Issue #5 resolved

Problem with Edge-pro

Inge Alexander Raknes
created an issue

The edge-pro galaxy tool seems to be looking for bowtie in current working directory which makes it impossible to run the tool. Any solution would be appreciated.

PREPROCESSING:
Getting sizes
Combining ptt and rnt files

ALIGNING READS TO GENOME
Can't exec "./bowtie2-build": No such file or directory at /data/nels-galaxy/tool_dependencies/edge-pro/1.3.1/crs4/edge_pro/bad8a51514dd/bin/edge.pl line 98.
Can't exec "./bowtie2": No such file or directory at /data/nels-galaxy/tool_dependencies/edge-pro/1.3.1/crs4/edge_pro/bad8a51514dd/bin/edge.pl line 109.

PROCESSING ALIGNMENTS
Calculating per base coverage...
Can't exec "./count": No such file or directory at /data/nels-galaxy/tool_dependencies/edge-pro/1.3.1/crs4/edge_pro/bad8a51514dd/bin/edge.pl line 117.
can't open edge_out.uniqueCounts_0

Comments (4)

  1. Nicola Soranzo

    Hi, thanks for the bug report!

    I think there is a bug in our tool_dependencies.xml file, can you try to run the following commands and let me know if they work?

    $ cd /data/nels-galaxy/tool_dependencies/edge-pro/1.3.1/crs4/edge_pro/bad8a51514dd/bin
    $ cp edge.pl edge.pl.sav
    $ sed -i -e 's|$sourceDir/||' edge.pl
    
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