit: more attempts to get rid of sandbox ACCESS VIOLATION ↵Martin Mokrejs2012-02-072-2/+5
| | | | | | SUMMARY errors (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/OBO-Edit: more attempts to get rid of sandbox ACCESS VIOLATION ↵Martin Mokrejs2012-02-074-5/+76
| | | | | | SUMMARY errors (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology-sra_sdk-2.1.9: preserve libs written directly into at the end ↵Martin Mokrejs2012-02-063-5/+14
| | | | | | of src_compile() and install them later on (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/sra_sdk-2.1.6: dropping an old crapMartin Mokrejs2012-02-061-73/+0
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* two more Makefiles needed a DESTDIR patch, in conjunction with an ugly ↵Martin Mokrejs2012-02-064-29/+112
| | | | | | symlink hack in one can build the stuff; dobin does not transfer symliks so every binary appears installed 3 times; upstream bug http://jira.be-md.ncbi.nlm.nih.gov/browse/TR-10207 (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/sra_sdk-2.1.9: version bump and almost correct DESTDIR patchMartin Mokrejs2012-02-065-9/+172
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* sci-biology/seaview: and the path to the helpfile was corrected in the ↵Martin Mokrejs2012-01-301-0/+4
| | | | Makefile to match intended location specified in ebuild
* sci-biology/seaview: version bump; add missing symlink so that the C++ ↵Martin Mokrejs2012-01-304-0/+99
| | | | | | header can be found; remove calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not include path) to /usr/include/fltk-1 so that svg.o gets included during linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*) (Portage version: 2.1.10.44/git/Linux x86_64, unsigned Manifest commit)
* sci-biology/wgs-assembler-7.0: version bump, would be nice if we could stop ↵Martin Mokrejs2012-01-274-0/+92
| | | | | | compilation of the kmer/ subdir (an r1916 snapshot) and DEPEND on the external http://kmer.sourceforge.net complete bundle instead (Portage version: 2.1.10.44/git/Linux i686, unsigned Manifest commit)
* version bump and some fixes so that it works with webappconfig again?Martin Mokrejs2012-01-174-0/+238
| | | | (Portage version: 2.1.10.44/git/Linux i686, unsigned Manifest commit)
* sci-biology/lastz: A pairwise DNA sequence aligner (also chromosome to ↵Martin Mokrejs2012-01-174-0/+48
| | | | chromosome), a BLASTZ replacement
* sci-biology/YASRA: Yet Another Short Read Assembler to reference using LASTZMartin Mokrejs2012-01-174-0/+44
| | | | (Portage version: 2.1.10.43/git/Linux i686, unsigned Manifest commit)
* sci-biology/gbrowse: added dev-perl/TermReadKey to dependenciesMartin Mokrejs2012-01-173-13/+18
| | | | (Portage version: 2.1.10.43/git/Linux i686, unsigned Manifest commit)
* sci-biology/libgtextutils: Gordon text utils libraryMartin Mokrejs2012-01-164-0/+41
| | | | (Portage version: 2.1.10.43/git/Linux i686, unsigned Manifest commit)
* Convert to thin manifests (as suggested by alexxy and jlec)Andreas K. Huettel (dilfridge)2012-01-1493-693/+0
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* Removed because the sources cannot be fetchedAndreas K. Huettel (dilfridge)2012-01-143-27/+5
| | | | (Portage version: 2.1.10.44/git/Linux x86_64, unsigned Manifest commit)