[galaxy-user] Question about formattung mouse (mm9) GTF
I have read in the mailing list that you have a workflow which can modify the human GTF file so that it will be compatible with Top Hat. Will it also work with Ensembl mm9 GTF or there is a different work flow. Thanks ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] using lastz
Hi, I have been using Lastz to perform assemblies of 454 data and I have run into a problem where, after the job has been added to the queue, a message appears saying that: Job is waiting to run. It remains like this indefinitely and when I click the 'edit attributes' button, a message says: 'Required metadata values are missing. Some of these values may not be editable by the user'. I am confused since I was able to previously run Lastz with the same samples and parameters and it worked fine. I have tried changing the parameters around a bit but the job still will not run. I would really appreciate any advice anyone could give on how to resolve this issue. Thanks, Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Problem starting galaxy on Cygwin
Dear All, There are related posts but it is unclear from them how to resolve the following. I'm trying to start a Galaxy server on Cygwin and it fails when trying to fetch an egg relying on NumPy. Could you kindly advise how to resolve the error? This uses the Cygwin python 2.6.5. I tried to point Cygwin to the Windows python (2.7.2 in my case) but that was even worse, the Mako egg threw a KeyError: 'Mako' exception up front. Thank you so much, Oren $ python --version Python 2.6.5 oren@oren-PC /cygdrive/c/web/galaxy-central $ sh run.sh --reload Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py, line 345, i n resolve egg.resolve() File /cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py, line 195, i n resolve return self.version_conflict( e.args[0], e.args[1] ) File /cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py, line 226, i n version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File /cygdrive/c/web/galaxy-central/lib/pkg_resources.py, line 565, in resol ve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] My tophat jobs are stuck in the queue
Hello Daniel, Please attempt a re-run of your jobs and let us know if delays are still an issue. Thanks, Jen Galaxy team On 10/12/11 1:47 AM, Daniel Lundin wrote: Hi, I've been running small tophat jobs as part of a student exercise, but since yesterday morning (about 7 am CET, or 24 hours ago) my tophat jobs does not start. Earlier (Monday) jobs started and finished fine. Other jobs like trimming, getting data from the Main table etc. works. /D -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
