User: Politz, Samuel M.

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Posts by Politz, Samuel M.

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How to save sequence data and analysis results outside of Galaxy
... I have some important data and an entire analysis of the data saved on Galaxy since 2013. I don't have a local instance of Galaxy. Is there some way I can save everything locally so that I can put it back into Galaxy if I need to work on it again or document the results? I still have the raw data ...
galaxy alignment assembly written 12 months ago by Politz, Samuel M.70 • updated 12 months ago by Jennifer Hillman Jackson24k
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Comment: C: Galaxy Server Error
... I am also dead in the water. I sent a post to this effect last week. Last Friday I left a job queued up on the main server and as of this morning, it still had not run after 2-1/2 days. Can someone notify us about what is wrong, and what is being done to fix it? Best regards, Sam _______________ ...
written 4.5 years ago by Politz, Samuel M.70
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Slow Galaxy Server
... This is a followup to my previous post on this topic. The exact message (in red) that I see after a long delay in running a tool is "An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists." I have seen this message twice while waiting ...
galaxy written 4.5 years ago by Politz, Samuel M.70 • updated 4.5 years ago by Jennifer Hillman Jackson24k
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Very Slow Server
... Hello, for the last week or so the main Galaxy server has not completed any of my jobs. These were jobs that were successfully queued, but I deleted them after 48 hours passed without completion. I started a job last night (BEDtools BedGraph of genome coverage on a BAM file). This morning I got an ...
bedtools written 4.5 years ago by Politz, Samuel M.70 • updated 4.5 years ago by Jennifer Hillman Jackson24k
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Comment: C: Problem With Sam-To-Bam Conversion
... Oh sorry, you are using Cb datatase, so embarrassing. Sorry! But the same approach is good, use the same database for all steps, and try to find a way to put it in your history. Best, Sam To: fbesnard@biologie.ens.fr; galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Problem with SAM-to-BAM ...
written 4.6 years ago by Politz, Samuel M.70
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Answer: A: Problem With Sam-To-Bam Conversion
... Hi Fabrice, I work on C. elegans too, and I have found that you need to have the same ce genome database for all steps; otherwise, some tools won't work later in your workflow. With some help from the Galaxy staff, I discovered that there is a version of ce10 in the CloudMap shared information on t ...
written 4.6 years ago by Politz, Samuel M.70
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Problem With Gatk Tools Not Accepting Bam File As Input
... I am using GATK tools on the useGalaxy main server to detect variants in a mutant C. elegans whole genome sequence obtained with an Illumina instrument (my own data). The first GATK tool I tried to use, Realigner Target Creator, gave me an error message. In the tool window, my input file (a BAM fi ...
galaxy written 4.7 years ago by Politz, Samuel M.70 • updated 4.7 years ago by Jennifer Hillman Jackson24k

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