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.travis.yml
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.travis.yml
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before_install:
- sudo add-apt-repository -y "deb http://archive.ubuntu.com/ubuntu/ trusty main universe"
- sudo apt-get -qq update
install:
- sudo apt-get install --yes --force-yes circos build-essential wget fasttree hmmer lua5.1 blast2 ncbi-blast+ unzip cpanminus mummer python-setuptools exonerate snap infernal mafft
- sudo ln -s /usr/bin/fasttree /usr/bin/FastTree
- sudo test/travis.setup-augustus.sh > /dev/null
- sudo test/travis.setup-gt.sh > /dev/null
- sudo test/travis.setup-last.sh > /dev/null
- sudo test/travis.setup-orthomcl.sh > /dev/null
- sudo test/travis.setup-aragorn.sh > /dev/null
- sudo test/travis.setup-gff3toembl.sh > /dev/null
- sudo cpanm -q --force Carp Storable Bio::SearchIO List::Util Getopt::Long
- curl -fsSL get.nextflow.io | bash
- wget -q http://geneontology.org/ontology/go.obo
- wget -q http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
- zcat Pfam-A.hmm.gz | test/split-hmm.lua 1000 > Pfam-A.hmm
- hmmpress Pfam-A.hmm
- rm -f Pfam-A.hmm
cache:
directories:
- work
env:
global:
- ROOTDIR="$TRAVIS_BUILD_DIR"
script:
- cd test/testsuite
- ./testsuite.rb -threads 2
- cd ../..
- ./nextflow -c loc_travis.config -c params_default.config run annot.nf -resume --do_circos=false