Using genairics on UGent HPC (instructions for Mac users)¶
Request account¶
Open a terminal: make the key combination CMD-space and type terminal, click on Terminal with the black ‘terminal’ icon.
In the terminal copy paste the following line:
ssh-keygen
Press enter, and press enter for every question (in total 4x enter). Now you are ready to go and request a vsc account, by clicking on the following link: https://account.vscentrum.be/.
Once you are logged in, go to the Edit Account section.
At the bottom of the screen you can upload the key that you made earlier with ssh-keygen.
To reach the .ssh folder where you can find the file to select (id_rsa.pub) type CMD-SHIFT-G and fill in ~/.ssh.
When you have uploaded the key, you should receive a mail that your account will be activated. You should also be notified of your unique vsc id number vscXXXX. In the following, whenever vscXXXX is written, replace it with your own number.
Prepare your work environment¶
Open a terminal, or continue to work in one already opened. And execute the following lines one by one.
ssh vscXXX@gengar.ugent.be
wget -O ~/.bashrc https://raw.githubusercontent.com/dicaso/genairics/master/genairics/scripts/gax_bash_vsc.sh
source ~/.bashrc
mkdir -p $GAX_RESOURCES/repos $GAX_DATADIR $GAX_RESULTSDIR
module load pandas
pip install --user genairics
genairics -h
If all went well, the last line gives you the genairics help output. You are now ready to start and use genairics.
GAX dependencies¶
If you are installing genairics as part of a personal account on the hpc, or your vo group has not yet been setup to run genairics, the following step is also required in order to use genairics.
In your ssh session, start up a console with genairics console and execute the following line:
InstallDependencies()
Get your BASESPACE_API_TOKEN accessToken¶
If you want to run analyses starting from an Illumina Basespace project you need to have an accessToken to be able to download your data in the pipelines. Follow the steps 1-5 from this link:
https://help.basespace.illumina.com/articles/tutorials/using-the-python-run-downloader/
emacs ~/.BASESPACE_API #Store your accessToke here, instead of emacs use any editor you like
chmod 600 ~/.BASESPACE_API #For security, only rw access for your user
Optional: ssh config¶
TODO: (sshconfig -> ssh vsc)
Submit job to different cluster¶
Example submit on golett.
- Find out server name
module swap cluster/golett
qstat -q
QSERVER=master19.golett.gent.vsc
module swap cluster/delcatty
Submit job with queue argument –cluster-Q
genairics –job-launcher qsub –cluster-Q @master19.golett.gent.vsc –remote-host vsc ATACseq NSQ_Run240
