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* sci-biology/tablet-bin: version bump, ebuild cleanupMartin Mokrejs2019-03-252-5/+6
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/MolBioLib: fix RDEPEND.suspect at leastMartin Mokrejs2019-03-251-9/+10
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bamql: bump to EAPI7Martin Mokrejs2019-03-252-2/+2
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bamql: bump to version with less greedy LLVM linkingMartin Mokrejs2019-03-252-1/+1
| | | | | | | | | | | | | | | | | | | | | The https://github.com/BoutrosLaboratory/bamql/blob/master/m4/ax_llvm.m4#L31 forces preference for static libs. The code was improved by Andre Masella. Although the original code is based on ax_llvm.m4 which is 4 versions behind current version at http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_llvm.m4 it does better job at the moment. https://github.com/BoutrosLaboratory/bamql/issues/14#issuecomment-475947032 Many thanks to François Bissey (@kiwifb) and Andre Masella (@apmasell) for discussion and Andre for the changes in https://github.com/BoutrosLaboratory/bamql/commit/9441772 which enable use to overcome the requirement for static libs and proceed with shared versions using: `--enable-static=no --enable-static-llvm=no` Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bamql: add IUSE="static-libs"Martin Mokrejs2019-03-233-7/+21
| | | | | | | | | | | | | Provided one specifies `--enable-static=no --enable-static-llvm=no` the patch in https://github.com/BoutrosLaboratory/bamql/commit/94417720bc7653a90cd9edd932ba6ba52d7bb89b is really needed (as these two args are enough to compile bamql-1.6 and llvm with only shared libs). See https://github.com/BoutrosLaboratory/bamql/issues/14 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* dev-python/traits: version bump 5.0.0Horea Christian2019-03-222-0/+51
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* dev-python/grabbit: version bumpHorea Christian2019-03-222-0/+28
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* dev-python/traits: migrated from main treeHorea Christian2019-03-184-0/+109
| | | | | | | See bug #672412 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-mathematics/slepc: version bump to 3.10.2Matthias Maier2019-03-092-0/+75
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/petsc: version bump to 3.10.4Matthias Maier2019-03-092-0/+197
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-biology/CAT: add missing -lstdc++ -lm and drop -wMartin Mokrejs2019-03-072-8/+16
| | | | | | | Use proper env variables Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/CAT: new packageMartin Mokrejs2019-03-074-0/+58
| | | | | | | Does not compile, probably requires some older C++ standard? Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/ParaAT: add missing default in src_prepare()Martin Mokrejs2019-03-071-0/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/KaKs_Calculator: new packageMartin Mokrejs2019-03-074-7/+80
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/ParaAT: new packageMartin Mokrejs2019-03-073-0/+42
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/afni: version bumpHorea Christian2019-03-023-0/+70
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sys-cluster/openmpi: bump 2.1.6Justin Bronder2019-02-253-5/+5
| | | | | Signed-off-by: Justin Bronder <jsbronder@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
* sci-biology/canu: respect CXXFLAGSMartin Mokrejs2019-02-202-4/+143
| | | | | Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/canu: add live package of a new toolMartin Mokrejs2019-02-202-0/+62
| | | | | Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bowtie: removing not working -1.2.2 ebuildMartin Mokrejs2019-02-192-78/+0
| | | | | Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bowtie: removing -9999 ebuildMartin Mokrejs2019-02-191-81/+0
| | | | | Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bowtie: working 1.2.2 snapshotMartin Mokrejs2019-02-193-0/+184
| | | | | | | | | | This ebuild keeps the bundled SeqAn-1.1 sources (a library of headers) and does not insist on system-wide installed SeqAn-1.4 (for which too many patches are needed and I am unable to evaluate/apply them all). Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bowtie: add some compile patches from DebianMartin Mokrejs2019-02-188-0/+236
| | | | | | | | | | Seems both bowtie1 and bowtie2 are bound too much to SeqAn-1.1 and need more patches for SeqAn-1.4. Per reports on github it seems one should be able to compile bowtie-1.2.2 using -std=c++03 (but not me). Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/samri_bidsdata: deprecated versionHorea Christian2019-02-122-24/+0
| | | | | Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/samri_bidsdata: version bumpHorea Christian2019-02-122-0/+22
| | | | | Package-Manager: Portage-2.3.59, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-physics/qcl: remove old versionsAndrew Savchenko2019-01-304-150/+0
| | | | | Package-Manager: Portage-2.3.58, Repoman-2.3.12 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sci-physics/qcl: multiple improvementsAndrew Savchenko2019-01-303-3/+128
| | | | | | | | | | | - Update to EAPI 7 - Fix dependencies (RDEPEND were wrong) - Install additional documentation - Respect CFLAGS for qc lib as well - Fix install paths so that qcl can find its lib Package-Manager: Portage-2.3.58, Repoman-2.3.12 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sci-biology/biobambam2: upstream moved from github to gitlabMartin Mokrejs2019-01-222-7/+9
| | | | | Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-libs/libmaus2: upstream moved from github to gitlabMartin Mokrejs2019-01-223-15/+13
| | | | | | | https://github.com/gt1/libmaus2/issues/28#issuecomment-456336598 Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-libs/io_lib: add libdeflate to USE flags and require itMartin Mokrejs2019-01-222-3/+6
| | | | | Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* app-arch/libdeflate: make a patch to fix EPREFIX installationsMartin Mokrejs2019-01-222-6/+57
| | | | | Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* app-arch/libdeflate: respect EPREFIX and use get_libdirMartin Mokrejs2019-01-221-0/+3
| | | | | Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-libs/io_lib: version bumpMartin Mokrejs2019-01-223-29/+72
| | | | | | | | | | | | | | Add a new version with experimental CRAM support. Force dependency on libdeflate although it could/should be maybe protected by USE flag. However, it is recommended by upstream authors. https://github.com/jkbonfield/io_lib/issues/11 https://github.com/jkbonfield/io_lib/issues/12 https://github.com/jkbonfield/io_lib/issues/13 Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* app-arch/libdeflate: new packageMartin Mokrejs2019-01-223-0/+42
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add highly CPU optimized implementation of deflate/zlib/gzip The package is highly preferred due to its speed by: sci-biology/io_lib-1.14.11 sci-libs/htslib-1.9 and maybe some more * Searching for libdeflate ... * Contents of app-arch/libdeflate-1.2: /usr /usr/bin /usr/bin/libdeflate-gunzip /usr/bin/libdeflate-gzip /usr/include /usr/include/libdeflate.h /usr/lib /usr/lib/libdeflate.so -> libdeflate.so.0 /usr/lib/libdeflate.so.0 /usr/share /usr/share/doc /usr/share/doc/libdeflate-1.2 /usr/share/doc/libdeflate-1.2/NEWS.bz2 /usr/share/doc/libdeflate-1.2/README.md.bz2 Seems the libdeflate-gunzip and libdeflate-gzip have statically linked in /usr/lib/libdeflate.a (which is deleted but later in src_install() unless USE=static-libs . Probably something to inspected but more experienced devs. I am not interested in maintaining this package in Gentoo (I would be happy if somebody from other herds take this over). Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/samri: dropped python2 supportHorea Christian2019-01-171-1/+1
| | | | | Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/samri: added prefix supportHorea Christian2019-01-171-4/+14
| | | | | Package-Manager: Portage-2.3.56, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/blasr: partial improvements of the ebuildMartin Mokrejs2019-01-171-8/+22
| | | | | Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/pbbam: new package needed by sci-biology/blasrMartin Mokrejs2019-01-172-0/+61
| | | | | | | | | | Builds and install for me, make cmake/clang deps could be improved. https://github.com/PacificBiosciences/pbbam/issues/25 Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/ABI-expression-data: new packageTina Segessemann2019-01-163-0/+51
| | | | | Package-Manager: Portage-2.3.54, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/ABI-connectivity-data:Tina Segessemann2019-01-163-0/+49
| | | | | Package-Manager: Portage-2.3.54, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-libs/nipype: Updated license, copyright, EAPIHorea Christian2019-01-151-23/+21
| | | | | | | tests, and PYTHON_COMPAT Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-libs/nipype: added python_2* dependencyHorea Christian2019-01-151-2/+4
| | | | | Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-libs/nipype: Deprecated versionHorea Christian2019-01-152-35/+0
| | | | | Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/samri: testing required atlasesHorea Christian2019-01-142-2/+6
| | | | | Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-libs/pmx: Now upstream is https://github.com/deGrootLab/pmxAlexey Shvetsov2019-01-141-4/+4
| | | | | Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-biology/samri: PYTHON_COMPAT bumpHorea Christian2019-01-122-3/+15
| | | | | | | and testing dependency update Package-Manager: Portage-2.3.55, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* Checking for and creating config dir if neededHorea Christian2019-01-111-1/+4
| | | | | | and improved comment style and grammar Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/irsabi_bidsdata: Description correct.Horea Christian2019-01-061-1/+1
| | | | | Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/irsabi_bidsdata: new packageHorea Christian2019-01-064-0/+55
| | | | | Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/samri: dependency updateHorea Christian2019-01-061-1/+0
| | | | | Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>