Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Yeah, pretty sure I'm up to date.
$ hg branches
default10411: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: thondeb...@me.com
mailto:thondeb...@me.com
Public profile on LinkedIn
http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/
From: Jeremy Goecks [mailto:jeremy.goe...@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.goe...@emory.edu
mailto: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/DATATE
ST/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.j
son
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata
_in_HistoryDatasetAssociation_2551_XsCZer,/mnt/ngs/analysis/svcgalaxy/DATATE
ST/job_working_directory/001/1916/metadata_kwds_HistoryDatasetAssociation_25
51_iNUAr_,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/191
6/metadata_out_HistoryDatasetAssociation_2551_ZHhosg,/mnt/ngs/analysis/svcga
laxy/DATATEST/job_working_directory/001/1916/metadata_results_HistoryDataset
Association_2551_tqtiIX,,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_di
rectory/001/1916/metadata_override_HistoryDatasetAssociation_2551_MOfd8w
echo $?
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy_1
916.ec
Regards,
Thon
Thon deBoer Ph.D
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.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
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) Regards, Thon Thon deBoer Ph.D., Bioinformatics Guru California, USA |p: +1 (650) 799-6839 |m: mailto:thondeb...@me.com thondeb...@me.com Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/ 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: mailto:thondeb...@me.com thondeb...@me.com Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/ 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. image001.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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: mailto:thondeb...@me.com thondeb...@me.com Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/ 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) Regards, Thon Thon deBoer Ph.D., Bioinformatics Guru California, USA |p: +1 (650) 799-6839 |m: mailto:thondeb...@me.com thondeb...@me.com Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/ LinkedIn From: galaxy-dev-boun...@lists.bx.psu.edu mailto: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: mailto:thondeb...@me.com thondeb...@me.com Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/ 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. image001.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
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 -g
tool-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.j
son
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/metadata
_in_HistoryDatasetAssociation_2551_XsCZer,/mnt/ngs/analysis/svcgalaxy/DATATE
ST/job_working_directory/001/1916/metadata_kwds_HistoryDatasetAssociation_25
51_iNUAr_,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/191
6/metadata_out_HistoryDatasetAssociation_2551_ZHhosg,/mnt/ngs/analysis/svcga
laxy/DATATEST/job_working_directory/001/1916/metadata_results_HistoryDataset
Association_2551_tqtiIX,,/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_di
rectory/001/1916/metadata_override_HistoryDatasetAssociation_2551_MOfd8w
echo $?
/mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy_1
916.ec
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: mailto:thondeb...@me.com
thondeb...@me.com
Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/
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: mailto:thondeb...@me.com
thondeb...@me.com
Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/
LinkedIn
From: galaxy-dev-boun...@lists.bx.psu.edu
mailto: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)
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru
California, USA |p: +1 (650) 799-6839 |m: mailto:thondeb...@me.com
thondeb...@me.com
Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/
LinkedIn
From: galaxy-dev-boun...@lists.bx.psu.edu
mailto:galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun
Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Hi Thon double check your datatypes_conf.xml (which was not touched/changed during the update process, since it is listed in the .hgignore file, I guess) with the new datatypes_conf.xml.sample file for any changes regarding converters for bed files Regards, Hans-Rudolf On 08/22/2013 02:51 AM, Anthonius deBoer wrote: Yep... $ bedtools --version bedtools v2.17.0 Thon On Aug 21, 2013, at 01:40 PM, sam guerler aysam.guer...@gmail.com wrote: Hi Anthonius, Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers. I hope this helps, Sam On Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer thondeb...@me.com mailto:thondeb...@me.com wrote: Hi, I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files... Am I missing a converter? And why would a BED file even needed to be converted? Thanks Thon datatype extension=bed type=galaxy.datatypes.interval:Bed display_in_upload=true converter file=bed_to_gff_converter.xml target_datatype=gff/ converter file=interval_to_coverage.xml target_datatype=coverage/ converter file=bed_to_bgzip_converter.xml target_datatype=bgzip/ converter file=bed_to_tabix_converter.xml target_datatype=tabix depends_on=bgzip/ converter file=bed_to_summary_tree_converter.xml target_datatype=summary_tree/ converter file=bed_to_fli_converter.xml target_datatype=fli/ !-- display file=ucsc/interval_as_bed.xml / -- !-- display file=genetrack.xml / -- display file=igb/bed.xml / /datatype datatype extension=bedgraph type=galaxy.datatypes.interval:BedGraph display_in_upload=true converter file=bedgraph_to_bigwig_converter.xml target_datatype=bigwig/ /datatype datatype extension=bedstrict type=galaxy.datatypes.interval:BedStrict / !-- datatype extension=bed6 type=galaxy.datatypes.interval:Bed6 converter file=bed_to_genetrack_converter.xml target_datatype=genetrack/ /datatype -- datatype extension=bed12 type=galaxy.datatypes.interval:Bed12 / datatype extension=len type=galaxy.datatypes.chrominfo:ChromInfo display_in_upload=true converter file=len_to_linecount.xml target_datatype=linecount / /datatype datatype extension=bigbed type=galaxy.datatypes.binary:BigBed mimetype=application/octet-stream dis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Hi Anthonius, Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers. I hope this helps, Sam On Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files... Am I missing a converter? And why would a BED file even needed to be converted? Thanks Thon datatype extension=bed type=galaxy.datatypes.interval:Bed display_in_upload=true converter file=bed_to_gff_converter.xml target_datatype=gff/ converter file=interval_to_coverage.xml target_datatype=coverage/ converter file=bed_to_bgzip_converter.xml target_datatype=bgzip/ converter file=bed_to_tabix_converter.xml target_datatype=tabix depends_on=bgzip/ converter file=bed_to_summary_tree_converter.xml target_datatype=summary_tree/ converter file=bed_to_fli_converter.xml target_datatype=fli/ !-- display file=ucsc/interval_as_bed.xml / -- !-- display file=genetrack.xml / -- display file=igb/bed.xml / /datatype datatype extension=bedgraph type=galaxy.datatypes.interval:BedGraph display_in_upload=true converter file=bedgraph_to_bigwig_converter.xml target_datatype=bigwig/ /datatype datatype extension=bedstrict type=galaxy.datatypes.interval:BedStrict / !-- datatype extension=bed6 type=galaxy.datatypes.interval:Bed6 converter file=bed_to_genetrack_converter.xml target_datatype=genetrack/ /datatype -- datatype extension=bed12 type=galaxy.datatypes.interval:Bed12 / datatype extension=len type=galaxy.datatypes.chrominfo:ChromInfo display_in_upload=true converter file=len_to_linecount.xml target_datatype=linecount / /datatype datatype extension=bigbed type=galaxy.datatypes.binary:BigBed mimetype=application/octet-stream dis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Yep...$ bedtools --versionbedtools v2.17.0ThonOn Aug 21, 2013, at 01:40 PM, sam guerler aysam.guer...@gmail.com wrote:Hi Anthonius,Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers.I hope this helps,SamOn Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer thondeb...@me.com wrote:Hi,I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check mydatatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files...Am I missing a converter? And why would a BED file even needed to be converted?ThanksThon datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" converter file="bed_to_gff_converter.xml" target_datatype="gff"/ converter file="interval_to_coverage.xml" target_datatype="coverage"/ converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/ converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/ converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/ converter file="bed_to_fli_converter.xml" target_datatype="fli"/ !-- display file="ucsc/interval_as_bed.xml" / -- !-- display file="genetrack.xml" / -- display file="igb/bed.xml" / /datatype datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/ /datatype datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" / !-- datatype extension="bed6" type="galaxy.datatypes.interval:Bed6" converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/ /datatype -- datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" / datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true" converter file="len_to_linecount.xml" target_datatype="linecount" / /datatype datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" dis___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
