Hi,
   I'm not sure if this is related or not but I'm also noticed a
similar problem where the program is not found in the path, but it
exists. I have it submitted as an issue , but it could be related here
so mentioned here. The problem started when I recently upgraded my
Galaxy installation(It was running in cluster with SGE, in Red hat
linux). Currently, I'm running Galaxy with drmaa in a cluster in Red
Hat linux, where the web server  is running in one Server, and the
execution is being performed in another. I noticed that programs like
ClustalW, dialign-tx etc, which uses a wrapper, is giving error as
follows:
sh: dialign-tx: command not found
The original command line in the wrapper is as follows:
command = "dialign-tx %s/dialign-tx %s %s -g%s -n%s -D %s %s" %
(GALAXY_DATA_INDEX_DIR, options, sensitivity, max_frag_length,
length_low_score_pos, input_file_name, output_file)

Even though, the programs are present in the Execution node's path,
and if I add, explicit path, like "/usr/local/bin" in the command as
bellow:
command = "/usr/local/bin/dialign-tx %s/dialign-tx %s %s -g%s -n%s -D
%s %s" % (GALAXY_DATA_INDEX_DIR, options, sensitivity,
max_frag_length, length_low_score_pos, input_file_name, output_file)

Then the programs works fine without any error.

I compared, the wrapper files with my old installation and the current
installation, and both are 100% same. So, I guess the path to the
executable is missing from the environment. I searched a lot, but
couldn't find any solution to rectify this issue.
Can someone please point out where I need to change to avoid adding
explicit path to each programs.
Thanks in advance.


With Regards,
----------------
Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,


On Fri, Jan 20, 2012 at 11:07 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> 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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>
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