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* sci-libs/pybids: new packageHorea Christian2018-05-234-0/+92
| | | | Package-Manager: Portage-2.3.38, Repoman-2.3.9
* dev-python/num2words: new package (pybids dep)Horea Christian2018-05-233-0/+48
| | | | Package-Manager: Portage-2.3.38, Repoman-2.3.9
* dev-python/grabbit: new package (pybids dependency)Horea Christian2018-05-233-0/+49
| | | | Package-Manager: Portage-2.3.38, 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
* dev-python/pynrrd: new packageHorea Christian2018-05-183-0/+46
| | | | Package-Manager: Portage-2.3.31, 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
* dev-cpp/highwayhash: initial commitChristoph Junghans2018-05-173-0/+39
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-libs/dealii: update Manifest (again)Matthias Maier2018-05-141-1/+1
| | | | Package-Manager: Portage-2.3.36, Repoman-2.3.9
* sci-libs/dealii: update tarballMatthias Maier2018-05-132-2/+2
| | | | Package-Manager: Portage-2.3.36, Repoman-2.3.9
* sci-libs/dealii: version bump to 9.0.0Matthias Maier2018-05-112-0/+146
| | | | Package-Manager: Portage-2.3.36, Repoman-2.3.9
* sci-libs/dealii: remove really old versionsMatthias Maier2018-05-114-263/+0
| | | | 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-libs/tensorflow: Move our flags to bazel-get-flags()Mark Wright2018-05-031-14/+18
| | | | Package-Manager: Portage-2.3.33, Repoman-2.3.9
* dev-util/bazel: Set our flags for #861 prefixMark Wright2018-05-033-0/+125
| | | | Package-Manager: Portage-2.3.33, Repoman-2.3.9
* sci-libs/tensorflow: Use CPPFLAGS, CXXFLAGS, LDFLAGS.Mark Wright2018-05-021-7/+33
| | | | | | | | | | Setting CPPFLAGS should help #861 sci-libs/tensorflow: respect EPREFIX. Require [${PYTHON_USEDEP}] on Python deps, which should help the dev-python/wheel not working in #849 sci-libs/tensorflow: new package, ebuilds with IUSE="cuda mpi" need improvements. 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
* sci-biology/jellyfish: version bump and a few tweaksMartin Mokrejs2018-05-023-5/+4
| | | | | | | | | | Install properly PDF documentation. Use ${PV} in SRC_URI. Update SRC_URI to reflect github hosting these days. Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-libs/tensorflow: Fix the C++ header findMark Wright2018-05-011-4/+3
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-libs/tensorflow: Bump to 1.8.0, build C and C++ APIsMark Wright2018-05-012-0/+173
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/bamql: add live ebuildMartin Mokrejs2018-05-011-0/+28
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-libs/gmsh: version bump to 3.0.6Matthias Maier2018-04-242-0/+94
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/jellyfish: install bundled PDF manualMartin Mokrejs2018-04-233-3/+54
| | | | | | And do not download an old version at all. Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-mathematics/petsc: avoid double prefixMatthias Maier2018-04-231-1/+1
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-mathematics/petsc: remove upstream workaround for -j1 in 3.9.0Matthias Maier2018-04-221-9/+0
| | | | | | Apparently this is not needed anymore. *hooray* Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-mathematics/slepc: version bump to 3.9.0Matthias Maier2018-04-222-0/+75
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-mathematics/petsc: vesrion bump to 3.9.0Matthias Maier2018-04-223-0/+223
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/kat: properly install python filesMartin Mokrejs2018-04-233-105/+59
| | | | | | | | | | | | Thanks to kiwifb. Drop -8888, update -9999 and -2.4.1 to link against system-wide boost. No ebuilds left which would let the bundled boost slip in as a static library. See: https://github.com/TGAC/KAT/issues/94#issuecomment-383385701 Closes: https://github.com/gentoo/sci/issues/867 Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/megahit: respect cuda USE flagMartin Mokrejs2018-04-232-6/+24
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/SOAPdenovo2: Respect CC/CXX/CFLAGS/CXXFLAGS variablesMartin Mokrejs2018-04-233-9/+216
| | | | | | | | | | | | | | | | | This commit cleans up the Makefiles a bit. 1. Do not override user's environment if the variables were are set. 2. Prefer site-wide installation of samtools-0.1.x if existing. 3. Do not force -L/lib or -L/usr/lib64, that is handled by the compiler/linker and very importantly, properly. 4. Cleanup spaces and other style inconsistencies. https://github.com/aquaskyline/SOAPdenovo2/pull/44 Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/kat: add missing DEPENDencyMartin Mokrejs2018-04-223-5/+7
| | | | Package-Manager: Portage-2.3.31, Repoman-2.3.9
* sci-biology/BlastToSam: move the -9999 ebuild to 1.1 versionMartin Mokrejs2018-04-221-5/+7
| | | | | | ant is complaining about jython missing but seems harmless Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/samstat: version bumpMartin Mokrejs2018-04-222-14/+4
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/kat: improve -8888 ebuildMartin Mokrejs2018-04-226-250/+132
| | | | | | | | | | | | | | | | | | | | | Try call setup.py on our own so that it could receive ${DESTDIR} contents. This still does not work. The ebuild drops bundled boost copy but retains bundled seqan headers and the modified copy of jellyfish. They won't interfere with with site-wide installed packages of those tools in Gentoo. The modified jellyfish is linked-in statically and binaries have 'kat_' prefix. The kat-2.4.1.ebuild and -9999.ebuild should later get same logic like appears in -8888.ebuild. Currently they stick to upstream's approach of using bundled boost too. All ebuilds suffer same problem: the python files do not get installed at all. Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/kat: remove lines commented outMartin Mokrejs2018-04-221-12/+0
| | | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/kat: ignore site-wide boost-build/site-config.jamMartin Mokrejs2018-04-225-6/+343
| | | | | | | Introduce -8888 ebuild which zaps bundled stuff altogether and uses system-wide boost and jellyfish2 files. Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/kat: execute the build_boost.sh and autogen.sh logicMartin Mokrejs2018-04-222-5/+31
| | | | | | | | Execute the commands from within ebuild to ease debugging of errors. See https://github.com/TGAC/KAT/issues/92 Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/sailfish: update comments with URLsMartin Mokrejs2018-04-222-5/+5
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/jellyfish: install the pdf manual tooMartin Mokrejs2018-04-211-0/+1
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/ESTate: update checksumsMartin Mokrejs2018-04-211-1/+1
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/gatk: comment out copy&pasted commandMartin Mokrejs2018-04-211-1/+3
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/jellyfish: SLOT jellyfish to support concurrent ver. {1,2}Martin Mokrejs2018-04-2118-49/+257
| | | | | | | | | | | | | | This renames the resulting binaries, pkg-config file contents, headers, and all packages currently depending on sci-biology/jellyfish. sci-biology/quorum: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/Rcorrector: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/SEECER: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/amos: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/kraken: SLOT jellyfish to support concurrent ver. {1,2} sci-biology/wgs-assembler: SLOT jellyfish to support concurrent ver. {1,2} Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/trinityrnaseq: rename patch filenameMartin Mokrejs2018-04-212-2/+2
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/trinityrnaseq: version bump (no KEYWORDS set)Martin Mokrejs2018-04-217-6/+106
| | | | | | | | | | | | The perl include paths are not matching the paths in *.pm files all *.pm need to be patched so that they could be placed into site_perl subdirectory. In brief, the package still does not support installation into a site-wide directory. users are supposed to executed off the unpacked tarball directly. Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/salmon: document install procedure issuesMartin Mokrejs2018-04-213-7/+28
| | | | | | | | The building procedure is still a mess. https://github.com/COMBINE-lab/salmon/issues/19 Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/sailfish: fix filename with a patchMartin Mokrejs2018-04-212-3/+3
| | | | | | Anyway, it does not compile with gcc-7.3.0 at least. Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/sailfish: drop KEYWORDS, version bumpMartin Mokrejs2018-04-213-14/+25
| | | | | | | | | This package automatically downloads 3rd-party sources instead of just compiling. https://github.com/kingsfordgroup/sailfish/issues/80 Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/kat: version bumpMartin Mokrejs2018-04-214-40/+55
| | | | | | | | | | | | | Lets require >=python-3.5 for best feature availability. The source code contain bundled sci-libs/boost and sci-biology/seqan. It also contain (unfortunately modified) sci-biology/jellyfish-2.2.0 https://github.com/TGAC/KAT/issues/92 Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-biology/gatk: add the missing licenseMartin Mokrejs2018-04-211-0/+26
| | | | | I always forget that repoman ignores license files scheduled for commit and that I have to use 'git commit' solely for that.
* sci-biology/tigmint: new packageMartin Mokrejs2018-04-213-0/+44
| | | | | | | It is not yet enabled because an install procedure is missing. Bug: https://github.com/bcgsc/tigmint/issues/10 Package-Manager: Portage-2.3.28, Repoman-2.3.9