Kevin, You should install samtools to your operating system and put the executable file to your /usr/local/bin or somewhere in a path that galaxy user can call. Best, Alper From: Kevin <changk16@byramhills.net> Date: Friday, August 29, 2014 at 10:44 AM To: Alper Kucukural <alper@kucukural.com> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Problem Running TopHat2 The error message was the same thing as before: Traceback (most recent call last): File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found Thanks, Kevin Chang From: Alper Kucukural <mailto:alper@kucukural.com> Sent: Friday, August 29, 2014 10:16 AM To: Kevin <mailto:changk16@byramhills.net> Cc: galaxy-dev@lists.bx.psu.edu What was the error? From: Kevin <changk16@byramhills.net> Date: Thursday, August 28, 2014 at 11:17 PM To: Alper Kucukural <alper@kucukural.com> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Problem Running TopHat2 Hi Alper, Thank you for the advice. After you suggested that I install the samtools and not just the samtools binary, I went to the Galaxy Main Tool Shed and installed the ³package_samtools_0_1_18². After running TopHat2 again for around 36 hours, the same error message came up again. It appears that installing the samtools themselves did not fix the problem. Are there any other ways to try and fix this problem? Thanks for taking the time to help me out, Kevin Chang Sent from Windows Mail From: Alper Kucukural <mailto:alper@kucukural.com> Sent: Tuesday, August 26, 2014 1:21 PM To: Kevin <mailto:changk16@byramhills.net> Cc: galaxy-dev@lists.bx.psu.edu Hey Kevin, You need to install samtools and bowtie(2) into your system. I assume, the package you installed to galaxy is just a wrapper to call samtools. It doesn¹t come with samtools binary. Best, Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: Alper.Kucukural@umassmed.edu On Aug 26, 2014, at 11:36 AM, Kevin <changk16@byramhills.net> wrote:
Hello All,
I am running a Galaxy instance on Linux and have installed tools from the Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable to complete the job before I get the following error message:
Traceback (most recent call last): File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
So far, I have made sure that the samtools do appear to be installed since they can be found listed under "Managed Installed Tool Shed Repositories". Is it possible that they were installed incorrectly? Any help is much appreciated.
Thanks for taking the time to read this, Kevin Chang
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