From 57686b6b25ca6bc1400d66691dd6346c113cbe02 Mon Sep 17 00:00:00 2001 From: Fabio Erculiani Date: Wed, 23 Nov 2011 14:34:15 +0100 Subject: [PATCH] [sci-biology] new particle --- weekly/sci-biology.particle | 170 ++++++++++++++++++++++++++++++++++++ 1 file changed, 170 insertions(+) create mode 100644 weekly/sci-biology.particle diff --git a/weekly/sci-biology.particle b/weekly/sci-biology.particle new file mode 100644 index 0000000..bf7a96e --- /dev/null +++ b/weekly/sci-biology.particle @@ -0,0 +1,170 @@ +# Entropy Matter, Automated Entropy Packages Build Service, example spec file + +# List of packages required to be built. +# Comma separated, example: app-foo/bar, bar-baz/foo +# Mandatory, cannot be empty +packages: + sci-biology/GBrowse, + sci-biology/aaindex, + sci-biology/abyss, + sci-biology/amos, + sci-biology/ariadne, + sci-biology/augustus, + sci-biology/bfast, + sci-biology/biogrep, + sci-biology/bioperl, + sci-biology/bioperl-db, + sci-biology/bioperl-network, + sci-biology/bioperl-run, + sci-biology/biopython, + sci-biology/bioruby, + sci-biology/biosql, + sci-biology/blat, + sci-biology/blossoc, + sci-biology/bowtie, + sci-biology/bwa, + sci-biology/cd-hit, + sci-biology/clustal-omega, + sci-biology/clustalw, + sci-biology/clustalw-mpi, + sci-biology/clustalx, + sci-biology/cutg, + sci-biology/dialign-tx, + sci-biology/elph, + sci-biology/embassy, + sci-biology/emboss, + sci-biology/eugene, + sci-biology/exonerate, + sci-biology/fasta, + sci-biology/fasttree, + sci-biology/finchtv, + sci-biology/foldingathome, + sci-biology/gibbs, + sci-biology/gmap, + sci-biology/goby-cpp, + sci-biology/hmmer, + sci-biology/iedera, + sci-biology/infernal, + sci-biology/iqpnni, + sci-biology/kalign, + sci-biology/lagan, + sci-biology/last, + sci-biology/mafft, + sci-biology/maq, + sci-biology/maqview, + sci-biology/mcl, + sci-biology/meme, + sci-biology/mosaik, + sci-biology/mothur, + sci-biology/mrbayes, + sci-biology/mummer, + sci-biology/muscle, + sci-biology/ncbi-tools, + sci-biology/njplot, + sci-biology/pals, + sci-biology/paml, + sci-biology/phylip, + sci-biology/phyml, + sci-biology/piler, + sci-biology/pilercr, + sci-biology/plink, + sci-biology/poa, + sci-biology/prank, + sci-biology/primer3, + sci-biology/prints, + sci-biology/prosite, + sci-biology/qrna, + sci-biology/raxml, + sci-biology/readseq, + sci-biology/rebase, + sci-biology/recon, + sci-biology/rnaview, + sci-biology/samtools, + sci-biology/shrimp, + sci-biology/sibsim4, + sci-biology/sim4, + sci-biology/snpfile, + sci-biology/stride, + sci-biology/t-coffee, + sci-biology/transfac, + sci-biology/tree-puzzle, + sci-biology/treeviewx, + sci-biology/trnascan-se, + sci-biology/ucsc-genome-browser, + sci-biology/unafold, + sci-biology/vaal, + sci-biology/velvet, + sci-biology/vienna-rna, + sci-biology/wise, + sci-biology/yass + +# Entropy repository where to commit packages +# Mandatory, cannot be empty +repository: sabayon-hell + +# Allow Source Package Manager (Portage) repository change? +# Valid values are either "yes" or "no" +# Default is: no +spm-repository-change: no + +# Allow compiling package even if it's not actually installed on system? +# Valid values are either "yes" or "no" +# Default is: no +not-installed: no + +# Allow dependencies to be pulled in? +# Valid values are either "yes" or "no" +# Default is: no +dependencies: yes + +# Allow package downgrade? +# Valid values are either "yes" or "no" +# Default is: no +downgrade: no + +# Allow package rebuild? +# Valid values are either "yes" or "no" +# Default is: no +rebuild: no + +# Make possible to continue if one or more packages fail to build? +# Valid values are either "yes" or "no" +# Default is: no +keep-going: yes + +# Allow new USE flags? +# Valid values are either "yes" or "no" +# Default is: no +new-useflags: yes + +# Allow removed USE flags? +# Valid values are either "yes" or "no" +# Default is: no +removed-useflags: yes + +# Package pre execution script hook +# Valid value is path to executable file +# Env vars: +# BUILDER_PACKAGE_NAME = name of the package that would be built +# pkgpre: /home/fabio/repos/entropy/services/matter_examples/pkgpre.sh + +# Package build post execution script hook, executed for each package +# Valid value is path to executable file +# Env vars: +# BUILDER_PACKAGE_NAME = name of the package that would be built +# pkgpost: /home/fabio/repos/entropy/services/matter_examples/pkgpost.sh + +# Env vars: +# MATTER_PACKAGE_NAME = name of the package that would be built. It does +# not reflect the name of the failing package, because it could be just a +# dependency of it. +# MATTER_PORTAGE_FAILED_PACKAGE_NAME = exact name (atom, CPV) of the failing +# package, the one that triggered the buildfail hook. +# MATTER_PORTAGE_REPOSITORY = Portage repository from where the package +# comes from +# MATTER_PORTAGE_BUILD_LOG_DIR = directory containing all the build logs of +# the failed package +buildfail: /particles/hooks/buildfail.sh + +# For more info regarding exported environment variables, please see: +# matter --help