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
Sent: ‎Friday‎, ‎August‎ ‎29‎, ‎2014 ‎10‎:‎16‎ ‎AM
To: Kevin
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 “package_samtools_0_1_18”. 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
Sent: Tuesday, August 26, 2014 1:21 PM
To: Kevin
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 doesn’t 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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