Hi Folks,
I got the galaxy docker image and played with it. However, I keep getting this when I use dexseq:
Fatal error: Exit code 1 () Could not import pysam, which is needed to process BAM file (though not to process text SAM files). Please install the 'pysam' library from https://code.google.com/p/pysam/
Looks like there is a conda env that is built on the fly and it doesn't have some dependencies installed. If I do the following
biocLite("DEXSeq")
inside the conda-env, then pysam is imported properly. Seems it installs the dexseq 1.22. I looked at the package in /tool_deps/_conda/ __bioconductor-dexseq@1.20.1, it's 1.20.1 as the name says. I'm not sure how this could be fixed...my thought would be update the conda env dependency to include dexseq 1.22 not 1.20, but I'm not familiar with conda...Could someone give me a hand? :-)
Thanks, Rui