Its sounds like bedGraphToBigWig has not been installed.
https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwig/
The README says:
Ensure the following command line tools are on the system path:
pysam - Python interface to samtools (http://code.google.com/p/pysam/) genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/) bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
However, the tool does appear to declare the dependencies via the Tool Shed mechanism - did you install them via the Tool Shed?
Peter
On Fri, Aug 5, 2016 at 2:23 PM, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
Dear All,
I get the following errors when I try to Convert BAM to BigWig
Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 103, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 48, in main convert_to_graph(bam_file, split, config, temp_handle) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 76, in convert_to_graph subprocess.check_call(cl, stdout=out_handle) File "/usr/lib/python2.7/subprocess.py", line 535, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
The tool produced the following additional output:
Have 93 references Calculating coverage...
or
Fatal error: Exit code 1 () bedtools: /galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by bedtools) needLargeMem: trying to allocate 0 bytes (limit: 100000000000) Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 122, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 57, in main convert_to_bigwig(temp_file, sizes, config, outfile) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 104, in convert_to_bigwig subprocess.check_call(cl) File "/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmp2F67r6', '/export/galaxy-central/database/files/003/dataset_3116-sizes.txt', '/export/galaxy-central/database/files/003/dataset_3116.dat']' returned non-zero exit status 255
The tool produced the following additional output:
Have 93 references Calculating coverage... Converting 0 MB graph file to bigwig..
depending what version of the tool i am using.
Any idea what this can be?
I am using the latest Docker-galaxy-stable version (16.04) but I think this is not related to docker. All tools are updated.
Thank you very much for your help,
Philipp
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