On Jan 20, 2012, at 12:12 AM, ambarish biswas wrote:

> 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.

I replied to your bitbucket ticket first, just in case you don't see it, here 
it is:

https://bitbucket.org/galaxy/galaxy-central/issue/702/program-command-not-found-in-path

--nate

> 
> 
> 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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