This profile configures Snakemake to run on the SURFsara Grid.
Then, install Miniconda 2 (in order to not interfere with python 2 grid tools).
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod +x Miniconda2-latest-Linux-x86_64.sh
./Miniconda2-latest-Linux-x86_64.sh -b -p /cvmfs/softdrive.nl/$USER/Miniconda2
And add the installation to the PATH (put the following into your .bashrc):
export PATH=/cvmfs/softdrive.nl/$USER/Miniconda2/bin:$PATH
Finally, setup the channel order for bioconda:
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda create -n snakemake snakemake python=3.6 pandas cookiecutter
The name (given to -n) is mandatory here, because the submission scripts of this profile assume this environment to exist.
Finally, softdrive has to be published with
publish-my-softdrive
It will take some time (up to half an hour) until other nodes will have access to the update.
To deploy this profile, login to your grid UI and run
mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
cookiecutter https://github.com/snakemake-profiles/surfsara-grid.git
When asked for the storage path, insert whatever shall be the place where your data analysis results shall be stored. It has to be a subdirectory of gridftp.grid.sara.nl:2811/pnfs/grid.sara.nl/data/.
Then, you can run Snakemake with
snakemake --profile surfsara-grid ...
so that jobs are submitted to the grid. If a job fails, you will find the "external jobid" in the Snakemake error message. You can investigate the job via this ID as shown here. If Snakemake is killed and restarted afterwards, it will automatically resume still running jobs.
Note that Snakemake needs valid proxy certificates throughout its runtime. It is advisable to use maximum lifetimes for those, i.e., generate them with
voms-proxy-init --voms <voms> --valid 168:00
myproxy-init -d -n -c 744 -t 744
glite-wms-job-delegate-proxy -d $USER
while replacing <voms> with your value (e.g. lsgrid:/lsgrid/Project_MinE).