Amir,

Uploading a BAM file in Galaxy requires the Samtools package. You can download it from http://samtools.sourceforge.net/, but if you want more information about installing it (and other NGS tools) in Galaxy, see our wiki page: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup .


Let us know if you need any further assistance.

Thanks,
Kelly



On Fri Jun 24, at 3:46 PM, Amirhossein Kiani 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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