Get Gentoo!
gentoo.org sites
gentoo.org Wiki Bugs Forums Packages
Planet Archives Sources
Infra Status
aboutsummaryrefslogtreecommitdiff
path: root/sci-biology
Commit message (Collapse)AuthorAgeFilesLines
* sci-biology/nilearn: fixed testsHorea Christian2018-08-024-6/+51
| | | | Package-Manager: Portage-2.3.44, Repoman-2.3.10
* sci-biology/nilearn: version bumpHorea Christian2018-08-022-0/+52
| | | | Package-Manager: Portage-2.3.44, Repoman-2.3.10
* sci-biology/nilearn: EAPI and PYTHON_COMPAT bumpHorea Christian2018-08-022-4/+4
| | | | Package-Manager: Portage-2.3.44, Repoman-2.3.10
* sci-biology/samri_bindata: Updated manifestHorea Christian2018-07-281-1/+1
| | | | | | version replaced inplace by upstream Package-Manager: Portage-2.3.43, Repoman-2.3.10
* sci-biology/mouse-brain-atlases: version bumpHorea Christian2018-07-192-2/+2
| | | | Package-Manager: Portage-2.3.43, Repoman-2.3.10
* sci-biology/mouse-brain-atlases: Updated homepageHorea Christian2018-07-194-4/+4
| | | | Package-Manager: Portage-2.3.41, Repoman-2.3.9
* sci-biology/mouse-brain-atlases: version bumpHorea Christian2018-07-192-0/+46
| | | | Package-Manager: Portage-2.3.41, Repoman-2.3.9
* sci-biology/mouse-brain-atlases: version bumpHorea Christian2018-07-173-0/+49
| | | | Package-Manager: Portage-2.3.41, Repoman-2.3.9
* sci-biology/samri_bindata: version bumpHorea Christian2018-07-172-0/+22
| | | | Package-Manager: Portage-2.3.41, Repoman-2.3.9
* sci-biology/samri_bindata: updated sourceHorea Christian2018-07-041-1/+1
| | | | Package-Manager: Portage-2.3.41, Repoman-2.3.9
* sci-biology/mouse-brain-atlases: updated sourceHorea Christian2018-07-041-1/+1
| | | | Package-Manager: Portage-2.3.41, Repoman-2.3.9
* sci-biology/mouse-brain-atlases: version bumpHorea Christian2018-07-042-0/+28
| | | | Package-Manager: Portage-2.3.41, Repoman-2.3.9
* sci-biology/mouse-brain-atlases: requirement checkHorea Christian2018-07-011-1/+7
| | | | | | | And EAPI downgrade, since eclass does not yet support EAPI 7. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/poretools: change LICENSE, add missing DEPENDencyMartin Mokrejs2018-06-281-3/+4
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/stringtie: version bump, accepted new upstream patch, worksMartin Mokrejs2018-06-273-75/+70
| | | | | | | | CXX/CXXFLAGS are still not respected for bundled samtools subdirectory. https://github.com/gpertea/stringtie/issues/185#issuecomment-400637035 Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/samri: new packageHorea Christian2018-06-264-0/+136
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: fix variablenamesMartin Mokrejs2018-06-263-2/+15
| | | | | | | | | Thanks to @kiwifb for spotting two improperly used variablenames https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493393 https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493465 Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: fix testsMartin Mokrejs2018-06-263-2/+14
| | | | | | | | Thanks to @kiwifb https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493393 Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/stringtie: drop KEYWORDS as it does not compileMartin Mokrejs2018-06-261-1/+2
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/gclib: removed as uselessMartin Mokrejs2018-06-264-79/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | https://github.com/gpertea/gclib/issues/2#issuecomment-400125651 There is a bit of confusion here, this "library" is not meant to be a typical object library (no binary static file is being built) and certainly not meant to be built and installed globally into some ${prefix}/lib/ with corresponding headers under ${prefix}/include or so... It's just a loose collection of reusable source code which I directly include/source into a few of my bioinformatics projects, at compile time, as needed. As such there should be no reason to install it separately, system wide! (and I would advise against it). Moreover, the Makefile included here was simply meant for some quick testing during development, not for distribution. I have some simple scripts included in the actual projects themselves (e.g. gffread) which are pulling the minimum necessary source code files from the gclib directory in the process of creating a custom release tarball for distribution, which can then be found on the official release web page for each project (e.g. for gffread is http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.12.tar.gz). That "official" source code release tarball already includes the gclib source files that are needed to build the project -- so I would advise various distributions to use those releases instead as they should build properly with the gclib code "frozen" at the time of that particular release. Since gclib code is in continuous development/tweaking, as the various projects using it are too, there is no guarantee that the various automatic github releases are going to be all build compatible all the time (though I do try to keep the "master" branches in sync and ready to build, but beyond those "official", manually tested releases, it's hard to keep multiple projects in sync all the time).
* sci-biology/stringtie: keep modified bundled copy of samtools-0.1.18Martin Mokrejs2018-06-262-14/+10
| | | | | | | | | | | https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090 https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844 Therefore, keep local copy of gclib and samtools. Still it does not compile for me with gcc-7.3.0 Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/gffread: fetch gclib and use during compilationMartin Mokrejs2018-06-263-6/+9
| | | | | | | | | | | | | | | The soucre tree is not made to use site-wide installed headers from gclib. I am not going to figure out git commit tag of gclib automagically bundled into some gffread binary when gffread was released (to make a dedicated gclib-$commitnr.tar.gz file for Gentoo/Debian/etc. and to include it into SRC_URI here so gffread could use it. It is the task for upstream author to properly document required versions of dependencies and release them properly. https://github.com/gpertea/gffread/issues/26#issuecomment-400134376 Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/gffcompare: new packageMartin Mokrejs2018-06-264-0/+124
| | | | | | | Is a mixture of gclib object and gffcompare objects, hence the download of two tar.gz files. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/afni: Added unstable x86 keywordHorea Christian2018-06-261-1/+1
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/ants: Version bump and improvementsHorea Christian2018-06-264-12/+47
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/stringtie: patch cleanupMartin Mokrejs2018-06-261-34/+28
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/gffread: new packageMartin Mokrejs2018-06-264-0/+70
| | | | | | Does not compile, will report upstream. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/stringtie: document bundled sci-biology/gclib copyMartin Mokrejs2018-06-261-2/+5
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/gclib: new packageMartin Mokrejs2018-06-264-0/+79
| | | | | | | Appears bundled in sci-biology/gffread , sci-biology/stringtie and probably in even more packages. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/stringtie: drop bundled samtools-0.18.1, fix MakefileMartin Mokrejs2018-06-252-1/+130
| | | | | | | Also use properly named CXX and CXXFLAGS variables, respect their initial values. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: add missing DEPENDency on app-arch/unzipMartin Mokrejs2018-06-252-0/+2
| | | | | | https://github.com/COMBINE-lab/salmon/issues/181#issuecomment-367800400 Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: bring -9999 in sync with 0.10.2.ebuildMartin Mokrejs2018-06-252-38/+10
| | | | | | | The -9999 won't work as the SRC_URI section is not respected, hence is commented out. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: drop calls to curl, fix libdirMartin Mokrejs2018-06-255-10/+249
| | | | | | | | This zaps all calls to curl downloads during compile time except those for Google tbb. It should not get executed anyway as the dev-cpp/tbb dependency is enforced. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: drop deps on static boost, some ebuild cleanupMartin Mokrejs2018-06-2511-135/+94
| | | | | | | | | | | | | | | | | | | Document zillions of cryptic dependencies of a lousy package https://github.com/Kingsford-Group/libgff/issues/1 https://github.com/COMBINE-lab/salmon/issues/236 https://github.com/COMBINE-lab/salmon/issues/19 Incomplete install docs are deemed to be at: http://salmon.readthedocs.io/en/latest/building.html#requirements-for-building-from-source Try the command below to see yourself: salmon-0.10.2 $ find . -type f | xargs grep curl 2>/dev/null Thanks to @kiwifb for comments at https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/afni: new packageHorea Christian2018-06-254-0/+154
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: bump version of required dev-cpp/tbbMartin Mokrejs2018-06-242-3/+3
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: add URL linkMartin Mokrejs2018-06-241-0/+1
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/salmon: version bump, attempts to get boost picked upMartin Mokrejs2018-06-246-8/+34
| | | | | | | cmake does not detect boost for me although the errors speak of pthread and not boost. Older version could probably be dropped soon. Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/bwa: version bumpMartin Mokrejs2018-06-244-0/+73
| | | | | | Also fix HOMEPAGE which does not listen on https (anymore?) Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/mouse-brain-atlases: new packageHorea Christian2018-06-243-0/+38
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/samri_bindata: new packageHorea Christian2018-06-243-0/+37
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/bru2nii: version bumpHorea Christian2018-06-232-0/+33
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* drop due to broken depsJustin Lecher2018-06-213-54/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/trimmomatic: version bumpMartin Mokrejs2018-06-062-4/+4
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/nilearn: new versionsHorea Christian2018-06-054-11/+48
| | | | Package-Manager: Portage-2.3.40, Repoman-2.3.9
* sci-biology/dipy: version bump and improved depsHorea Christian2018-05-233-3/+43
| | | | Package-Manager: Portage-2.3.38, Repoman-2.3.9
* sci-biology/SPAdes: version bump, drop oldMartin Mokrejs2018-05-174-110/+14
| | | | Package-Manager: Portage-2.3.36, Repoman-2.3.9
* sci-biology/kat: removing patches for 2.4.1 versionMartin Mokrejs2018-05-082-58/+0
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/kat: various fixes for issue #867François Bissey2018-05-0711-229/+308
| | | | | | | | | | | | | | | | | | | | | | | many thanks to @kiwifb and @maplesond for on fixing the package and ebuild ax_check_zlib is in use. A hint for zlib location has to be provided otherwise system zlib will be used on prefix. make sure zlib is a dependency. develop branch has switched to proper library detection. fixing rpath. enabling python support (but broken right now). make sure a suitable python3 is setup at configure time bump to 2.4.2 fix typo in /DEPPEND/DEPEND/, cleanup comments Closes: https://github.com/gentoo/sci/issues/867 Closes: https://github.com/gentoo/sci/pull/868 Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/quorum: drop oldMartin Mokrejs2018-05-022-29/+0
| | | | | | | Anyway it doe snot compile with gcc-7.3.0, see https://github.com/gmarcais/Jellyfish/issues/122 Package-Manager: Portage-2.3.31, Repoman-2.3.9