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

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?

Matt Shirley
Ph.D Candidate - BCMB
Pevsner Lab <http://pevsnerlab.kennedykrieger.org/>
Johns Hopkins Medicine
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:


Reply via email to