User: deane

gravatar for deane
deane30
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30
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2 months ago
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1 year, 1 month ago
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d****@blazie.net

Posts by deane

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Comment: A: Local instance upgrade caused error: need to upgrade database from 132 to 134
... Yes, I'm trying to find instructions on how to backup the existing database. Then I can update the database with manage_db.py. But first I need to unload it, back it up. Thanks, Deane ...
written 9 weeks ago by deane30
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Comment: C: Local instance upgrade caused error: need to upgrade database from 132 to 134
... Because I have already done the git upgrade, the version.py file shows 17.05. So I don't know what version I came from but I'm guessing 16.07 My question is this: How do I backup the existing database. The links all show how to upgrade the database with the manage_db.py script but now how to back ...
written 9 weeks ago by deane30
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Comment: C: Local instance upgrade caused error: need to upgrade database from 132 to 134
... I don't know how to find the current version I updated from because it won't run. But it was installed around June 2016. I'm running on Linux. Thanks for the help. ...
written 10 weeks ago by deane30
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Local instance upgrade caused error: need to upgrade database from 132 to 134
... I recently updated a local instance of Galaxy to revision_17 using git checkout release_17.05 && git pull --ff-only origin release_17.05 Now the instance will not run, telling me I need to upgrade the database from 132 to 134 after I backup. I am using the default database (sqlite/alchemy? ...
17.05 local upgrade git admin written 10 weeks ago by deane30
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Answer: A: Local Tophat Error "OSError: [Errno 2] No such file or directory"
... I solved this by adding a link to /usr/local/bin to the galaxy directory where the tool-shed installed samtools. My search on the galaxy forums showed this to be a pretty common error. I can see where it may not be a samtools bug, but it would save a lot of research time if Galaxy took care of it ...
written 13 months ago by deane30
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Answer: A: Tophat execution error
... This issue should be fixed by the tophat tool maintainer. All other tools that I have used put the proper path in the tool definition. For some reason Tophat (even old versions) need the path in the environment of the galaxy server. I spent over a week trying to find the cause of the error. The ...
written 13 months ago by deane30
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Comment: A: Top Hat Error
... Hi, did you ever solve this error? I have the same error running Tophat on a local server. My failure seems to be related to setting metadata for the Accepted Hits file. See below. This propagates to the "finish method" Job wrapper which gives the error you stated in your post. galaxy.jobs.outp ...
written 13 months ago by deane30
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Comment: C: Local Tophat Error "OSError: [Errno 2] No such file or directory"
... Thank you for the response. I did try this but got the same error. Samtools was loaded and all dependencies seemed to be satisfied. The stdio error seems to indicate that it could not write to the database to store Metadata: galaxy.jobs.output_checker INFO 2016-10-18 21:58:11,363 Job 7: Log: tool ...
written 13 months ago by deane30
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Answer: A: Error running tophat2
... I am having this same issue with 16.07 I tried tophat2 and older versions and got the same error. galaxy.jobs.runners.local DEBUG 2016-10-18 12:33:03,293 execution finished: /home/galaxy/galaxy/database/jobs_directory/000/6/galaxy_6.sh galaxy.jobs.output_checker INFO 2016-10-18 12:33:03,305 Job 6 ...
written 14 months ago by deane30
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Local Tophat Error "OSError: [Errno 2] No such file or directory"
... I have created a local Galaxy server to run RNA analysis. I am trying to run TOPHAT on a fastasanger file and am using a reference genome from my history. I was able to successfully run the Fasta-Groomer on my raw fasta file to create the fasta-sanger file. But running tophat on the Groomer outpu ...
samtools local admin tophat path written 14 months ago by deane30 • updated 13 months ago by Jennifer Hillman Jackson23k

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