Dilmurat Yusuf

@bgruening I am trying to update the dexseq wrappers to use the available conda pkgs. so far, it went well with dexseq.xml. for dexseq_count.xml, an environmental variable $DEXSEQ_ROOT is required...

@bgruening yes for sure, that can be done at the level of conda package. I was just wondering any solution from Galaxy so that I need not go to bioconda...

@bgruening regarding the tophat failure, the following error might be the culprit, /export/galaxy-central/database/job_working_directory/000/36/conda-env/bin/tophat2: /export/tool_deps/_conda/pkgs/tophat-2.1.0-py35_0/bin/tophat: /opt/anaconda1anaconda2anaconda3/bin/python: bad interpreter: No such file or directory this might be the issue related to the...

@bgruening I did planemo test on the galaxy tophat2 tool (in my ubuntu), there was no error with conda dependencies. then is it possible something wrong with docker setting in...

@bgruening so what would be the plan to make tophat work? a workbench without this aligner does not sound promising.