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TSRchitect HOWTO - embedding TSRchitect in workflows

Preparation

At this stage, you should have completed the TSRchitect installation steps documented in the INSTALL document; we'll assume that you have downloaded the tsr.sif singularity container. We explain how you can use bash and Rscript scripts to exectute the examples in the TSRchitectUsersGuide.

Example 1

This example only requires the xdemo1 script you will find in this directory. Take a look at the script: it's simply a compilation of the instructions from the relevant section in the TSRchitectUsersGuide, to be executed in your shell. The following command may need to be adjusted to your needs. Here we assume that the the tsr.sif container is located in the parent of your current working directory.

singularity exec -e -B${PWD}/.. ../tsr.sif  ./xdemo1

Example 2

As with the previous example, first we must download the raw data. In this case we have only a single alignment file to retrieve, which is found here: https://oregonstate.app.box.com/s/3lb3spmqbiuofhbubovc1z8bfthmxh6f . Once download of the file peat.sorted.bam is complete, please move it to subdirectory "PEATbam/". Then execution of xdemo2 should work (see Example 1 for setup details):

singularity exec -e -B /projects/vbrendel/TMP /DATA/GROUP/prj/SINGULARITY/tsr.simg  ./xdemo2

Example 3

singularity exec -e -B /projects/vbrendel/TMP /DATA/GROUP/prj/SINGULARITY/tsr.simg  ./xdemo3