This is a focused collection of makefiles and scripts to for analysis on Illumina sample data. While this probably can't be directly used by someone not in our lab, it might be a useful reference for others.
In order to set up these scripts, checkout the repository. There are some environment variables to set:
- STAMPIPES -- full path to the installation directory
- LIMS_API_URL -- URL to the LIMS API
- LIMS_API_TOKEN -- Auth to the LIMS API
- MODULELOAD -- Full path to the GNU modules init script
- HOTSPOT_DIR -- Path to HOTSPOT, defaults to
~/hotspot/hotspot-distr- download at [https://github.com/rthurman/hotspot] - PYTHON3_ACTIVATE -- A virtualenv activation script for python3.
A python version that includes pip needs to be installed for proper python package version recording.
The current modules to load for working the pipeline are:
bcl2fastq/1.8.4bcl2fastq2/2.15.0.4bedops/2.4.35-typicalbedtools/2.25.0bowtie/1.0.0bwa/0.7.12coreutils/8.25cufflinks/2.2.1fastqc/0.11.5gcc/4.7.2git/2.3.3hotspot2/2.1htslib/1.6.0jdk/1.8.0_92kallisto/0.43.1- `kentutil/302
picard/2.8.1pigz/2.3.3pysam/0.9.0python/2.7.11python/3.5.1R/3.2.5RSEM/1.2.30samtools/1.3STAR/2.4.2atophat/2.0.13numpy/1.11.0atlas-lapack/3.10.2scipy/1.0.0scikit-learn/0.18.1stringtie/1.3.4d
If $MODULELOAD is set, then the processing scripts should load the required modules automatically.