It appears you are missing some updates. This issue was fixed in this changeset
9992:
--
changeset: 9992:7105c53139d4
branch: stable
parent: 9990:f35c0441e374
user: jeremy goecks <jeremy.goe...@emory.edu>
date: Tue Jun 11 17:34:26 2013 -0400
files: lib/galaxy/tools/actions/__init__.py
description:
Use len_file_path config option rather than hardcoded path for chromInfo tool
parameter.
--
You might have missed this changeset if you updated to the late June release
soon after it came out. However, it is definitely included in the August
release. Can you confirm that you're running the August release?
Thanks,
J.
On Aug 23, 2013, at 9:08 PM, Thon de Boer wrote:
> Ofcourse I spoke too soon…
>
> I get a problem in that the conversion of my dataset reports that it cannot
> find the chromosome length files, even though trickster itself has no problem
> showing it…
>
> I looked at the problem script and it is showing below
>
> It seems that the script is passed the path to the chromosome files like this
> “tool-data/shared/ucsc/chrom/hg19-decoy.len”
>
> This will clearly never work since this file is not relative to the working
> directory..
> SO somewhere a script forgets to add the ${GALAXY_DATA_DIR} or whatever that
> parameter is…..
>
> I could probably hardcode the location of the tool-data directory, but I
> don’t think that should be the solution…
>
> Why do I only have this issue? SHOULD I have hardcoded the location of
> tool-data?
>
> The universe_wgi.ini.sample file does not hardcode this…
>
> Am I missing some updates?
>
> Thanks,
>
> Thon
>
> #!/bin/sh
> GALAXY_LIB="None"
> if [ "$GALAXY_LIB" != "None" ]; then
> if [ -n "$PYTHONPATH" ]; then
> PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
> else
> PYTHONPATH="$GALAXY_LIB"
> fi
> export PYTHONPATH
> fi
> TMPDIR=/mnt/ngs/analysis/svcgalaxy/DATATEST/TMP
> export TMPDIR
>
> cd /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916
> grep -v '^#' /mnt/ngs/analysis/svcgalaxy/DATATEST/files/002/dataset_2288.dat
> | sort -k1,1 | bedtools genomecov -bg -split -i stdin
> -gtool-data/shared/ucsc/chrom/hg19-decoy.len > temp.bg ;
> bedGraphToBigWig temp.bg
> tool-data/shared/ucsc/chrom/hg19-decoy.len/mnt/ngs/analysis/svcgalaxy/DATATEST/files/002/dataset_2315.dat;
> cd /mnt/ngs/analysis/svcgalaxy/galaxy-test;
> /mnt/ngs/analysis/svcgalaxy/galaxy-test/set_metadata.sh
> /mnt/ngs/analysis/svcgalaxy/DATATEST/files
> /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916 .
> /mnt/ngs/analysis/svcgalaxy/galaxy-test/universe_wsgi.ini
> /mnt/ngs/analysis/svcgalaxy/DATA/TMP/tmp2KAn7W
> /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy.json
>
> /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_in_HistoryDatasetAssociation_2551_XsCZer,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_kwds_HistoryDatasetAssociation_2551_iNUAr_,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_out_HistoryDatasetAssociation_2551_ZHhosg,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_results_HistoryDatasetAssociation_2551_tqtiIX,,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata_override_HistoryDatasetAssociation_2551_MOfd8w
> echo $? >
> /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy_1916.ec
>
> Regards,
>
> Thon
>
> Thon deBoer Ph.D., Bioinformatics Guru
> California, USA |p: +1 (650) 799-6839 |m: thondeb...@me.com
> Public profile on LinkedIn
>
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer
> Sent: Friday, August 23, 2013 5:47 PM
> To: 'Jeremy Goecks'
> Cc: 'Galaxy-dev Galaxy-dev'
> Subject: Re: [galaxy-dev] Why does my trackster complain about not being able
> to display BED files?
>
> I tracked it down to a problem with the API proxy configuration.
>
> I had the API calls diverted to a different server since I wanted to ensure
> that API calls would be handled by a different server, but that does not seem
> to work correctly for the API calls used in trickster…
>
> Issue resolved…
>
> Regards,
>
> Thon
>
> Thon deBoer Ph.D., Bioinformatics Guru
> California, USA |p: +1 (650) 799-6839 |m: thondeb...@me.com
> Public profile on LinkedIn
>
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer
> Sent: Friday, August 23, 2013 5:12 PM
> To: 'Jeremy Goecks'
> Cc: 'Galaxy-dev Galaxy-dev'
> Subject: Re: [galaxy-dev] Why does my trackster complain about not being able
> to display BED files?
>
> I now have a different problem with a different (production) version of
> galaxy trickster.
>
> I always get this message “Could not load chroms for this dbkey”
>
> I have checked that I have files with the [key].len in
> tool-data/shared/ucsc/chrom and I have twobit files etc.
>
> The weird thing is, that the “Create visualization” shows the genome keys I
> have but this window shows nothing for the dbkey it things it should be
> getting…
>
> So somewhere it “looses” the key…
>
> Any ideas?
>
> (I’m running the latest update)
>
>
> <image001.png>
>
> Regards,
>
> Thon
>
> Thon deBoer Ph.D., Bioinformatics Guru
> California, USA |p: +1 (650) 799-6839 |m: thondeb...@me.com
> Public profile on LinkedIn
>
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer
> Sent: Friday, August 23, 2013 11:02 AM
> To: 'Jeremy Goecks'
> Cc: 'Galaxy-dev Galaxy-dev'
> Subject: Re: [galaxy-dev] Why does my trackster complain about not being able
> to display BED files?
>
> Thanks Jeremy,
>
> I did what you suggested and now it no longer complains!
> Not sure if I had edited datatypes_conf.xml but just copying the sample
> worked and let’s just hope I did not break any of my changes
>
> Regards,
>
> Thon
>
> Thon deBoer Ph.D., Bioinformatics Guru
> California, USA |p: +1 (650) 799-6839 |m: thondeb...@me.com
> Public profile on LinkedIn
>
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
> Sent: Thursday, August 22, 2013 11:11 AM
> To: Anthonius deBoer
> Cc: sam guerler; Galaxy-dev Galaxy-dev
> Subject: Re: [galaxy-dev] Why does my trackster complain about not being able
> to display BED files?
>
>
> Am I missing a converter?
>
> Yes, you are missing the bed_to_bigwig converter.
>
> If you haven't made changes to your datatypes_conf.xml file, you can just
> copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed
> converters.
>
> If you've made changes to datatypes_conf.xml, you'll need to manually add the
> needed converters. We recently transitioned all the *_to_summary_tree
> converters to *_to_bigwig, so you'll want to remove the summary_tree
> converters and replace them with the bigwig converters.
>
>
> And why would a BED file even needed to be converted?
>
> Converter = indexer for visualizations. Datasets are indexed so that (a)
> aggregate (coverage) data is readily available when viewing a large region
> and (b) finding features in a small region (when zoomed in) is fast.
>
> J.
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