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INSTALL.rst

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Installation

On localhost

Please install the following programs use your favouriate package manager or from source, and put their executables in PATH.

  • Python-2.7.x
  • wget (in case ascp fails, wget will try to download the same file from a different url)
  • Aspera ascp
  • fastq-dump from SRA Toolkit
  • [optional] If you need to run rsem on the localhost, as well. For example, when doing the analysis on a small number of GSMs for testing purpose, install bowtie (dependency of RSEM) and RSEM, too.

Then install the pipeline,

$ pip install virtualenv
$ virtualenv <DIR>
$ source <DIR>/bin/activate
$ pip install git+https://github.com/bcgsc/rsempipeline.git#egg=rsempipeline

On remote cluster

Please install the following packages

Example for setting up cron jobs

. code-block:

*/30 * * * *  RSEM_DIR=/path/to/data/batchx; . /path/to/venv/bin/activate; cd ${RSEM_DIR};  rp-run -v 1 -s soft/* -i GSE_species_GSM.csv -T gen_qsub_script -j 7  --qsub_template 0_submit_genesis.jinja2 &> ~/rp-run.log
*/20 * * * *  RSEM_DIR=/path/to/data/batchx; . /path/to/venv/bin/activate; cd ${RSEM_DIR};  rp-transfer -s soft/* -i GSE_species_GSM.csv &> ~/rp-transfer.log