l.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/l
t;
Date: Thursday, August 28, 2014 at 11:17 PM
To: Alper Kucukural <al...@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
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
;
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
What was the error?
From: Kevin
Date: Thursday, August 28, 2014 at 11:17 PM
To: Alper Kucukural
Cc: "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 no
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 Plantatio
