Yes I did. All tools are installed and I see no error message. Philipp
---Philipp on the road--- Am 05.08.2016 um 15:31 schrieb Peter Cock <p.j.a.c...@googlemail.com <mailto:p.j.a.c...@googlemail.com> >: 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/ > <http://code.google.com/p/pysam/> ) > genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/ > <http://code.google.com/p/bedtools/> ) > bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/ > <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.rath...@ibc.uni-stuttgart.de <mailto:philipp.rath...@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 > > <http://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 > > <http://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 > > <http://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 > > <http://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 > > <http://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 > > <http://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 > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ><http://galaxyproject.org/search/mailinglists/>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
