This is due to a mismatch is chromosome names between your hg19.len file (UCSC
naming) and the VCF (Ensembl naming). This should be handled better by Galaxy,
and I’ve created a card for it:
https://trello.com/c/bjmNesZj
In the meantime, I used this command to convert chromosome names for this
I am trying to visualise VCF exported from:
ftp://ngs.sanger.ac.uk/production/cosmic/CosmicCodingMuts_v68.vcf.gz
However I get the following error: (Both on Galaxy Main and Local installation)
Input error: Chromosome 1 found in your input file but not in your genome file.
needLargeMem: trying to
Hello,
I am developing a web application, where I want to show a Trackster
visualization in an iframe from our local Galaxy Server.
The problem is that I am not able to specify over a locus via the URL
when I am not the owner of the visualization.
(When we click saved Visualization we can
This is a good idea, and I’ve implemented it in this -central changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/c055181847a46dc3199458d899d28d559ae43c38
If you’re working with galaxy-dist, you can pull this one changeset and use it
until the next release. Let me know if you have
To: Liisa Koski liisa.ko...@basf.com
Cc: galaxy-dev@lists.bx.psu.edu Dev galaxy-dev@lists.bx.psu.edu
Date: 11/04/2014 03:12 AM
Subject:Re: [galaxy-dev] trackster is not working on the
vrelease_2014.02.10--2--29ce93a13ac7
Hi Liisa,
For us, it was only copying the directory
Hi Liisa,
For us, it was only copying the directory
“galaxy-dist/static/scripts/packed/viz” from a fresh install to the
installation we wanted to update.
I hope that helps!
Cheers,
Sajoscha
On Apr 10, 2014, at 5:57 PM, Liisa Koski liisa.ko...@basf.com wrote:
Hello,
I just updated to
Hello,
I just updated to Feb.10 and also noticed that Trackster is not working. I
too get the blank screen. Could you please tell me how to manually update
the vis packed files? I do not know what these are.
Thanks in advance,
Liisa
___
Hi Jeremy,
I reverted the files that I have changed, and also cleaned the cache once
again. The error messages are the same:
Failed to load resource: the server responded with a status of 404 (Not Found)
require.js:1:1910Error: Script error for: libs/backbone/backbone-relational
Hi Jeremy,
We found that the vis packed files were somehow not updated when we did the
Galaxy updates. So, we manually update these files and now the trackster is
working fine.
Thank you very much for the help!!
Best,
Shu-Yi
On Mar 29, 2014, at 7:51 PM, Jeremy Goecks wrote:
I cloned
Hi Jeremy,
Which version you download, the most latest one or
vrelease_2014.02.10--2--29ce93a13ac7?
Thank you very much.
Best,
Shu-Yi
On Mar 28, 2014, at 10:47 PM, Jeremy Goecks wrote:
I just downloaded a fresh copy of galaxy-dist and everything worked fine with
Trackster. This suggests
I cloned directly from galaxy-dist:
% hg clone https://bitbucket.org/galaxy/galaxy-dist/
which gives you the latest release, and it is 2014.02.10--2–29ce93a13ac7
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Mar 29, 2014, at 3:02 AM,
I just downloaded a fresh copy of galaxy-dist and everything worked fine with
Trackster. This suggests that your Galaxy installation is somehow corrupted.
You’ll need to rollback any changes to your repository and/or start from a
fresh copy.
Let us know if you need help doing this.
Best,
J.
Hi Jeremy,
I cleaned the catche on both safari and firefox, but it doesn't work. It still
shows the same error messages.
Thank you very much for the help!!
Best,
Shu-Yi
On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote:
This sounds like a cache issue. Both of these scripts have been removed
Hi Jeremy,
After checking, the two js scripts are absent from the release:
backbone-relational.js ( static/scripts/packed/libs/backbone/ )
galaxy.utils.js ( static/scripts/packed/utils/ )
bw
C
On 25 Mar 2014, at 16:16, Shu-Yi Su wrote:
Hi Jeremy,
Thank you very much for the reply.
This sounds like a cache issue. Both of these scripts have been removed from
the distribution, so they should be absent from the distribution. Can you try
clearing your cache and see if that fixes the issue?
Thanks,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George
The next step then is to revert all the changes that you pulled from -central
and report back the errors you’re seeing. Manually pulling selected change sets
can be problematic if you don’t get all the dependencies.
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George
Providing some additional information will help diagnose the problem:
*are you running galaxy-dist? If so, have you manually pulled and applied
commits from galaxy-central? If so, which ones?
*which Web browser are you using?
*can you please open the JavaScript console in your browser and
Hi Jeremy,
Thank you very much for the reply.
Yes, we are running on galaxy-dist, and manually pulled to update our
installation. The release version is vrelease_2014.02.10--2--29ce93a13ac7.
I have tried safari and firefox. Both are not working.
Here is the error massage from console:
[Error]
Hi Jeremy,
Thank you so much for reply.
You are right…..I just took the first few lines in fastq file and mapped with
bowtie. Now it works with this small dataset.
I am trying to find the error in my complete dataset, but haven't spotted any
yet.
Do you think the error is from reading the
When visualizing a BAM dataset, Galaxy generates a bigwig dataset of read
coverage. Trying to visualize this dataset is causing the issue. You could try
to convert the BAM to BigWig manually (click on dataset's pencil icon --
convert format -- convert to bigwig) and see if there are any issues
Hey guys,
we want to use trackster in our local galaxy instance (rev. 10392:1ae95b3aa98d
release_2013.08.12) and followed the instructions at
http://wiki.g2.bx.psu.edu/Learn/Visualization .
We tested it with a custom Build of 96 sequences in a fasta file, where all
bams were mapped against
Hi all,
I have a problem that the mappings of an experiment suddenly don't show
up anymore in Trackster, only when I choose 'squish' as visualisation
format. 'Coverage' and 'dense' provide the expected output. So 'squish'
shows nothing. But 'Pack' shows only the names, without the bars.
Update: the 'dense' option does not work neither. So in summary: the
alignment can only be viewed in 'coverage' mode.
Thanks,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/05/2013 09:52 AM, Joachim Jacob | VIB | wrote:
Hi all,
I have a problem
I suspect there is an issue with Trackster when changing from one mode to
another. Can you confirm that by saving and refreshing the visualization, you
can view the dataset in different modes?
Thanks,
J.
On Sep 5, 2013, at 4:06 AM, Joachim Jacob | VIB | wrote:
Update: the 'dense' option does
bedtools genomecov -bg -split -i stdin -g
/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
However this crashes. After looking in my computer, I find that bedtools do
not contain the file genomecov. Is this an erroneous assumption of mine or
have I installed something
Thank you for your quick response. However, I have checked and bedtools are
indeed in the galaxy path. When reviewind the log, I get the following:
galaxy.jobs.runners.local DEBUG 2013-07-09 16:59:15,937 execution
finished: grep -v '^#'
Dear all,
As I was trying to do visualize my data set in trackster, I get the following
error:
/bin/sh: 1: bedtools: not found
sort: fflush failed: standard output: Broken pipe
sort: write error
needLargeMem: trying to allocate 0 bytes (limit: 1000)
When doing a sudo find / -name
You'll need to make sure that bedtools is in your Galaxy user's path.
Best,
J.
On Jul 9, 2013, at 6:40 PM, Perez, Ricardo wrote:
Dear all,
As I was trying to do visualize my data set in trackster, I get the following
error:
/bin/sh: 1: bedtools: not found
sort: fflush failed: standard
Dear all,
I updated to the latest Galaxy stable code, and updated the
datatypes_conf.xml.
Trackster displays an error after opening a saved view:
***
Error: The requested genome file
(/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not
be opened.
Hi Linda,
1- Should the "Set display mode" give out different output?Not yet.VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.)What you're seeing is the display of individual variants; of course, trying to view so many
Thank you Jeremy.
The new wiki page looks great!
Regards,
Linda
From: Jeremy Goecks jeremy.goe...@emory.edu
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: galaxy-dev@lists.bx.psu.edu
Date: 06/11/2013 12:56 PM
Subject:Re: [galaxy-dev] Trackster set display mode - Output looks
Trackster displays an error after opening a saved view:
***
Error: The requested genome file
(/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be
opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open
Hi Jeremy,
Thanks for you assistance. I would love to try your suggestions, but
Galaxy won't start anymore.
I have found the root cause of the problems: my home partition has
become too small, due to a fat 'job_working_directory'. I didn't expect
it to become so big (especially with tophat
Hi Joachim,
It looks like your integrated_tool_panel.xml file has been corrupted somehow.
You can move this file to a backup location (or delete) and it should be
automatically regenerated on Galaxy startup. If this fixes the issue, could you
share a copy of the file? It might be helpful for
1) The dist is most recent:
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 7982:12fcd068b12e
tag: tip
user:Daniel Blankenberg d...@bx.psu.edu
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
2)
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.
I've seen this once or twice before but haven't been able to track down the
issue yet.
Here are two workaround that may help you out:
(1) Add the dataset to a
Thanks for your suggestion, Hans-Rudolf. Unfortunately, no success.
Looking into it bit deeper. Keep suggestions coming ;-)
Joachim
On 11/08/2012 05:00 PM, Hans-Rudolf Hotz wrote:
Hi Joachim
This might be completely unrelated, but your situation reminds me of
our case when we did the last
Can you please verify that you're running the most recent dist?
In the most recent dist, requireJS modules are used, so Dataset is prefixed
with its module, e.g.
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Nearly all saved viz's just show a blank main window, while just
displaying the Galaxy header and the trackster header bar.
In contrast, one visualisation gives this error:
ConverterDependencyException: 'A
Try clearing your browser cache and see if that does the trick.
If not, please open your JavaScript console and report the errors that you're
seeing.
Thanks,
J.
On Nov 8, 2012, at 4:56 AM, Joachim Jacob wrote:
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Clearing cache did not solve it.
The Js console reports (when trying to visualize an short-read alignment):
Uncaught ReferenceError: Dataset is not defined visualization.js:1
Uncaught ReferenceError: Dataset is not defined tracks.js:1
Uncaught ReferenceError: Dataset is not defined
Hi Joachim
This might be completely unrelated, but your situation reminds me of our
case when we did the last update (to Oct 5th release):
All previously stored visualizations didn't work any more a first. I had
to modify the datatypes_conf.xml file by adding
the following line:
datatype
I will modify the gff file as you mentioned and update galaxy.
Thanks a lot.
Yec'han
Yec'han LAIZET
Ingenieur
Plateforme Genome Transcriptome
Tel: 05 57 12 27 75
_
INRA-UMR BIOGECO 1202
Equipe Genetique
69 route
Whatever the file type I set for the gff file (gff3, gff or gtf), I get the
transcript_id error:
Traceback (most recent call last):
File
/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py,
line 91, in
main()
File
Hi all,
I want to view two interval-type datasets in trackster on genome hg19
together with one BAM dataset.
The interval datasets give an error (while the BAM is displayed nicely):
[ti_index_core] bug in BGZF: 80048ed5001b 80048ed5
Thanks for any input,
Joachim
--
Joachim
Here are the links to get the gff and the related genome files:
http://genomeportal.jgi-psf.org/Crypa2/download/Cparasiticav2.GeneCatalog20091217.gff.gz
http://genomeportal.jgi-psf.org/Crypa2/download/Cryphonectria_parasiticav2.nuclearAssembly.unmasked.gz
Whatever the file type I set for the
Can you please share the datasets that are generating this errors?
Thanks,
J.
On Oct 24, 2012, at 4:19 AM, Joachim Jacob wrote:
Hi all,
I want to view two interval-type datasets in trackster on genome hg19
together with one BAM dataset.
The interval datasets give an error (while the
The error you saw was generated by tabix (which is used for fast random access
to interval files), so it's possible that you hit tabix's upper bound. You
might consider following up with the tabix folks to see what the issue is.
As you noted, your dataset is definitely better formatted as a
FYI, trackster supports BigWig directly (no conversion or additional
indexing) and quite efficiently, so you will likely have the most luck
with that.
-- jt
On Wed, Oct 24, 2012 at 3:09 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
bigwig file.
Yes, you should be able to use a single GFF for the complete genome.
This error stems from the same issue as before, namely that Galaxy is treating
your GFF file as GTF.
If you think your GFF is well formatted and there is an issue with Galaxy's
handling of GFF, please send me your GFF and
On Sep 15, 2012, at 11:05 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
is there a way to determine whether Trackster is the cause?
The only place where Trackster caches data is in the SummaryTreeDataProvider.
In galaxy-central, the relevant line is 709 in
is there a way to determine whether Trackster is the cause?
The only place where Trackster caches data is in the SummaryTreeDataProvider.
In galaxy-central, the relevant line is 709 in
lib/galaxy/visualization/genome/data_providers.py :
--
CACHE = LRUCache( 20 ) # Store 20 recently accessed
We're seeing an odd issue that seems to be related to Trackster's caching of
track information, mainly that memory in the web server processes increases.
It appears that tracks are being cached in memory per web process.
If I create a new visualization (and monitor our web processed via top)
This bug has been fixed in galaxy-central changeset 0b58ac6510c5
Thanks for reporting,
J.
On Aug 15, 2012, at 5:41 AM, SHAUN WEBB wrote:
Hi, not sure if this has been reported yet.
If I use the dataset icon to view in trackster then select view in saved
visualisation, the saved
Hello,
I try to use the visualization tool of my local instance of galaxy under
ubuntu. Everytime I try to create a feature track from a sam file, I get the
following error:
/bin/sh samtools not found
I have installed samtools from ubuntu reposotories and it works well as I can
call it from
Hello,
It's likely that samtools is not in Galaxy's path because Trackster uses the
same path as Galaxy does. Also, many tools in Galaxy use the Galaxy PySam egg
rather than the samtools binary, so it's possible that you can run a tool that
uses samtools without the binary in Galaxy's path.
Hello,
Please see the section titled 'Setup for Local Instances' section on this page
to read about how to get .len files for various builds.
Best,
J.
On May 24, 2012, at 10:24 PM, Xu, Jianpeng wrote:
Hi,
I am trying to install the Trackster on the local galaxy. I read the webpage
Hi,
I have been trying to use trackster on the main Galaxy server for a couple
of days now. It was working fine for me early yesterday, I was looking at
(larger) BAM files, then it just stopped and would not display the data of
the loaded tracks (but did display the track title). I have tried to
Mo,
This was a temporary problem and has been fixed.
However, the datasets you tried to visualize are now in an error state, so
you'll have to copy them (History Menu -- Copy Datasets) to create new ones,
which you can then visualize. You can copy datasets to the same history without
It seems that trackster does not know how to display INTERVAL files?Is that true? Surely there is an easy way to support those kinds of simple files without having to convert them?Am I missing something?I also don't seem to be able to convert an interval file into a BED file?Thanks,Thon
Oh wait..It's in the info section...Weird place for a conversion tool but it is there :)On Mar 19, 2012, at 12:02 PM, Anthonius deBoer thondeb...@me.com wrote:It seems that trackster does not know how to display INTERVAL files?Is that true? Surely there is an easy way to support those kinds of
Thon,
It seems that trackster does not know how to display INTERVAL files?
Is that true?
Yes, this is currently a limitation. However, most of the work is done that is
necessary to make this happen, so it should be done soon, definitely in the
next month or two.
Surely there is an easy way
Hello,
I am getting consistent breakage for a C. Cerevisiae reference and mapped
dataset when trying to visualize the mapped data in Trackster. I'm running the
latest galaxy-dist and Trackster appears to be generally working since I added
a couple of reference genomes and users were able to
Alex,
Generally cPickle errors when loading summary trees are a result of indexing
gone bad.
Here are a couple notes that should save you some work:
*your bowtie indices and 2bit files do not need to be rebuilt; they are not
generating these errors;
*converting your SAM files to BAM may
Hi
I am sorry to be a pain in the neck, but as part of our quarterly
upgrade procedure, I am stumbling across the next problem:
Can anybody confirm, that the visualization does not work with the
June 23, 2011 release (changeset: 5743:720455407d1c) when using IE8
or IE7 on windows XP?
(it
Hi Hans,
We haven't done much testing of Trackster with IE yet, and I wouldn't be
surprised if it's broken because IE doesn't follow standards in many important
areas. Trackster should work with Chrome, Safari, and Firefox in all cases.
We'll continue to work to improve Trackster functionality
Colin,
How is it possible to preinstall a reference genome for trackster (hg19)
within galaxy.
i tried to find a dedicated help page but could not find any. Could you
please link me to relevant information?
See the section titled 'Setup for local instances' on this page:
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