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-fo... --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 <nate@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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