Closed:Defining path to installed tools within Singularity simg

Question

[Barry Digby]

Hey guys,

I have a question re working within a singularity image, and specifying its installed tools path.

I have put together an image locally that contains the necessary tools, and python version to run circ-seq.

Circ-Seq uses a configuration file to point to where paths of tools are like so (this is not the singularity.def file):

#### tools
BOWTIE=/home/bdigby/bin/circ-seq/bowtie2-2.1.0
PYTHON=/home/bdigby/.local/easybuild/software/Anaconda3/4.4.0/envs/py2/bin/python
SAMTOOLS=/home/bdigby/bin/circ-seq/samtools-0.1.18
BEDTOOLS=/home/bdigby/bin/circ-seq/bedtools2/bin
BLAT=/home/bdigby/bin/circ-seq
WORKFLOW_PATH=/data/bdigby/circ/CircSeq_standalone

#### env variables
PYTHONPATH=/home/bdigby/.local/easybuild/software/Anaconda3/4.4.0/envs/py2/bin/

Now, let's say I wanted to stay current and trendy and run this on a singularity image, how would I go about telling the configuration file where each tool resides (within the image) after running

singularity shell -B /data/bdigby circ-seq.simg

?

The end goal in mind is to submit these containers as a SLURM job using exec, but I am still testing things out.

Thanks,

Barry