User: jdv

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jdv20
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Posts by jdv

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debug warnings from delayed job(s) bloating log file
... On a local Galaxy instance, the main log is being filled with lines like this, printing every few seconds repeatedly: galaxy.workflow.run DEBUG 2017-11-22 14:15:50,713 Marking step 10769 outputs of invocation 5849 delayed (dependent step [10768] delayed, so this step must be delayed) galaxy ...
log debug galaxy admin written 20 days ago by jdv20 • updated 20 days ago by Jennifer Hillman Jackson23k
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Comment: C: Galaxy failed to unzip gz files after uploading
... I can wait, but this is great - it is a long-desired feature to be able to handle compressed read data transparently. Is this a fundamental datatype (i.e. can it be set as an output format for tools that can natively write compressed fastq or which we can pipe through gzip when history size is more ...
written 10 months ago by jdv20
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Comment: C: Galaxy failed to unzip gz files after uploading
... I would love to be able to do this on a local instance. Is this feature only available on the main public server or will it be in the next release as well? ...
written 10 months ago by jdv20
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Answer: C: Error running multi-input workflow after upgrade
... After testing, I found that changing the relevant line (line 191 in $INSTALL//lib/galaxy/workflow/run_request.py) from #nh_name = '%s on %s and %s' % ( nh_name, ', '.join( ids[ 0:-1 ] ), ids[ -1 ] ) to nh_name = '%s on %s and %s' % ( nh_name, ', '.join( map(str,ids[ 0:-1 ] )), ids[ -1 ] ...
written 10 months ago by jdv20
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Error running multi-input workflow after upgrade
... After upgrading a local Galaxy instance to 16.10 (from 16.01), I now get an error trying to start a workflow with multiple input files. This happens even with a newly-created barebones testing workflow. The steps taken are: 1. Select workflow to run 2. Select multiple linked datasets for forward an ...
galaxy software error written 10 months ago by jdv20
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Comment: C: mixing collections and "multiple" input tools
... Bjoern, As I understand the tool (and have been using it), if you specify a single FASTQ and two BAM files (say the FASTQ file mapped against two different databases), the tool should discard (or keep, depending on settings) all reads with mappings in any of the BAM files. This has always worked as ...
written 12 months ago by jdv20
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mixing collections and "multiple" input tools
... I'm trying to modify a workflow to work on list collections. Most tools work as expected without change, but I'm running into difficulty with tools that have an input with the 'multiple="true"' attribute set. For these tools, the input in question is expanded into ALL inputs in the collection, which ...
collections written 12 months ago by jdv20
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Answer: A: Help configuring dynamic resource allocation
... For the record, I came up with the following working solution: from galaxy.jobs import JobDestination import os import ast def phyml(job): # Allocate extra time/cores to bootstrap jobs params = dict( [ (p.name, p.value) for p in job.parameters ] ) ...
written 18 months ago by jdv20
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Help configuring dynamic resource allocation
... I'm trying (for the first time) to set up dynamic resource allocation for some jobs on a local Galaxy instance. I've read the docs [here][1] and can get a toy example working, but I know very little Python and don't fully understand how to access the job parameters from within the rules script. The ...
python galaxy written 18 months ago by jdv20

Latest awards to jdv

Scholar 10 months ago, created an answer that has been accepted. For A: Help configuring dynamic resource allocation
Scholar 18 months ago, created an answer that has been accepted. For A: Help configuring dynamic resource allocation

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