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* sci-libs/p4est: Remove, moved to ::gentooMatthias Maier2017-05-265-343/+0
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* dev-util/numdiff: Remove, moved to ::gentooMatthias Maier2017-05-264-101/+0
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* sci-physics/quinoa: fix depsChristoph Junghans2017-05-251-1/+1
| | | | | | Ref: quinoacomputing/quinoa#140 Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-mathematics/slepc: ensure that environment is saneMatthias Maier2017-05-251-0/+7
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/libStatGen: version bump, use ${PV}Martin Mokrejš2017-05-253-1/+23
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/verifyBamID: another attempt at removing the -WerrorMartin Mokrejš2017-05-251-4/+3
| | | | | | | Somehow the sed calls do not work, disable -Werror append by defining the variable non-empty Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/verifyBamID: work around compile error with g++-7.1.0Martin Mokrejš2017-05-251-0/+3
| | | | | | https://github.com/statgen/verifyBamID/issues/7 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/dealii: add support for slepcMatthias Maier2017-05-253-3/+10
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/slepc: initial commitMatthias Maier2017-05-253-0/+83
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/petsc: fix licenseMatthias Maier2017-05-254-55/+5
| | | | | | petsc 3.5 and newer is released under a two-clause BSD license Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/dealii: update metadataMatthias Maier2017-05-251-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/petsc: update metadataMatthias Maier2017-05-251-15/+19
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/petsc: version bump to 3.6.5, major overhaulMatthias Maier2017-05-259-452/+53
| | | | | | | | | | | | | - bump to EAPI 6 - respect upstream decision to install in a monolithic way. Now, the full petsc distribution is installed into /usr/lib/petsc - add metis support Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/dealii: remove erroneous package versionMatthias Maier2017-05-253-5/+2
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/trilinos: fix installation pathsMatthias Maier2017-05-241-0/+5
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/ncbi-tools++: do not add $(PCRE_LIBS) unless necessary (from ↵Martin Mokrejš2017-05-238-198/+97
| | | | | | Aaron Ucko) Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/fast5: remove blank lineMartin Mokrejš2017-05-231-1/+0
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/fast5: removing KEYWORDs until src_install is fixedMartin Mokrejš2017-05-231-1/+18
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/fast5: new packageMartin Mokrejš2017-05-234-0/+65
| | | | | | Will be needed for sci-biology/nanopolish (once ebuild arrives in sci tree). Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/cortex_var: fix compilation error on PREFIXed hostsMartin Mokrejš2017-05-221-1/+2
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SOAPdenovo2: add Debian manpageMartin Mokrejš2017-05-223-5/+25
| | | | | | https://manpages.debian.org/testing/soapdenovo2/soapdenovo2.1.en.html Package-Manager: Portage-2.3.5, Repoman-2.3.2
* Drop obsolete maskJustin Lecher2017-05-221-5/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/samtools: Add missing SLOT operatorsJustin Lecher2017-05-226-9/+9
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/cortex_var: EAPI bump and QA FixesJustin Lecher2017-05-222-11/+15
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/angsd: QA FixesJustin Lecher2017-05-221-1/+1
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/vcftools: QA FixesJustin Lecher2017-05-222-4/+5
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* dev-util/nvidia-cuda-gdk: Drop oldJustin Lecher2017-05-225-627/+0
| | | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* profiles: Mask old version of dev-util/nvidia-cuda-gdkDavid Seifert2017-05-221-0/+5
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* dev-cpp/eigen: Update yearDavid Seifert2017-05-221-1/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-biology/cutadapt: add recent new dependencyMartin Mokrejš2017-05-212-2/+6
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* dev-python/xopen: new package (needed by sci-biology/cutadapt)Martin Mokrejš2017-05-213-0/+32
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/htslib: note version lib along the SLOTMartin Mokrejš2017-05-211-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* net-misc/cernbox-client: Bump to 2.3.2 release, drop old.Oliver Freyermuth2017-05-204-133/+1
| | | | | | | Following new owncloud-client version. Package-Manager: Portage-2.3.5, Repoman-2.3.2 Closes: https://github.com/gentoo/sci/pull/788
* sci-biology/MaSuRCA: version bumpMartin Mokrejš2017-05-163-58/+35
| | | | | | | The package is actually a bundle of many, including SOAPdenovo2 somewhat patched so that it compiles (unlike vanilla 2.04-r240). Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SOAPdenovo2: a bit cleanup of the build processMartin Mokrejš2017-05-161-2/+28
| | | | | | Will need to bring in Debian med patches from git://anonscm.debian.org/debian-med/soapdenovo2.git Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SOAPdenovo2: new packageMartin Mokrejš2017-05-153-0/+33
| | | | | | Does not respect CFLAGS, compile fails Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/quorum: improve DESCRIPTION textMartin Mokrejš2017-05-152-3/+3
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/jellyfish: point SRC_URI to proper tarball, drop yaggo DEPENDencyMartin Mokrejš2017-05-152-5/+3
| | | | | | | This tarball really doe snot need yaggo for building. See for whole discussion: https://github.com/gmarcais/Jellyfish/issues/87 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* dev-lang/yaggo: remove doubbed '/usr'Martin Mokrejš2017-05-151-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* dev-lang/yaggo: add missing 'install' argumentMartin Mokrejš2017-05-151-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* dev-lang/yaggo: also respect ${EPREFIX}Martin Mokrejš2017-05-151-0/+5
| | | | | | https://github.com/gmarcais/yaggo/issues/7 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/jellyfish: CDEPEND does not work?Martin Mokrejš2017-05-151-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/jellyfish: version bump, add new CDEPEND on dev-lang/yaggoMartin Mokrejš2017-05-152-6/+14
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* dev-lang/yaggo: new package required by sci-biology/jellyfish-2.2.6Martin Mokrejš2017-05-153-0/+35
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/quorum: version bumpMartin Mokrejš2017-05-152-4/+6
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: drop DEPENDency on boostMartin Mokrejš2017-05-141-6/+8
| | | | | | | Upstream says SPAdes uses bundled while modified local copy. Fix URL to new official site. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: install the package directly using cmakeMartin Mokrejš2017-05-141-3/+5
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SPAdes: fix compile issue but drop KEYWORDS because of QA issuesMartin Mokrejš2017-05-133-10/+49
| | | | | | | | | | Use patch from https://github.com/Homebrew/homebrew-science/pull/5616 The package install its own *.py files outside of PYTHON's site-packages/. The "make install" procedure is flakey shellscript and there is no setup.py so we could reuse common infrastructure for pythonic packages. There are plenty of bundled 3rd-party apps, some of them compiling statically. Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/pfft: Fix HOMPAGE and SRC_URIJustin Lecher2017-05-133-6/+6
| | | | | | | Fixes gentoo/sci#786 Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* dev-cpp/eigen: Merge tree changes FixesJustin Lecher2017-05-133-11/+3
| | | | | | | | Fixes gentoo/sci#707 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=601170 Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>