[galaxy-dev] Trackster error
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 Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/
Re: [galaxy-dev] Trackster error
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 BAM is displayed nicely): > > [ti_index_core] bug in BGZF: 80048ed5001b < 80048ed5 > > > Thanks for any input, > > Joachim > > -- > Joachim Jacob, PhD > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > ___ > 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/ ___ 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/
Re: [galaxy-dev] Trackster error
It appears the my interval file is too big, and actually in the wrong format: I think it would be better in wig (or other) format since I have only one bp intervals. Anyway, I have pasted the first 500 000 lines of the output of a liftover file (which is in interval format). https://dl.dropbox.com/u/18352887/Galaxy48-%5BSelect_first_on_data_23%5D.interval As you can see, every interval is only one bp long... Thanks Joachim On 10/24/2012 03:27 PM, Jeremy Goecks wrote: 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 BAM is displayed nicely): [ti_index_core] bug in BGZF: 80048ed5001b < 80048ed5 Thanks for any input, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/ ___ 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/
Re: [galaxy-dev] Trackster error
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 wiggle/bigwig file. Best, J. On Oct 24, 2012, at 10:14 AM, Joachim Jacob wrote: > It appears the my interval file is too big, and actually in the wrong format: > I think it would be better in wig (or other) format since I have only one bp > intervals. > > Anyway, I have pasted the first 500 000 lines of the output of a liftover > file (which is in interval format). > https://dl.dropbox.com/u/18352887/Galaxy48-%5BSelect_first_on_data_23%5D.interval > > As you can see, every interval is only one bp long... > > Thanks > Joachim > > On 10/24/2012 03:27 PM, Jeremy Goecks wrote: >> 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 BAM is displayed nicely): >>> >>> [ti_index_core] bug in BGZF: 80048ed5001b < 80048ed5 >>> >>> >>> Thanks for any input, >>> >>> Joachim >>> >>> -- >>> Joachim Jacob, PhD >>> >>> Rijvisschestraat 120, 9052 Zwijnaarde >>> Tel: +32 9 244.66.34 >>> Bioinformatics Training and Services (BITS) >>> http://www.bits.vib.be >>> @bitsatvib >>> >>> ___ >>> 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/ >> >> > ___ 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/
Re: [galaxy-dev] Trackster error
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 wrote: > bigwig file. ___ 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/
[galaxy-dev] Trackster : Error visualising VCF
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 allocate 0 bytes (limit: 1000) The input file seems to be conforming to VCF4.1 format. Is this an issue with trackster instead? Saket ___ 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/
[galaxy-dev] Trackster error after upgrade
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 dependency (bgzip) was in an error state.' Any help appreciated, thanks. Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/
Re: [galaxy-dev] Trackster : Error visualising VCF
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 VCF: sed -E 's/^[0-9XY]+/chr&/‘ input.vcf | sed -E 's/^MT/chrM/' You may need to massage it depending on your platform and sed version. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 20, 2014, at 11:27 AM, Saket Choudhary wrote: > 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 allocate 0 bytes (limit: 1000) > > > The input file seems to be conforming to VCF4.1 format. Is this an > issue with trackster instead? > > > Saket > ___ > 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] Trackster error after upgrade
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. > > 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 dependency (bgzip) was in an error state.' > > Any help appreciated, thanks. > > Joachim > > -- > Joachim Jacob, PhD > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > ___ > 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/ ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
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 tracks.js:1 Thanks, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 11/08/2012 04:14 PM, Jeremy Goecks wrote: 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. 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 dependency (bgzip) was in an error state.' Any help appreciated, thanks. Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/ ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
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: type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/> and add and to the bed and gff definitions, respectively. (the differences are easy to spot when you compare your 'datatypes_conf.xml' file with the new 'datatypes_conf.xml.sample' file.) After making the changes and restarting the server, the saved visualization were re-indexed as soon as I tried to open them, but finally, the were visible again. Regards, Hans-Rudolf On 11/08/2012 04:21 PM, Joachim Jacob wrote: 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 tracks.js:1 Thanks, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 11/08/2012 04:14 PM, Jeremy Goecks wrote: 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. 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 dependency (bgzip) was in an error state.' Any help appreciated, thanks. Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
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 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: type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/> and add and to the bed and gff definitions, respectively. (the differences are easy to spot when you compare your 'datatypes_conf.xml' file with the new 'datatypes_conf.xml.sample' file.) After making the changes and restarting the server, the saved visualization were re-indexed as soon as I tried to open them, but finally, the were visible again. Regards, Hans-Rudolf On 11/08/2012 04:21 PM, Joachim Jacob wrote: 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 tracks.js:1 Thanks, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 11/08/2012 04:14 PM, Jeremy Goecks wrote: 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. 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 dependency (bgzip) was in an error state.' Any help appreciated, thanks. Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
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. https://bitbucket.org/galaxy/galaxy-dist/src/12fcd068b12eb844d7eded11bd70826c4275021c/static/scripts/viz/visualization.js?at=default#cl-726 However, the errors you're reporting indicate no module is used. Another thing to try: repacking/reminifying the JavaScript files: % cd /static/scripts % python pack_scripts.py If that still doesn't work, you could try commenting out the apache rewrite rule for packed scripts and see if that solves the problem. If so, then the problem is narrowed down to the packed scripts, one way or another. J. On Nov 9, 2012, at 12:37 AM, Joachim Jacob wrote: > 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 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: >> >> > type="galaxy.datatypes.tabular:FeatureLocationIndex" >> display_in_upload="false"/> >> >> >> and add >> >> >> and >> >> to the bed and gff definitions, respectively. >> >> (the differences are easy to spot when you compare your 'datatypes_conf.xml' >> file with the new 'datatypes_conf.xml.sample' file.) >> >> >> After making the changes and restarting the server, the saved visualization >> were re-indexed as soon as I tried to open them, but finally, the were >> visible again. >> >> >> Regards, Hans-Rudolf >> >> >> On 11/08/2012 04:21 PM, Joachim Jacob wrote: >>> 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 tracks.js:1 >>> >>> >>> Thanks, >>> Joachim >>> >>> Joachim Jacob, PhD >>> >>> Rijvisschestraat 120, 9052 Zwijnaarde >>> Tel: +32 9 244.66.34 >>> Bioinformatics Training and Services (BITS) >>> http://www.bits.vib.be >>> @bitsatvib >>> >>> On 11/08/2012 04:14 PM, Jeremy Goecks wrote: 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. > > 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 dependency (bgzip) was in an error > state.' > > Any help appreciated, thanks. > > Joachim > > -- > Joachim Jacob, PhD > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > ___ > 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/ >>> >>> ___ >>> 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/ >> >> > ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
1) The dist is most recent:
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 7982:12fcd068b12e
tag: tip
user:Daniel Blankenberg
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
2) executed [galaxy_home]/static/scripts/pack_scripts.py
This solved the problem for all, but one visualisation!
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.
URL: http://localhost/visualization/trackster?id=968205d9ed31733d
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
160 in __call__
body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 94 in decorator
return func( self, trans, *args, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/visualization.py',
line 710 in trackster
viz_config = self.get_visualization_config( trans, vis )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line
516 in get_visualization_config
tracks.append( pack_track( drawable_dict ) )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line
467 in pack_track
source='data' )
File
'/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py',
line 94 in get_data_provider
data_provider = self.get_data_provider( trans,
name=data_provider_name, original_dataset=original_dataset )
File
'/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py',
line 74 in get_data_provider
converted_dataset = original_dataset.get_converted_dataset( trans, name )
File '/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py', line 1152
in get_converted_dataset
raise ConverterDependencyException("A dependency (%s) was in an error
state." % dependency)
ConverterDependencyException: 'A dependency (bgzip) was in an error state.'
Thanks,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 11/09/2012 08:34 PM, Jeremy Goecks wrote:
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.
https://bitbucket.org/galaxy/galaxy-dist/src/12fcd068b12eb844d7eded11bd70826c4275021c/static/scripts/viz/visualization.js?at=default#cl-726
However, the errors you're reporting indicate no module is used.
Another thing to try: repacking/reminifying the JavaScript files:
% cd /static/scripts
% python pack_scripts.py
If that still doesn't work, you could try commenting out the apache
rewrite rule for packed scripts and see if that solves the problem. If
so, then the problem is narrowed down to the packed scripts, one way
or another.
J.
On Nov 9, 2012, at 12:37 AM, Joachim Jacob wrote:
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 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:
type="galaxy.datatypes.tabular:FeatureLocationIndex"
display_in_upload="false"/>
and add
and
to the bed and gff definitions, respectively.
(the differences are easy to spot when you compare your
'datatypes_conf.xml' file with the new 'datatypes_conf.xml.sample'
file.)
After making the changes and restarting the server, the saved
visualization were re-indexed as soon as I tried to open them, but
finally, the were visible again.
Regards, Hans-Rudolf
On 11/08/2012 04:21 PM, Joachim Jacob wrote:
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 R
Re: [galaxy-dev] Trackster error after upgrade
> 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 new/saved visualization and then click 'try again' to try reindexing the dataset; (2) copy the dataset using History Options --> Copy Datasets, then delete the failing dataset and try indexing the new dataset. If the dataset continues to fail, please make it available to me and I'll take a look. Best, J. ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
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 output). Now I have the
job_working_directory mounted on our network share. So I restart
Galaxy, and got this error:
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line
36, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 85, in
__init__
self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path,
self )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
84, in __init__
self.load_integrated_tool_panel_keys()
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
236, in load_integrated_tool_panel_keys
tree = util.parse_xml( self.integrated_tool_panel_config )
File "/home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line
143, in parse_xml
tree = ElementTree.parse(fname)
File
"/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 859, in parse
tree.parse(source, parser)
File
"/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 584, in parse
self._root = parser.close()
File
"/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 1251, in close
self._parser.Parse("", 1) # end of data
ExpatError: unclosed token: line 109, column 4
Removing PID file main.pid
Before dragging up my backup, any idea how to fix this otherwise? I
suspect that mercurial could not pull all changes in, is that possible?
Cheers,
Joachim
On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote:
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 new/saved visualization and then click 'try again' to
try reindexing the dataset;
(2) copy the dataset using History Options --> Copy Datasets, then delete the
failing dataset and try indexing the new dataset.
If the dataset continues to fail, please make it available to me and I'll take
a look.
Best,
J.
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Re: [galaxy-dev] Trackster error after upgrade
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 us to try to figure out what
happened to it.
Thanks for using Galaxy,
Dan
On Nov 14, 2012, at 4:25 AM, Joachim Jacob wrote:
> 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 output). Now I have the job_working_directory
> mounted on our network share. So I restart Galaxy, and got this error:
>
> Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line
> 36, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 85, in __init__
> self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
> File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 84, in
> __init__
> self.load_integrated_tool_panel_keys()
> File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 236, in
> load_integrated_tool_panel_keys
> tree = util.parse_xml( self.integrated_tool_panel_config )
> File "/home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in
> parse_xml
> tree = ElementTree.parse(fname)
> File
> "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
> line 859, in parse
> tree.parse(source, parser)
> File
> "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
> line 584, in parse
> self._root = parser.close()
> File
> "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
> line 1251, in close
> self._parser.Parse("", 1) # end of data
> ExpatError: unclosed token: line 109, column 4
> Removing PID file main.pid
>
>
> Before dragging up my backup, any idea how to fix this otherwise? I suspect
> that mercurial could not pull all changes in, is that possible?
>
>
> Cheers,
> Joachim
>
>
> On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote:
>>> 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 new/saved visualization and then click 'try again'
>> to try reindexing the dataset;
>>
>> (2) copy the dataset using History Options --> Copy Datasets, then delete
>> the failing dataset and try indexing the new dataset.
>>
>> If the dataset continues to fail, please make it available to me and I'll
>> take a look.
>>
>> Best,
>> J.
>>
> ___
> 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/
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[galaxy-dev] Trackster error when loading a gff file
Hello,
when I try to load a gff file in trackster on a galaxy instance (ubuntu
server), I get the following error:
Traceback (most recent call last):
File
"/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py",
line 91, in
main()
File
"/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py",
line 30, in main
for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
File
"/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line
375, in read_unordered_gtf
transcript_id = line_attrs[ 'transcript_id' ]
KeyError: 'transcript_id'
I guess it's because not all the lines in the file have a transcript_id.
Is it a specification in gff file format?
I made it work by changing the line 65 of
/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py by this:
transcript_id = line_attrs.get('transcript_id' , 0)
You may want to change the default 0 value by something more
pertinent... if it is really a bug and not a mistake from myself.
Best regards
Yec'han
Yec'han LAIZET
Ingenieur
Plateforme Genome Transcriptome
Tel: 05 57 12 27 75
_
INRA-UMR BIOGECO 1202
Equipe Genetique
69 route d'Arcachon
33612 CESTAS
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Re: [galaxy-dev] trackster error for viewing rat data (rn5)
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 read name or position or something else…..this could help me to dig out the error in the file? Thank you again for the help….without this piece of useful information, i might had spent days and days on this : ) Best regards, Shu-Yi On Nov 22, 2013, at 2:40 AM, Jeremy Goecks wrote: > This appears to be an issue with the dataset that you're trying to view, not > the build or visualization. It appears that the (bigwig? bigbed?) dataset is > malformed in some way. Can you inspect the dataset to look for errors? Are > you able to view a different rn5 dataset? > > J. > > On Nov 21, 2013, at 10:43 AM, Shu-Yi Su wrote: > >> Hi, >> >> I am trying to view rat data (rn5) using trackster with data format bam or >> bigwig on our galaxy installation, but it isn't working. It works with other >> organisms, such as dm3 or hg19. There is error message in the log: >> >> 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET >> /galaxy-dev/api/genomes/rn5?low=0&num=100 HTTP/1.1" 200 - >> "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922b&hda_ldda=hda"; >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 >> (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" >> 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET >> /galaxy-dev/api/datasets/83c20bbc7104922b?hda_ldda=hda&data_type=track_config >> HTTP/1.1" 200 - >> "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922b&hda_ldda=hda"; >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 >> (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" >> galaxy.webapps.galaxy.api.datasets ERROR 2013-11-20 16:14:21,795 Error in >> dataset API at listing contents: 'BinaryFileReader' object has no attribute >> 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' >> Traceback (most recent call last): >> File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", line >> 44, in show >> is_true( kwd.get( 'retry', False ) ) ) >> File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", line >> 106, in _converted_datasets_state >> if not data_provider.has_data( chrom ): >> File >> "/g/funcgen/galaxy-dev/lib/galaxy/visualization/data_providers/genome.py", >> line 1078, in has_data >> all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ >> File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query >> (lib/bx/bbi/bbi_file.c:5596) >> File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query >> (lib/bx/bbi/bbi_file.c:5210) >> File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize >> (lib/bx/bbi/bbi_file.c:4475) >> File "bbi_file.pyx", line 248, in >> bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) >> File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find >> (lib/bx/bbi/bpt_file.c:1388) >> File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find >> (lib/bx/bbi/bpt_file.c:1154) >> AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' >> >> I also attached the first few lines in our rn5.len: >> chr1 290094216 >> chr2 285068071 >> chr4 248343840 >> chr3 183740530 >> chr5 177180328 >> chr6 156897508 >> chrX 154597545 >> chr7 143501887 >> chr8 132457389 >> chr9 121549591 >> chr13118718031 >> chr14115151701 >> chr15114627140 >> chr10112200500 >> chr1193518069 >> chr1792503511 >> chr1690051983 >> chr1887229863 >> chr1972914587 >> chr2057791882 >> chr1254450796 >> chr4_AABR06109730_random 227955 >> chrUn_JH620568 73090 >> chr2_JH620298_random 62026 >> chr5_JH620330_random 58807 >> chrUn_JH620520 57992 >> chrUn_JH620553 56877 >> chr1_AABR06109393_random 52834 >> chr18_JH620420_random51685 >> chr9_JH620364_random 51490 >> chrX_JH620445_random 49212 >> chrUn_JH620623 47760 >> chr10_JH620371_random44089 >> >> I have looked into this error for a while and still can't figure it out. Any >> idea or suggestions are very appreciated. >> >> Thank you very much. >> Best regards, >> Shu-Yi >> >> >> ___ >> 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 subscr
Re: [galaxy-dev] trackster error for viewing rat data (rn5)
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 generating the dataset. You could then try visualizing that dataset directly to see if anything unusual happens. Finally, there was a bug in bx-python that was fixed a while back: https://bitbucket.org/james_taylor/bx-python/commits/24893a84ce13a18815e3006c9f89b3828022ac96 if you're using an old version of Galaxy, you might try updating and see if that fixes the issue. Best, J. On Nov 22, 2013, at 8:18 AM, Shu-Yi Su wrote: > 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 read name or position or something > else…..this could help me to dig out the error in the file? > > Thank you again for the help….without this piece of useful information, i > might had spent days and days on this : ) > > Best regards, > Shu-Yi > > On Nov 22, 2013, at 2:40 AM, Jeremy Goecks wrote: > >> This appears to be an issue with the dataset that you're trying to view, not >> the build or visualization. It appears that the (bigwig? bigbed?) dataset is >> malformed in some way. Can you inspect the dataset to look for errors? Are >> you able to view a different rn5 dataset? >> >> J. >> >> On Nov 21, 2013, at 10:43 AM, Shu-Yi Su wrote: >> >>> Hi, >>> >>> I am trying to view rat data (rn5) using trackster with data format bam or >>> bigwig on our galaxy installation, but it isn't working. It works with >>> other organisms, such as dm3 or hg19. There is error message in the log: >>> >>> 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET >>> /galaxy-dev/api/genomes/rn5?low=0&num=100 HTTP/1.1" 200 - >>> "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922b&hda_ldda=hda"; >>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 >>> (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" >>> 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET >>> /galaxy-dev/api/datasets/83c20bbc7104922b?hda_ldda=hda&data_type=track_config >>> HTTP/1.1" 200 - >>> "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922b&hda_ldda=hda"; >>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 >>> (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" >>> galaxy.webapps.galaxy.api.datasets ERROR 2013-11-20 16:14:21,795 Error in >>> dataset API at listing contents: 'BinaryFileReader' object has no attribute >>> 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' >>> Traceback (most recent call last): >>> File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", >>> line 44, in show >>> is_true( kwd.get( 'retry', False ) ) ) >>> File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", >>> line 106, in _converted_datasets_state >>> if not data_provider.has_data( chrom ): >>> File >>> "/g/funcgen/galaxy-dev/lib/galaxy/visualization/data_providers/genome.py", >>> line 1078, in has_data >>> all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ >>> File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query >>> (lib/bx/bbi/bbi_file.c:5596) >>> File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query >>> (lib/bx/bbi/bbi_file.c:5210) >>> File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize >>> (lib/bx/bbi/bbi_file.c:4475) >>> File "bbi_file.pyx", line 248, in >>> bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) >>> File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find >>> (lib/bx/bbi/bpt_file.c:1388) >>> File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find >>> (lib/bx/bbi/bpt_file.c:1154) >>> AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' >>> >>> I also attached the first few lines in our rn5.len: >>> chr1290094216 >>> chr2285068071 >>> chr4248343840 >>> chr3183740530 >>> chr5177180328 >>> chr6156897508 >>> chrX154597545 >>> chr7143501887 >>> chr8132457389 >>> chr9121549591 >>> chr13 118718031 >>> chr14 115151701 >>> chr15 114627140 >>> chr10 112200500 >>> chr11 93518069 >>> chr17 92503511 >>> chr16 90051983 >>> chr18 87229863 >>> chr19 72914587 >>> chr20 57791882 >>> chr12 54450796 >>> chr4_AABR06109730_random227955 >>> chrUn_JH620568 73090 >>> chr2_JH620298_random62026 >>> chr5_JH620330_random58807 >>> chrUn_JH620520 57992 >>> chrUn_JH620553 56877 >>> chr1_AABR06109393_random
Re: [galaxy-dev] Trackster error when loading a gff file
The error suggests that Trackster thinks the dataset is in GTF format, not GFF
format.
Galaxy attempts to guess a format when a file is uploaded. If transcript_id and
gene_id are present in the attributes column, Galaxy will assign it a GTF
format. (In GTF format, attributes transcript_id and gene_id are required.) So
far, this heuristic has worked well, but perhaps it's problematic in your case?
You can manually change the format of a dataset in the main Galaxy UI by
clicking on the pencil icon next to a dataset, selecting the Datatype tab, and
choosing GFF. Once you've changed the format to GFF, you should be able to view
it in Trackster.
J.
23, 2012, at 9:08 AM, Yec'han Laizet wrote:
> Hello,
>
> when I try to load a gff file in trackster on a galaxy instance (ubuntu
> server), I get the following error:
>
> Traceback (most recent call last):
> File
> "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py",
> line 91, in
>main()
> File
> "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py",
> line 30, in main
>for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
> File "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line
> 375, in read_unordered_gtf
>transcript_id = line_attrs[ 'transcript_id' ]
> KeyError: 'transcript_id'
>
>
> I guess it's because not all the lines in the file have a transcript_id. Is
> it a specification in gff file format?
>
> I made it work by changing the line 65 of
> /home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py by this:
>
> transcript_id = line_attrs.get('transcript_id' , 0)
>
> You may want to change the default 0 value by something more pertinent... if
> it is really a bug and not a mistake from myself.
>
> Best regards
>
> Yec'han
>
>
>
>
> Yec'han LAIZET
> Ingenieur
> Plateforme Genome Transcriptome
> Tel: 05 57 12 27 75
> _
> INRA-UMR BIOGECO 1202
> Equipe Genetique
> 69 route d'Arcachon
> 33612 CESTAS
>
>
> ___
> 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/
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] Trackster error: not able to find the chrom len file
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. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory *** In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster len_file_path = /mnt/referencedata/trackster Thanks for any advice, Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___ 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] Trackster error: not able to find the chrom len file
I just have symlinked the files to the right location. Is this the correct solution? Further, I had to remove the 'chr' in the chrom len files to make it work. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 06/11/2013 03:26 PM, Joachim Jacob | VIB | wrote: 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. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory *** In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster len_file_path = /mnt/referencedata/trackster Thanks for any advice, Cheers, Joachim ___ 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] Trackster error: not able to find the chrom len file
>> 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 /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , >> No such file or directory >> *** >> >> In my universe_wsgi.ini I point to the correct directory where I keep my >> chrom len files. >> # Directory where chrom len files are kept, currently mainly used by >> trackster >> len_file_path = /mnt/referencedata/trackster This is a bug: Galaxy wasn't using this setting in converters. I've fixed this in -stable changeset 7105c53: https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2 > Further, I had to remove the 'chr' in the chrom len files to make it work. This is a problem between the UCSC chromosome naming convention (e.g., 'chr1') and the Ensembl naming convention (e.g. '1'). In most cases Galaxy handles this transparently, but the new converters do not. This is something that definitely needs to be implemented. Here's a card so that you can follow the feature's progress: https://trello.com/c/lai0uU9g Best, J.___ 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/
