User: rich_jp

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rich_jp0
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11 months ago
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3 years, 6 months ago
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r******@ucl.ac.uk

Posts by rich_jp

<prev • 11 results • page 1 of 2 • next >
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vcftools - errors running vcf-merge
... Hi all, I am trying to run the vcf-merge tool, which depends on the vcftools 0.1.11 package and tabix (with installed via toolshed) on a local Galaxy server. I keep getting error messages such as the following: Log: tool progress gunzip: error writing to output: Broken pipe gunzip: 0.vcf.sorted.gz ...
software error written 11 months ago by rich_jp0 • updated 11 months ago by Jennifer Hillman Jackson24k
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Comment: A: VariantsToTable? Extract AF from INFO column of VCF
... Both work great - thanks Björn :) Richard ...
written 24 months ago by rich_jp0
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VariantsToTable? Extract AF from INFO column of VCF
... Hi all, I would like to extract the AF from the INFO column of GATK Unified Genotyper VCF files (e.g. in tabular format) for downstream analysis. This can be done with GATK VariantsToTable for example but how can this be done inside Galaxy (not finding a good tool wrapper for this)? Cheers, Richard ...
vcf written 24 months ago by rich_jp0
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Answer: A: "\${GALAXY_SLOTS:-4}" usage help
... Hi Hans-Rudolf, Sorry - I had though that this forum and the galaxy-dev list were monitored by different sets of folks. Which would be the preferred place to post? Thanks, Richard ...
written 2.0 years ago by rich_jp0
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"\${GALAXY_SLOTS:-4}" usage help
... Could somebody point me to a good explanation of how to setup and use GALAXY_SLOTS correctly on my server? A basic explanation is good but I also make use of Pulsar to stage some jobs on our cluster here (my machine is 4-core and cluster I use is 12-core) so I am wondering if GALAXY_SLOTS can hand ...
multicore galaxy galaxy_slots multithreading slots written 2.0 years ago by rich_jp0 • updated 2.0 years ago by Jennifer Hillman Jackson24k
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Answer: A: suite_samtools_1_2 EOF marker absent error
... Hiya, thanks for this. I will try this out and let you know how it goes. What I find strange is that with some genomes the intermediate BAM files do not throw this error (suggesting then they may have been sorted) but others do, despite it always being the same pipeline. I also had noticed that when ...
written 2.8 years ago by rich_jp0
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suite_samtools_1_2 EOF marker absent error
... Hi all, so I'm experiencing a problem running SAM-to-BAM using samtools 1.2 from a toolshed install of suite_samtools_1_2. I have a pipeline that after mapping uses 'SAM-to-BAM', followed by GATK2 'realign target creator/indel realign' and then picard 'mark duplicate reads'. When I run this last pic ...
samtools gatk picard written 2.8 years ago by rich_jp0
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Comment: C: no PID in database, unable to stop
... Hi Jen - thanks to you and Nate for taking a look and fixing this :)   ...
written 3.0 years ago by rich_jp0
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Comment: C: no PID in database, unable to stop
... Hi Jen, thanks to you (and others - Nate!) for checking on this for me. Just to add that I actually first observed this issue quite a while ago, importantly before I updated to the latest Galaxy (17052:28113eeee212 ). So it is not something specific to the latest release but has been around a while. ...
written 3.0 years ago by rich_jp0
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Answer: A: no PID in database, unable to stop
... Hi Jen, So I am talking about jobs that are already running (yellow) and then trying to kill them via Admin>Manage Jobs and submitting a kill request. Its then that I get the 'no PID in database for job error, unable to stop'. Rich     ...
written 3.0 years ago by rich_jp0

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Popular Question 24 months ago, created a question with more than 1,000 views. For suite_samtools_1_2 EOF marker absent error

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