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.cock@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/)
> 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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