Those errors suggest that the samtools executable could not be found so
you'll need to install it and make sure it's available to executing jobs.

Galaxy tools rely on a large number of third party executables being
installed - these are maintained by other people - see
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies



On Sat, Jun 25, 2011 at 5:46 AM, Amirhossein Kiani <amirhki...@gmail.com>wrote:

> Hey there,
>
> I'm not an advanced python developer and have an issue setting up my own
> galaxy server. I followed the steps on getgalaxy.org and have added
> ~./galaxy-pyhon to my path.
>
> The server comes up and I can see stuff but when I try to import a BAM file
> I get the following error in the history:
>
> Traceback (most recent call last):
>  File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 382, in
>
>    __main__()
>  File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 374, in
> __main__
>    add_file( dataset, registry, json_file, output_path )
>  File "/Users/amir/galaxy-dist/tools/data_source/upload.py", line 314, in
> add_file
>    if datatype.dataset_content_needs_grooming( output_path ):
>  File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in
> dataset_content_needs_grooming
>    version = self._get_samtools_version()
>  File "/Users/amir/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in
> _get_samtools_version
>    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
>  File
> "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
> line 594, in __init__
>    errread, errwrite)
>  File
> "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
> line 1097, in _execute_child
>    raise child_exception
> OSError: [Errno 2] No such file or directory
>
> I tried it on my RedHat server as well and get the same error:
>
> Traceback (most recent call last):
>  File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py",
> line 382, in
>
>    __main__()
>  File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py",
> line 374, in __main__
>    add_file( dataset, registry, json_file, output_path )
>  File "/home/amir/galaxy-python/galaxy-dist/tools/data_source/upload.py",
> line 314, in add_file
>    if datatype.dataset_content_needs_grooming( output_path ):
>  File
> "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line
> 79, in dataset_content_needs_grooming
>    version = self._get_samtools_version()
>  File
> "/home/amir/galaxy-python/galaxy-dist/lib/galaxy/datatypes/binary.py", line
> 63, in _get_samtools_version
>    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
>  File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__
>    errread, errwrite)
>  File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child
>    raise child_exception
> OSError: [Errno 2] No such file or directory
>
> It's worth mentioning that I was able to import a FASTA file.
>
> I also checked the server logs and I see:
>
> galaxy.tools DEBUG 2011-06-24 12:21:34,430 Loaded tool: t_test_two_samples
> 1.0.0
> galaxy.tools DEBUG 2011-06-24 12:21:37,993 Loaded tool: sam_indel_filter
> 1.0.0
> galaxy.tools DEBUG 2011-06-24 12:21:38,015 Loaded tool: indel_sam2interval
> 1.0.0
> galaxy.tools DEBUG 2011-06-24 12:21:38,287 Loaded tool: sam_bw_filter 1.0.0
> galaxy.tools DEBUG 2011-06-24 12:21:38,304 Loaded tool: sam2interval 1.0.1
> galaxy.tools DEBUG 2011-06-24 12:21:38,319 Loaded tool: sam_to_bam 1.1.2
> galaxy.tools DEBUG 2011-06-24 12:21:38,331 Loaded tool: bam_to_sam 1.0.3
> galaxy.tools DEBUG 2011-06-24 12:21:38,343 Loaded tool: sam_merge 1.1.1
> galaxy.tools DEBUG 2011-06-24 12:21:38,371 Loaded tool: sam_pileup 1.1.1
> galaxy.tools DEBUG 2011-06-24 12:21:38,497 Loaded tool: samtools_flagstat
> 1.0.0
>
>
> So I'm not sure what the issue is...
>
> Many thanks in advance for your help!
> Amir
>
> ___________________________________________________________
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>



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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