commit: ba21795bddb7d2ad8e1359a93327a14b0435fc26 Author: Sébastien Fabbro <bicatali <AT> gentoo <DOT> org> AuthorDate: Mon Apr 4 17:24:03 2016 +0000 Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de> CommitDate: Mon Apr 4 17:24:03 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ba21795b
Merge branch 'master' of https://github.com/gentoo-science/sci .travis.yml | 8 +- dev-python/hdf5storage/Manifest | 1 + ...age-0.1.11.ebuild => hdf5storage-0.1.13.ebuild} | 0 dev-python/matplotlib2tikz/Manifest | 1 + ...z-0.5.4.ebuild => matplotlib2tikz-0.5.6.ebuild} | 0 sci-biology/CONTIGuator/CONTIGuator-2.7.3.ebuild | 31 +++ sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild | 17 -- sci-biology/CONTIGuator/Manifest | 1 + sci-biology/DisEMBL/DisEMBL-1.4.ebuild | 2 +- sci-biology/MolBioLib/Manifest | 1 + sci-biology/MolBioLib/MolBioLib-5.ebuild | 31 +++ .../{cross_genome => MolBioLib}/metadata.xml | 0 sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild | 6 +- sci-biology/TransDecoder/Manifest | 1 + ...oder-2.0.1.ebuild => TransDecoder-2.1.0.ebuild} | 8 +- ...s.patch => TransDecoder-2.1.0__fix_paths.patch} | 0 sci-biology/abyss/Manifest | 3 - sci-biology/abyss/abyss-1.3.3-r1.ebuild | 42 ---- sci-biology/abyss/abyss-1.3.4-r1.ebuild | 47 ---- sci-biology/abyss/abyss-1.3.6-r1.ebuild | 48 ---- .../abyss/files/abyss-1.3.3-ac_prog_ar.patch | 18 -- sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch | 15 -- sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch | 40 ---- sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch | 15 -- sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch | 40 ---- .../abyss/files/abyss-1.3.6-ac_prog_ar.patch | 18 -- sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch | 15 -- sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 ---- sci-biology/abyss/metadata.xml | 8 - sci-biology/act-bin/Manifest | 4 + sci-biology/act-bin/act-bin-13.0.0.ebuild | 50 ++++ sci-biology/{cross_genome => act-bin}/metadata.xml | 0 sci-biology/amos/amos-3.1.0-r2.ebuild | 9 +- sci-biology/amos/amos-9999.ebuild | 10 +- sci-biology/arachne/Manifest | 1 + sci-biology/arachne/arachne-46233.ebuild | 41 ++++ sci-biology/{cross_genome => arachne}/metadata.xml | 0 sci-biology/artemis-bin/Manifest | 4 +- sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild | 29 ++- sci-biology/artemis/Manifest | 3 +- sci-biology/artemis/artemis-9999.ebuild | 19 +- sci-biology/bamtools/Manifest | 1 + ...{bamtools-9999.ebuild => bamtools-2.4.0.ebuild} | 7 +- ...nbundle.patch => bamtools-2.4.0-unbundle.patch} | 0 sci-biology/cap3-bin/Manifest | 1 + ...in-20071221.ebuild => cap3-bin-20071015.ebuild} | 0 ...in-20071221.ebuild => cap3-bin-20150210.ebuild} | 14 +- sci-biology/cd-hit/Manifest | 2 +- sci-biology/cd-hit/cd-hit-4.6.1.ebuild | 44 ---- sci-biology/cd-hit/cd-hit-4.6.5.ebuild | 61 +++++ .../{4.6.1-gentoo.patch => 4.6.5-gentoo.patch} | 95 ++++++-- .../cd-hit/files/cd-hit-auxtools-manual.txt | 212 +++++++++++++++++ sci-biology/cg-cat/cg-cat-20150130.ebuild | 35 ++- sci-biology/consed/consed-29.ebuild | 12 +- .../cross_genome/cross_genome-20140822.ebuild | 2 +- sci-biology/cutadapt/Manifest | 4 +- sci-biology/cutadapt/cutadapt-1.4.1.ebuild | 18 -- sci-biology/cutadapt/cutadapt-1.5.ebuild | 18 -- ...cutadapt-1.2.1.ebuild => cutadapt-1.9.1.ebuild} | 2 +- sci-biology/cutadapt/cutadapt-9999.ebuild | 2 +- sci-biology/exomiser-bin/Manifest | 4 +- sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild | 23 -- sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild | 31 +++ sci-biology/fgap-bin/Manifest | 1 + sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild | 25 ++ .../{cross_genome => fgap-bin}/metadata.xml | 0 sci-biology/fgap/Manifest | 1 + sci-biology/fgap/fgap-1.8.1.ebuild | 26 +++ sci-biology/{cross_genome => fgap}/metadata.xml | 0 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +- sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 4 +- sci-biology/karect/Manifest | 1 + sci-biology/karect/karect-1.0.0.ebuild | 33 +++ sci-biology/{cross_genome => karect}/metadata.xml | 0 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 6 +- sci-biology/{cross_genome => perga}/metadata.xml | 0 sci-biology/perga/perga-9999.ebuild | 36 +++ sci-biology/perlprimer/perlprimer-1.1.21.ebuild | 2 +- sci-biology/reapr/Manifest | 2 + sci-biology/reapr/files/fix_sort_samtools13.patch | 16 ++ sci-biology/reapr/files/use_shared_libs.patch | 252 +++++++++++++++++++++ sci-biology/{cross_genome => reapr}/metadata.xml | 0 sci-biology/reapr/reapr-1.0.18.ebuild | 62 +++++ .../roche454ace2caf-20100812.ebuild | 6 +- .../scaffold_builder-20131122-r1.ebuild | 2 +- sci-biology/scbi_mapreduce/Manifest | 2 +- ...-0.0.40.ebuild => scbi_mapreduce-0.0.45.ebuild} | 2 +- sci-biology/scythe/scythe-0.992.ebuild | 2 +- sci-biology/staden/Manifest | 3 +- ...ags.patch => staden-2.0.0_beta10-ldflags.patch} | 0 ...9-zlib.patch => staden-2.0.0_beta10-zlib.patch} | 0 .../files/staden-2.0.0_beta9-libpng-1.5.patch | 16 -- ...0.0_beta9.ebuild => staden-2.0.0_beta10.ebuild} | 31 ++- sci-biology/staden/staden-9999.ebuild | 19 +- sci-biology/{staden => staden_doc}/Manifest | 1 - .../{cross_genome => staden_doc}/metadata.xml | 0 .../staden_doc/staden_doc-2.0.0_beta9.ebuild | 44 ++++ sci-biology/trimmomatic/Manifest | 4 +- ...momatic-0.32.ebuild => trimmomatic-0.35.ebuild} | 2 +- sci-chemistry/nwchem/Manifest | 14 ++ .../nwchem/files/nwchem-6.6-unique_tags.patch | 12 + sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild | 4 +- ...26243-r7.ebuild => nwchem-6.6_p27746-r2.ebuild} | 46 ++-- sci-libs/armadillo/Manifest | 3 +- ...llo-6.200.3.ebuild => armadillo-6.200.5.ebuild} | 0 ...llo-6.200.3.ebuild => armadillo-6.600.5.ebuild} | 0 sci-libs/calculix-ccx/Manifest | 6 +- ...-ccx-2.8_p2.ebuild => calculix-ccx-2.10.ebuild} | 15 +- ...0_Makefile_custom_cc_flags_spooles_arpack.patch | 35 +++ ...7_Makefile_custom_cc_flags_spooles_arpack.patch | 31 --- .../calculix-ccx/files/01_ccx_2.7_lapack.patch | 11 - ...2_Makefile_custom_cc_flags_spooles_arpack.patch | 32 --- sci-libs/calculix-cgx/Manifest | 4 +- ...-cgx-2.7-r1.ebuild => calculix-cgx-2.10.ebuild} | 31 +-- ...=> 01_cgx_2.10_Makefile_custom_cxx_flags.patch} | 33 ++- ...h => 02_cgx_2.10_menu_fix-freeglut_2.8.1.patch} | 35 ++- sci-libs/clfft/Manifest | 1 + .../{clfft-2.10.0.ebuild => clfft-2.10.2.ebuild} | 0 sci-libs/io_lib/Manifest | 1 + sci-libs/io_lib/io_lib-1.14.7.ebuild | 29 +++ sci-libs/{pg2plplot => io_lib}/metadata.xml | 12 +- sys-cluster/modules/modules-3.2.10-r1.ebuild | 2 +- 122 files changed, 1383 insertions(+), 792 deletions(-)
