Yeah, pretty sure I’m up to date…

$ hg branches

default 10411:c42567f43aa7

stable 10408:6822f41bc9bb (inactive)

[svcbioinfo@srv160 gs]$ hg branch

stable

[svcbioinfo@srv160 gs]$ hg tip

changeset: 10411:c42567f43aa7

tag: tip

user: greg

date: Mon Aug 19 13:19:56 2013 -0400

summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.

[svcbioinfo@srv160 gs]$ hg incoming

warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting)

comparing with https://bitbucket.org/galaxy/galaxy-dist/

searching for changes

no changes found

$ hg update release_2013.08.12

0 files updated, 0 files merged, 0 files removed, 0 files unresolved

Should I just take “lib/galaxy/tools/actions/__init__.py “ from a fresh install?

Regards,

Thon

Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: thondeboer@me.com

Public profile on LinkedIn

From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Sent: Saturday, August 24, 2013 7:39 AM
To: Thon de Boer
Cc: 'Galaxy-dev Galaxy-dev'
Subject: Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

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.goecks@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,

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:  thondeboer@me.com
Public profile on LinkedIn

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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:  thondeboer@me.com
Public profile on LinkedIn

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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:  thondeboer@me.com
Public profile on LinkedIn

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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:  thondeboer@me.com
Public profile on LinkedIn

From: Jeremy Goecks [mailto:jeremy.goecks@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.