Development¶
General setup for sys/vo admin¶
Choose a different prefix, if you want dependencies installed in different dir
git clone https://github.com/beukueb/genairics.git && cd genairics PREFIX=$VSC_DATA_VO/resources genairics/scripts/genairics_dependencies.sh
virtualenv settings¶
If installing within a virtual environment with mkvirtualenv you can set genairics locations relative to the environment:
GAXDIR=~/repos/genairics mkvirtualenv -a $GAXDIR -i ipython -r $GAXDIR/requirements.txt genairics echo “export GAX_REPOS=$VIRTUAL_ENV/repos” >> $VIRTUAL_ENV/bin/postactivate echo “export GAX_PREFIX=$VIRTUAL_ENV” >> $VIRTUAL_ENV/bin/postactivate echo “export GAX_RESOURCES=$VIRTUAL_ENV/resources” >> $VIRTUAL_ENV/bin/postactivate echo “unset GAX_REPOS GAX_PREFIX GAX_RESOURCES” >> $VIRTUAL_ENV/bin/predeactivate
git repo¶
For new version do git updatemaster, which automates working from dev branch, merging to master and updating version with following aliases in .git/config
[alias] repoversion = !echo 25 updaterepoversion = !git config –local alias.repoversion ‘!echo ‘$(($(git repoversion)+1)) && git repoversion updateversion = !sed -i -e ‘s/version = “.*”/version = “0.1.’$(git updaterepoversion)’”/’ setup.py && git commitversion commitversion = !git commit -am”subversion=$(git repoversion)” tagversion = !git tag -a v0.1.$(git repoversion) -m ‘genairics version 0.1.’$(git repoversion) && git push origin v0.1.$(git repoversion) updatemaster = !git updateversion && git checkout master && git merge dev && git tagversion && git push origin master && git checkout dev pulldev = !git pull origin dev && pip3 install –user –upgrade .
Testing¶
Tests can be run from the repo directory with python3 setup.py test. Tests are included for any pipelines referenced in papers and pipelines used by collaborators.
Mac OS X¶
Setup¶
Install brew: https://docs.brew.sh/Installation.html
brew install python3 bowtie2 brew install homebrew/core/fastqc homebrew/science/bedtools pip3 install –user genairics
Install fuse from https://osxfuse.github.io/ and sshfs from https://github.com/osxfuse/sshfs/releases
HPC¶
Interactive node for debugging¶
qsub -I -l walltime=09:50:00 -l nodes=1:ppn=12
Debug job¶
qsub -q debug -l walltime=00:50:00 -l nodes=1:ppn=4 -m n -v datadir=$VSC_DATA_VO_USER/data,project=NSQ_Run270,forwardprob=0,SET_LUIGI_FRIENDLY=,GENAIRICS_ENV_ARGS= $VSC_DATA_VO/resources/repos/genairics/genairics/RNAseq.py
Submit package to pypi¶
python setup.py sdist upload -r pypi
Docker¶
Build container¶
#docker build . –build-arg buildtype=development #for development docker build . –tag beukueb/genairics:latest docker push beukueb/genairics:latest docker tag beukueb/genairics:latest genairics
To debug, reset entrypoint:
docker run -it -v /tmp/data:/data -v /tmp/results:/results -v /Users/cvneste/mnt/vsc/resources:/resources –env-file ~/.BASESPACE_API –entrypoint bash bcaf446c7765
Cleaning docker containers/images¶
docker system prune -f
