On Jan 18, 2012, at 5:28 PM, Matt Shirley wrote:

> Hi all. I'm sorry if this has been answered before, but I've searched and 
> cannot find a solution other than "add SAMtools to your PATH", which I 
> already have done. I can invoke samtools from BASH while logged in as the 
> "galaxy" user I set up according to the production installation guide. When I 
> try to add .bam files to a shared data library, I get the following message:
> 
> Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in
> __main__()
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in 
> __main__
> add_file( dataset, registry, json_file, output_path )
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 327, in 
> add_file
> if link_data_only == 'copy_files' and 
> datatype.dataset_content_needs_grooming( output_path ):
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in 
> dataset_content_needs_grooming
> version = self._get_samtools_version()
> File "/home/galaxy/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 639, in __init__
> errread, errwrite)
> File "/usr/lib64/python2.6/subprocess.py", line 1220, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
> 
> I've taken a peek at the "dataset_content_needs_grooming" function and it 
> looks like there is an OS call that executes "$ samtools" and splits the 
> resulting string to access the version number of samtools (why couldn't the 
> developers add a --version flag?). It seems to me like samtools cannot be 
> executed, but I can't think of any reason why. Invoking samtools as user 
> "galaxy" (with the user's associated PATH) gives:
> 
> Program: samtools (Tools for alignments in the SAM format)
> Version: 0.1.12a (r862)
> Usage: samtools <command> [options]
> Command: view SAM<->BAM conversion
> sort sort alignment file
> pileup generate pileup output
> mpileup multi-way pileup
> faidx index/extract FASTA
> tview text alignment viewer
> index index alignment
> idxstats BAM index stats (r595 or later)
> fixmate fix mate information
> glfview print GLFv3 file
> flagstat simple stats
> calmd recalculate MD/NM tags and '=' bases
> merge merge sorted alignments
> rmdup remove PCR duplicates
> reheader replace BAM header
> 
> Does anyone know where I've gone wrong?

Hi Matt,

Are you running tools on a cluster?  If running locally, are you starting 
Galaxy by hand (i.e. run.sh) from that same shell in which you can run samtools?

--nate

>  
> -- 
> Matt Shirley
> Ph.D Candidate - BCMB
> Pevsner Lab
> Johns Hopkins Medicine
> 
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