Problem with "Map with Bowtie for Illumina" on a local Galaxy
Dear colleagues, I have a local installed Galaxy. When I try to run bowtie to align a small FASTQ file, I got the following message and the result was empty. """ empty, format: sam, database: Project-Id-Version: PACKAGE VERSION Report-Msgid-Bugs-To: POT-Creation-Date: 2008-09-21 18:33+0900 PO-Revision-Date: 2009-03-17 03:55-0400 Last-Translator: FULL NAME Language-Team: en Plural-Forms: nplurals=2; plural=(n != 1) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Generated-By: Babel 0.9.4 Info: """ It seems bowtie_wrapper.py wasn't executed at all. Has someone seen this message before and what could be the cause? Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231
Hello Leon, Are you still experiencing problems with your local install? Could you confirm that you have attempted this again with the current distribution (April 8th) and have completed the NGS Tool set up as described in our wiki? Once we know everything is current it will be easier to offer more help. https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup galaxy-dist% hg pull -u -r 50e249442c5a https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs Best! Jen Galaxy team On 3/19/11 10:30 AM, Leon Mei wrote:
Dear colleagues,
I have a local installed Galaxy. When I try to run bowtie to align a small FASTQ file, I got the following message and the result was empty.
""" empty, format: sam, database: Project-Id-Version: PACKAGE VERSION Report-Msgid-Bugs-To: POT-Creation-Date: 2008-09-21 18:33+0900 PO-Revision-Date: 2009-03-17 03:55-0400 Last-Translator: FULL NAME Language-Team: en Plural-Forms: nplurals=2; plural=(n != 1) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Generated-By: Babel 0.9.4 Info: """
It seems bowtie_wrapper.py wasn't executed at all. Has someone seen this message before and what could be the cause?
Thanks, Leon
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
Hi Jen, Thanks. Yes, the problem is solved. I was running it within our Galaxy VM which had some missing system files. Cheers, Leon On Tue, Apr 26, 2011 at 6:33 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Leon,
Are you still experiencing problems with your local install? Could you confirm that you have attempted this again with the current distribution (April 8th) and have completed the NGS Tool set up as described in our wiki? Once we know everything is current it will be easier to offer more help.
https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
galaxy-dist% hg pull -u -r 50e249442c5a https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs
Best!
Jen Galaxy team
On 3/19/11 10:30 AM, Leon Mei wrote:
Dear colleagues,
I have a local installed Galaxy. When I try to run bowtie to align a small FASTQ file, I got the following message and the result was empty.
""" empty, format: sam, database: Project-Id-Version: PACKAGE VERSION Report-Msgid-Bugs-To: POT-Creation-Date: 2008-09-21 18:33+0900 PO-Revision-Date: 2009-03-17 03:55-0400 Last-Translator: FULL NAME Language-Team: en Plural-Forms: nplurals=2; plural=(n != 1) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Generated-By: Babel 0.9.4 Info: """
It seems bowtie_wrapper.py wasn't executed at all. Has someone seen this message before and what could be the cause?
Thanks, Leon
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231
participants (2)
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Jennifer Jackson -
Leon Mei