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* sci-biology/ncbi-tools++: bring back USE=mesa although it is about OSMesaMartin Mokrejš2014-06-263-11/+9
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* sci-biology/ncbi-tools++: fix 'make install if USE=pchMartin Mokrejš2014-06-262-0/+12
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* sci-biology/ncbi-tools++: dropped USE=ftds as it is useless and recommended ↵Martin Mokrejš2014-06-263-24/+17
| | | | by upstream to be disabled altogether
* sci-biology/ncbi-tools++-12.0.0: drop forgotten IUSE=sslMartin Mokrejš2014-06-261-1/+1
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* sci-biology/ncbi-tools++-12.0.0: added a blocker with sci-biology/sra_sdkMartin Mokrejš2014-06-261-0/+1
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* sci-biology/ncbi-tools++-12.0.0: more places where to drop ':%=%'Martin Mokrejš2014-06-261-1/+1
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* sci-biology/ncbi-tools++-12.0.0: more entries to ↵Martin Mokrejš2014-06-261-0/+22
| | | | ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
* sci-biology/ncbi-tools++-12.0.0: added the patch istelf dropping :%=% from ↵Martin Mokrejš2014-06-261-0/+22
| | | | LIB settings
* sci-biology/ncbi-tools++-12.0.0: dropping :%=% from LIB settingsMartin Mokrejš2014-06-261-0/+1
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* sci-biology/ncbi-tools++-9.0.0*: dropped altogether openssl-related USE ↵Martin Mokrejš2014-06-262-13/+5
| | | | flags and configure arguments (per upstream info nothing in the public code uses openssl and the configure test is there for their internal reasonings); dropped gnutls[lzo] requirement which was only need for unpatched 9.0.0 version; however, --with-lzo is still advantageous for http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html
* sci-biology/ncbi-tools++-12.0.0: dropped altogether openssl-related USE ↵Martin Mokrejš2014-06-261-3/+1
| | | | flags and configure arguments (per upstream info nothing in the public code uses openssl and the configure test is there for their internal reasonings); dropped gnutls[lzo] requirement which was only need for unpatched 9.0.0 version; however, --with-lzo is still advantageous for http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html
* sci-biology/barrnap: working ebuild although installing a pre-compiled ↵Martin Mokrejš2014-06-262-0/+33
| | | | | | binary and until somebody hacks teh main perl code it need to be installed into /usr/share/{PN} and modifies PATH accordingly Package-Manager: portage-2.2.7
* sci-biology/ncbi-tools++-12.0.0: cleanup comments and shutdown a false alarm ↵Martin Mokrejš2014-06-261-2/+1
| | | | message from mv
* sci-biology/ncbi-tools++-12.0.0: dropped unneeded patchMartin Mokrejš2014-06-261-1660/+0
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* sci-biology/ncbi-tools++-12.0.0: dropped unneeded patches, added direct ↵Martin Mokrejš2014-06-263-67/+2
| | | | dependency on glew because the dependency on virtual/opengl does not work
* sci-biology/ncbi-tools++-12.0.0: re-added update patch to configure so that ↵Martin Mokrejš2014-06-252-44264/+67
| | | | we can avoid eautoconf until there is autoconf-2.59 system-wide
* sci-biology/ncbi-tools++-12.0.0: install colliding files under a name ↵Martin Mokrejš2014-06-251-2/+6
| | | | suffixed by a plus sign
* sci-biology/ncbi-tools++-12.0.0: first compile-able ebuild, wow, huge thanks ↵Martin Mokrejš2014-06-254-6/+444
| | | | to Aaron Ucko from NCBI developers on the cpp@ mailing list
* more changes to get ncbi-tools++-12.0.0 compiledMartin Mokrejš2014-06-256-1448/+1968
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* sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ depsMartin Mokrejš2014-06-242-0/+16
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* sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ depsMartin Mokrejš2014-06-242-0/+38
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* dropped the duplicate part from the patchMartin Mokrejš2014-06-231-1660/+0
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* add an extra patch for configure until we find a way to ensure user has ↵Martin Mokrejš2014-06-232-6/+46083
| | | | autoconf-2.59 or for ncbi-tools++-12.0.0 may have autoconf-2.60
* updating the ChangeLog to note where the ↵Martin Mokrejš2014-06-231-1/+8
| | | | ncbi-tools++-12.0.0-support-autoconf-2.60.patch comes from
* add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed)Martin Mokrejš2014-06-232-3/+1667
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* sci-biology/sgp2: new package, worksMartin Mokrejš2014-06-175-0/+141
| | | | Package-Manager: portage-2.2.7
* sci-biology/geneid: new package, worksMartin Mokrejš2014-06-175-0/+62
| | | | Package-Manager: portage-2.2.7
* sci-biology/ncbi-tools++: added a note about a taxonomy database add-on not ↵Martin Mokrejš2014-06-023-0/+12
| | | | yet installed by Gentoo
* Add new ebuildAlexey Shvetsov2014-06-024-0/+54
| | | | Package-Manager: portage-2.2.10
* sci-biology/cd-hit-auxtools: added HTML manual pageMartin Mokrejš2014-06-013-1/+8
| | | | Package-Manager: portage-2.2.7
* sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG ↵Martin Mokrejš2014-06-015-0/+109
| | | | | | to loosen g++ strictness Package-Manager: portage-2.2.7
* sci-biology/cd-hit-4.6.1: forgot to re-enable the reworked patchMartin Mokrejš2014-06-012-1/+4
| | | | Package-Manager: portage-2.2.7
* sci-biology/cd-hit-4.6.1: version bumpMartin Mokrejš2014-06-015-0/+195
| | | | Package-Manager: portage-2.2.7
* sci-biology/bedtools-2.20.1: version bumpMartin Mokrejš2014-05-303-1/+7
| | | | Package-Manager: portage-2.2.7
* sci-biology/khmer: Version BUmpJustin Lecher2014-05-154-1/+71
| | | | Package-Manager: portage-2.2.10
* Imported to treeJustin Lecher2014-05-0710-304/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Configure worksJustin Lecher2014-05-061-8/+8
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/trf-4.07b: version bump; install some HTML helpfiles as wellMartin Mokrejš2014-04-224-0/+61
| | | | Package-Manager: portage-2.2.7
* sci-biology/mira-4.0.2: version bumpMartin Mokrejš2014-04-202-1/+1
| | | | Package-Manager: portage-2.2.7
* sci-biology/biopython: ops, taking back my own testing patchesMartin Mokrejš2014-04-183-224/+4
| | | | Package-Manager: portage-2.2.7
* sci-biology/biopython: upstream patch to downgrade an assert to a warningMartin Mokrejš2014-04-188-1/+371
| | | | Package-Manager: portage-2.2.7
* sci-biology/bedtools: version bump per bug #505538Martin Mokrejš2014-04-154-0/+59
| | | | Package-Manager: portage-2.2.7
* sci-biology/VelvetOptimiser: add requirement for threaded perlMartin Mokrejš2014-04-152-1/+5
| | | | Package-Manager: portage-2.2.7
* sci-biology/VelvetOptimiser: new packageMartin Mokrejš2014-04-154-0/+48
| | | | Package-Manager: portage-2.2.7
* sci-biology/velvetk: new packageMartin Mokrejš2014-04-154-0/+48
| | | | Package-Manager: portage-2.2.7
* sci-biology/nesoni: new package, needs some dev-lang/R -based packages to be ↵Martin Mokrejš2014-04-154-0/+53
| | | | | | installed Package-Manager: portage-2.2.7
* sci-biology/barrnap: new package, package contains bundled binaries, untestedMartin Mokrejš2014-04-154-0/+41
| | | | Package-Manager: portage-2.2.7
* sci-biology/mira-4.0.1: bump to current recommended bugfix releaseMartin Mokrejš2014-04-123-0/+82
| | | | Package-Manager: portage-2.2.7
* sci-biology/consed: add a stub file for consedrc; refer to it via ↵Martin Mokrejš2014-04-059-0/+30
| | | | | | CONSED_PARAMETERS Package-Manager: portage-2.2.7
* sci-biology/consed: fix more hardcoded pathsMartin Mokrejš2014-04-059-8/+29
| | | | Package-Manager: portage-2.2.7