Problem with Edge-pro
Issue #5
resolved
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)
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reporter This solved the problem. Thanks for your help!
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- changed status to resolved
Fix
#5.→ <<cset 02ca83a438ed>>
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Fix
#5.→ <<cset 43c304d8c6be>>
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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?