User: bryan.hepworth

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7 months, 3 weeks ago
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b*************@newcasle.ac.uk

Posts by bryan.hepworth

<prev • 9 results • page 1 of 1 • next >
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Comment: C: sam to bam - Galaxy version 17.01
... Hi All After several tries at plain vanilla installation and failure at the same sam to bam step I resorted to Google and a few other suggestions, one here too - is it in your $PATH When I'd tried a which samtools previously it had come back with an answer, so I'd thought that wasn't the issue. ho ...
written 7 months ago by bryan.hepworth30
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Comment: C: sam to bam - Galaxy version 17.01
... Hi Jen Following on from my initial post I thought I'd write and ask for a best practice installation for a local installation. By trying to follow examples I've been dotting around pages that aren't in the wiki any more, suggesting going off elsewhere to read something that was originally there. ...
written 7 months ago by bryan.hepworth30
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Comment: C: sam to bam - Galaxy version 17.01
... Hi Jen First one is easily answered, I haven't adjusted any of the .loc files from a stock github install. All the index files have been built with the datamanager tools and show as: - Data Manager: all_fasta /galaxy/tool-data/hg19/seq/hg19.fa /galaxy/tool-data/hg18/seq/hg18.fa /ga ...
written 7 months ago by bryan.hepworth30
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Comment: C: sam to bam - Galaxy version 17.01
... Hi Jen It might be I'm missing a trick here with not being a bioinformatician and not knowing some of the intricacies. I have two fastq files that have been generated from an Illumina run. I've brought these in to the Galaxy instance with the Get Data tool. The workflow I was given just has steps ...
written 7 months ago by bryan.hepworth30
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Comment: C: sam to bam - Galaxy version 17.01
... Hi Devon I'm just looking through the output from the sh run.sh to see if I can spot other things happening before the failure, then I'll post in the galaxy-dev Thanks for taking the trouble to respond, much appreciated. Bryan ...
written 7 months ago by bryan.hepworth30
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Comment: C: sam to bam - Galaxy version 17.01
... Hi Hans-Rudolf Yes package_samtools_1_2 is installed it got pulled in as a dependency somewhere I believe, but can see it in the manage installed tools menu, ticked and green. Thanks Bryan ...
written 7 months ago by bryan.hepworth30
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Comment: C: sam to bam - Galaxy version 17.01
... Hi Devon I did cat ../..seq/hg19.fa in the directory with the symlink in and got the output from the file as expected., not sure where else to look for clues. Thank you Bryan ...
written 7 months ago by bryan.hepworth30
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Comment: C: sam to bam - Galaxy version 17.01
... Hi Devon I've had a quick look and they all exist although the first one is a symlink to ../../seq/hg19.fa I haven't changed any of the .loc locations from a default install and test from sh run.sh the galaxy.ini has only been changed to allow admin users and to point to the postgresql database T ...
written 7 months ago by bryan.hepworth30
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sam to bam - Galaxy version 17.01
... Hi All First of all I am not a bioinformatician, I'm looking at someone else's test workflow. I have successfully run it on usegalaxy to completion however on my local instance that I've set up I've bumped into an error at the sam to bam conversion process. Comparing the workflows side by side the ...
galaxy samtools local job-error written 7 months ago by bryan.hepworth30 • updated 7 months ago by Jennifer Hillman Jackson23k

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