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egaffo / circompara2

Improved bioinformatic pipeline to identify and quantify circRNA expression from RNA-seq data by combining multiple circRNA detection methods
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Error message in docker #12

Open bnorthoff opened 1 year ago

bnorthoff commented 1 year ago

Hi Egaffo, since I had some trouble with the old version of samtools in combination with SUSE, I've switched to your given docker image. This is the first docker image I'm using. After starting you docker image using docker run egaffo/circompara2:v0.1.2.1 I get the following message and the process gets aborted:

IOError: [Errno 2] No such file or directory: '/data/meta.csv':
  File "/circompara2/src/sconstructs/main.py", line 447:
    with open(env['META']) as csvfile:

Do you know how to continue? Thanks! Bernd

egaffo commented 1 year ago

You did not set the file paths properly in the config files. You need to understand how Docker set its paths (and mounts volumes) to properly set the vars.py and meta.csv configuration files.