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.travis.yml
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.travis.yml
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language: python
python:
- "3.6" # current default Python on Travis CI
- "3.7"
- "3.8"
- "3.9"
# install dependencies
install:
- pip install -r requirements.txt
- pip install .
- pip install coveralls
- pip install coverage
#install deps
#install samtools
- wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 -O /tmp/samtools.tar.bz2
- tar -xvjf /tmp/samtools.tar.bz2
- cd samtools-1.10
- ./configure --prefix=$(pwd)
- make && make install
- cd ..
- export PATH=$PATH:$PWD/samtools-1.10/bin/
#install sratoolkit
- wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6-1/sratoolkit.2.9.6-1-ubuntu64.tar.gz -O /tmp/sratools.tar.gz
- tar -xvzf /tmp/sratools.tar.gz
- export PATH=$PATH:$PWD/sratoolkit.2.9.6-1-ubuntu64/bin/
#install stringtie
- wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-2.0.6.Linux_x86_64.tar.gz -O /tmp/stie.tar.gz
- tar -xvzf /tmp/stie.tar.gz
- export PATH=$PATH:$PWD/stringtie-2.0.6.Linux_x86_64/
#install cufflinks
- wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz -O /tmp/cuff.tar.gz
- tar -xvzf /tmp/cuff.tar.gz
- export PATH=$PATH:$PWD/cufflinks-2.2.1.Linux_x86_64/
#install hisat2
- wget https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-Linux_x86_64/download -O /tmp/hisat2.zip
- unzip /tmp/hisat2.zip
- export PATH=$PATH:$PWD/hisat2-2.1.0/
#install STAR
- wget https://github.com/alexdobin/STAR/archive/2.7.3a.tar.gz -O /tmp/star.tar.gz
- tar -xvzf /tmp/star.tar.gz
- export PATH=$PATH:$PWD/STAR-2.7.3a/bin/Linux_x86_64/
#install bowtie2
- wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.5.1/bowtie2-2.3.5.1-linux-x86_64.zip/download -O /tmp/btie.zip
- unzip /tmp/btie.zip
- export PATH=$PATH:$PWD/bowtie2-2.3.5.1-linux-x86_64/
#install kallisto
- wget https://github.com/pachterlab/kallisto/releases/download/v0.46.1/kallisto_linux-v0.46.1.tar.gz -O /tmp/kallisto.tar.gz
- tar -xvzf /tmp/kallisto.tar.gz
- export PATH=$PATH:$PWD/kallisto/
#install salmon
- wget https://github.com/COMBINE-lab/salmon/releases/download/v1.1.0/salmon-1.1.0_linux_x86_64.tar.gz -O /tmp/salmon.tar.gz
- tar -xvzf /tmp/salmon.tar.gz
- export PATH=$PATH:$PWD/salmon-latest_linux_x86_64/bin/
#install cutadapt
- pip3 install --upgrade cutadapt
#install trim_galore
- wget https://github.com/FelixKrueger/TrimGalore/archive/0.6.5.tar.gz -O /tmp/tg.tar.gz
- tar -xvzf /tmp/tg.tar.gz
- export PATH=$PATH:$PWD/TrimGalore-0.6.5/
#install bbduk
- wget https://sourceforge.net/projects/bbmap/files/BBMap_38.73.tar.gz/download -O /tmp/bbtools.tar.gz
- tar -xvzf /tmp/bbtools.tar.gz
- export PATH=$PATH:$PWD/bbmap/
#install orfipy
- pip install orfipy --upgrade
#upgrade numpy
- pip install numpy --upgrade
# command to run tests
script:
- ls
- cp -r tests/test_files/params .
#- travis_wait 60 coverage run -m pytest tests/
- rm -rf tests/testout
- coverage run -m pytest tests/
- coverage report --show-missing -i
after_success:
- coveralls