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* Drop leftover from CVS in HEADERJustin Lecher2017-02-251184-1184/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/trilinos: added X depsChristoph Junghans2017-02-241-2/+4
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/tigr-foundation-libs: fix install phaseMartin Mokrejš2017-02-241-5/+4
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sys-cluster/ganglia_jobmonarch: Drop broken packageMarius Brehler2017-02-246-208/+0
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* Revert "depend.php.eclass: Import from main tree, required by ↵Marius Brehler2017-02-241-258/+0
| | | | | | ganglia_jobmonarch" This reverts commit 1c70956ce252680df94134953d0c4dae97223cc9.
* Merge branch 'master' of git+ssh://git.gentoo.org/proj/sciMartin Mokrejš2017-02-242-1/+259
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| * depend.php.eclass: Import from main tree, required by ganglia_jobmonarchMarius Brehler2017-02-241-0/+258
| | | | | | | | | | | | | | | | Import from: https://raw.githubusercontent.com/gentoo/gentoo/93a324d308b208d1ae629da846f2d89571a74355/eclass/depend.php.eclass Was dropped with commit: https://github.com/gentoo/gentoo/commit/e2d9f131cef171702b7427629a801ad46801bfac
| * Merge remote-tracking branch 'github/master'Marius Brehler2017-02-241-1/+1
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| | * dev-util/numdiff: update e-mail addressMatthias Maier2017-02-191-1/+1
| | | | | | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | | sci-libs/libStatGen: a standalone static libraryMartin Mokrejš2017-02-243-0/+36
| | | | | | | | | | | | | | | | | | | | | | | | This is to be used by sci-biology/verifyBamID but it requires some of the Makefiles from libStatGen source tree, and likely headers as well. Seem slike a lot of work to rewamp the build requirements. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | | sci-biology/verifyBamID: new package, would benefit unbundling of libStatGenMartin Mokrejš2017-02-243-0/+53
|/ / | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/genepop: version bump, install PDF docMartin Mokrejš2017-02-242-0/+43
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/Ray: fix typo in USE variableMartin Mokrejš2017-02-241-1/+1
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/picard: version bumpMartin Mokrejš2017-02-232-1/+1
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/bambus: remove direct dev-lang/perl DEPENDcyMartin Mokrejš2017-02-221-2/+1
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/Atlas_GapFill: remove dependency on sys-cluster/torqueMartin Mokrejš2017-02-211-2/+1
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/tablet: adding KEYWORDS to the latest release although building ↵Martin Mokrejš2017-02-211-1/+1
| | | | | | | | | | | | from SVN tag Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/SnpEff: version bumpMartin Mokrejš2017-02-202-3/+3
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/VarScan: version bumpMartin Mokrejš2017-02-202-0/+36
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/VarScan-bin: version bumpMartin Mokrejš2017-02-202-0/+33
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/tablet-bin: do not zap bundled jar files as we do not have a ↵Martin Mokrejš2017-02-201-0/+11
| | | | | | | | | | | | | | | | | | package for them in Gentoo Maybe except picard.jar while upstream uses picard-1.113 in tablet-1.16.09.06. We should be around 2.0.3 with sci-biology/picard-9999 as of now. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/tablet: do not zap jar files as we do not have a package for ↵Martin Mokrejš2017-02-203-20/+27
| | | | | | | | | | | | | | | | | | them in Gentoo Maybe except picard.jar while upstream uses picard-1.113 in tablet-1.16.09.06. We should be around 2.0.3 with sci-biology/picard-9999 as of now. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/tablet-bin: use two alternative sed calls to distinguish normal ↵Martin Mokrejš2017-02-201-5/+12
| | | | | | | | | | | | | | | | | | and EPREFIX installations Somehow the EPREFIX-enabled sed call breaks normal non-EPREFIX host installations. Document bundled jar files. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/sambamba: add a link to ldc-developers Gentoo overlayMartin Mokrejš2017-02-192-5/+3
| | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* | sci-biology/sambamba: multithreaded tool written in D languageMartin Mokrejš2017-02-194-0/+72
|/ | | | | | | | The ebuilds are incomplete as I need to figure out how to compile the thingie. Make does not exit upon error (released tarball does not contain htslib/). Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/yaha: Fix build with gcc-5 and respect build toolsJustin Lecher2017-02-193-5/+90
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/lumpy-sv: more tweaks to the install procedureMartin Mokrejš2017-02-191-2/+6
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/lumpy-sv: use CDEPEND for cmakeMartin Mokrejš2017-02-191-1/+2
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* Merge branch 'master' of git+ssh://git.gentoo.org/proj/sciMartin Mokrejš2017-02-1914-260/+40
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| * sys-cluster/pyslice: Bump to EAPI=6Justin Lecher2017-02-191-2/+2
| | | | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
| * sci-physics/tauola: Bump to EAPI=6Justin Lecher2017-02-199-181/+25
| | | | | | | | | | | | | | drop old Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
| * sys-cluster/blcr: Bump to EAPI=6Justin Lecher2017-02-193-63/+4
| | | | | | | | | | | | | | drop old Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
| * dev-cpp/icnc: Bump to EAPI=6Justin Lecher2017-02-191-14/+9
| | | | | | | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* | sci-biology/lumpy-sv: new package, inventing installation layoutMartin Mokrejš2017-02-192-0/+51
|/ | | | | | https://github.com/arq5x/lumpy-sv/issues/168 Package-Manager: Portage-2.3.3, Repoman-2.3.1
* Merge branch 'master' of git+ssh://git.gentoo.org/proj/sciMartin Mokrejš2017-02-191-1/+1
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| * sci-libs/cblas-reference: Fix installation pathJustin Lecher2017-02-191-1/+1
| | | | | | | | | | | | | | fixes GH #730 Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* | sci-biology/yaha: new package, does not respect CFLAGS/CXXFLAGS yetMartin Mokrejš2017-02-192-0/+40
|/ | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/tablet-bin: fix sed hackery for EPREFIX installationsMartin Mokrejš2017-02-191-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/tablet: version bumpMartin Mokrejš2017-02-193-7/+58
| | | | | | | | Fix required java version to 1.8 Seems 1.16.09.06 is under upstream's SVN commit #876. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/tablet-bin: version bumpMartin Mokrejš2017-02-192-6/+6
| | | | | | | | | | | | | Pass '-Djava.util.prefs.systemRoot=${TMPDIR}' to java to avoid permission denied when writing to /etc/.java/.systemPrefs (outside our sandbox) The /opt/Tablet/tablet wrapper falsely issues error although am on Oracle JDK 1.8.0.121 [oracle-jdk-bin-1.8]: java.lang.UnsupportedClassVersionError: tablet/gui/Tablet : Unsupported major.minor version 52.0 However, 'java -jar /opt/Tablet/lib/tablet.jar' runs fine. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/abacas: add eapply_userMartin Mokrejš2017-02-181-0/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/phusion: allmost corrected build processMartin Mokrejš2017-02-181-2/+20
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/phusion: respect EPREFIXMartin Mokrejš2017-02-181-2/+2
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/genometools: update DEPs, EAPI bumpMartin Mokrejš2017-02-181-2/+5
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/genometools: respect EPREFIXMartin Mokrejš2017-02-181-1/+5
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/jtreeview: remove forgotten reference to perlMartin Mokrejš2017-02-181-1/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/jtreeview: add 3.0_alpha version which executes fineMartin Mokrejš2017-02-181-0/+40
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/jtreeview: add deemed dependency on nanoxmlMartin Mokrejš2017-02-181-1/+2
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/jtreeview-bin: package using upstream's binaryMartin Mokrejš2017-02-183-0/+58
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/jtreeview: improve ebuildMartin Mokrejš2017-02-181-5/+21
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1