Re: [galaxy-dev] advanced parameters: all or nothing?
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu wrote: Hello, I was recently adjusting advanced parameters when running Tophat in Galaxy and noticed that when advanced parameters are used, every field is converted and submitted as command line parameter to the tool at runtime. Without changing any of the default values I get a different tophat result than if advanced parameters are left off. That sounds like a bug in the wrapper. I'm curious if the Galaxy team has considered a mechanism for disabling an individual parameter? Or perhaps a way of individually enabling parameters from within the Advanced Parameter block? Just trying to think of a way to use one advanced parameter without using all of them. Cheers, Andrew Warren This should be possible using optional parameters, as of: https://bitbucket.org/galaxy/galaxy-central/issue/403/ https://bitbucket.org/galaxy/galaxy-central/issue/661/ Peter ___ 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] Stalled upload jobs under Admin, Manage jobs
Hello all, I've noticed we have about a dozen stalled upload jobs on our server from several users. e.g. Job ID UserLast Update ToolState Command LineJob Runner PID/Cluster ID 235221 hours agoupload1 upload NoneNoneNone ... 233919 hours agoupload1 upload NoneNoneNone The job numbers are consecutive (2339 to 2352) and reflect a problem for a couple of hours yesterday morning. I believe this was due to the underlying file system being unmounted (without restarting Galaxy), and at the time restarting Galaxy fixed uploading files. Test jobs since then have completed normally - but these zombie jobs remain. Using the Stop jobs option does not clear these dead upload jobs. Restarting the Galaxy server does not clear them either. This is our production server and was running galaxy-dist, changeset 5743:720455407d1c - which I have now updated to the current release, 6621:26920e20157f - which makes no difference to these stalled jobs. Does anyone have any insight into what might be wrong, and how to get rid of these zombie tasks? Thanks, Peter ___ 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] Problem with self.object_store.exists in set_dataset_sizes.py
Hi all, I've just updated our Galaxy to the current release 26920e20157f which now includes quota support. This means I need to run set_dataset_sizes.py in order to record the current usage, as explained here: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas However, I have run into a problem: $ sudo -u galaxy python2.6 scripts/set_dataset_sizes.py Loading Galaxy model... Processing 3011 datasets... Completed 0% Traceback (most recent call last): File scripts/set_dataset_sizes.py, line 45, in module dataset.set_total_size() File lib/galaxy/model/__init__.py, line 702, in set_total_size if self.object_store.exists(self, extra_dir=self._extra_files_path or dataset_%d_files % self.id, dir_only=True): AttributeError: 'NoneType' object has no attribute 'exists' According to the comments in that file, self.object_store should be initialized in mapping.py (method init) by app.py - apparently that isn't happening. Has anyone else seen this? Thanks, Peter ___ 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] Batch limit on Wokflows
Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] advanced parameters: all or nothing?
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu wrote: Hello, I was recently adjusting advanced parameters when running Tophat in Galaxy and noticed that when advanced parameters are used, every field is converted and submitted as command line parameter to the tool at runtime. Without changing any of the default values I get a different tophat result than if advanced parameters are left off. That sounds like a bug in the wrapper. Recent Tophat versions have changed parameters and default values again. I made the following changes in 3bd8bed55631 to make the wrapper compatible with Tophat 1.4.0: *removed junctions_filter parameter *changed the default value for max-mismatches from 40 to 20 This should ensure that enabling advanced parameters but leaving them untouched yields the same results as using default parameters. 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] advanced parameters: all or nothing?
On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu wrote: Hello, I was recently adjusting advanced parameters when running Tophat in Galaxy and noticed that when advanced parameters are used, every field is converted and submitted as command line parameter to the tool at runtime. Without changing any of the default values I get a different tophat result than if advanced parameters are left off. That sounds like a bug in the wrapper. Recent Tophat versions have changed parameters and default values again. I made the following changes in 3bd8bed55631 to make the wrapper compatible with Tophat 1.4.0: *removed junctions_filter parameter *changed the default value for max-mismatches from 40 to 20 This should ensure that enabling advanced parameters but leaving them untouched yields the same results as using default parameters. J. Wouldn't it be better not to have the default value 40 (or 20) in the wrapper at all? i.e. Leave it out, so that by default that argument isn't used, so that tophat uses the default it wants to use. Peter ___ 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] advanced parameters: all or nothing?
Wouldn't it be better not to have the default value 40 (or 20) in the wrapper at all? i.e. Leave it out, so that by default that argument isn't used, so that tophat uses the default it wants to use. This would work but limits reproducibility and transparency because Galaxy wouldn't have a record of the parameter's actual value. Yes, this is a problem when default parameters are used as well and should be fixed. However, making more use of defaults when advanced setting are used could be especially problematic b/c I imagine that using advanced parameters generally implies that a user cares are default values more so than if using all defaults. FWIW, the Galaxy team has started thinking about how to better handle multiple tool versions and different parameter default values for different tool versions. If anyone has strong feelings, please feel free to start a discussion (in a new thread please) on this challenge. 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] Batch limit on Wokflows
What revision is your Galaxy instance at? I'm not seeing this behavior on tip with a simple test, it may have been something we've fixed in a more recent revision. -Dannon On Feb 10, 2012, at 11:14 AM, Petit III, Robert A. wrote: Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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] Problem with GMAP datatypes
Thon, I believe this is fixed in change set 6711:62fc9e053835, which is now available in out central repo. However, I do not have access to any data of the required type, so if you still encounter problems, could you send me some data that I can use to reproduce the behavior? Thanks! Greg On Feb 9, 2012, at 9:04 PM, Greg Von Kuster wrote: Hi Thon, I've been working on fixes which I believe may be related to this. When uploading a file, the proprietary datatypes / sniffers (datatypes included in installed tool shed repositories) are not correctly handled by the upload process. Also, when running jobs, if setting metadata externally, the same issue occurs. I'm very close to a fix for this - I just need to polish up the changes. I'm planning to have the fix committed tomorrow - I'll let you know. Thanks for reporting this. Greg On Feb 9, 2012, at 5:32 PM, Anthonius deBoer wrote: I tried to install the GMAP from the main toolshed, but I am getting this error when I actually try to run the GSNAP/GMAP tools It seems that there is a problem with the definition of the datatypes...When I check the paster.log it does complain a little, when loading GMAP stuff, but it seems just a problem with the markup of the help text Any ideas? Error in galaxy when running GSNAP WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmapdb': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmapsnpindex': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'splicesites.iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'introns.iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'snps.iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_annotation': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_splicesites': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_introns': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_snps': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmap PASTER.LOG == galaxy.util.shed_util DEBUG 2012-02-09 12:51:43,862 Installing repository 'gmap' galaxy.util.shed_util DEBUG 2012-02-09 12:51:43,914 Cloning http://toolshed.g2.bx.psu.edu/repos/jjohnson/gmap galaxy.util.shed_util DEBUG 2012-02-09 12:51:46,834 Updating cloned repository to revision 93911bac43da docutils WARNING 2012-02-09 12:51:47,128 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. galaxy.util.shed_util DEBUG 2012-02-09 12:51:47,190 Adding new row (or updating an existing row) for repository 'gmap' in the tool_shed_repository table. docutils WARNING 2012-02-09 12:51:47,238 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. docutils WARNING 2012-02-09 12:51:47,332 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. galaxy.tools DEBUG 2012-02-09 12:51:47,391 Reloading section: GMAP galaxy.tools DEBUG 2012-02-09 12:51:47,413 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_iit_store/2.0.0, version: 2.0.0. docutils WARNING 2012-02-09 12:51:47,445 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. galaxy.tools DEBUG 2012-02-09 12:51:47,462 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gsnap/2.0.1, version: 2.0.1. galaxy.tools DEBUG 2012-02-09 12:51:47,482 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_snpindex/2.0.0, version: 2.0.0. galaxy.tools DEBUG 2012-02-09 12:51:47,501 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_build/2.0.0, version: 2.0.0. galaxy.tools DEBUG 2012-02-09 12:51:47,534 Loaded tool id:
Re: [galaxy-dev] Problem with GMAP datatypes
I'll give it a try and let you know if I run into any more problemsThanksThonOn Feb 10, 2012, at 12:00 PM, Greg Von Kuster g...@bx.psu.edu wrote:Thon, I believe this is fixed in change set 6711:62fc9e053835, which is now available in out central repo. However, I do not have access to any data of the required type, so if you still encounter problems, could you send me some data that I can use to reproduce the behavior? Thanks! Greg On Feb 9, 2012, at 9:04 PM, Greg Von Kuster wrote: Hi Thon,I've been working on fixes which I believe may be related to this. When uploading a file, the proprietary datatypes / sniffers (datatypes included in installed tool shed repositories) are not correctly handled by the upload process. Also, when running jobs, if setting metadata externally, the same issue occurs. I'm very close to a fix for this - I just need to polish up the changes. I'm planning to have the fix committed tomorrow - I'll let you know.Thanks for reporting this.Greg On Feb 9, 2012, at 5:32 PM, Anthonius deBoer wrote:I tried to install the GMAP from the main toolshed, but I am getting this error when I actually try to run the GSNAP/GMAP toolsIt seems that there is a problem with the definition of the datatypes...When I check the paster.log it does complain a little, when loading GMAP stuff, but it seems just a problem with the markup of the help textAny ideas? Error in galaxy when running GSNAP WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmapdb': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmapsnpindex': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'splicesites.iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'introns.iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'snps.iit': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_annotation': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_splicesites': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_introns': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'gmap_snps': 'module' object has no attribute 'gmap' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmapPASTER.LOG ==galaxy.util.shed_util DEBUG 2012-02-09 12:51:43,862 Installing repository 'gmap' galaxy.util.shed_util DEBUG 2012-02-09 12:51:43,914 Cloning http://toolshed.g2.bx.psu.edu/repos/jjohnson/gmap galaxy.util.shed_util DEBUG 2012-02-09 12:51:46,834 Updating cloned repository to revision "93911bac43da" docutils WARNING 2012-02-09 12:51:47,128 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.galaxy.util.shed_util DEBUG 2012-02-09 12:51:47,190 Adding new row (or updating an existing row) for repository 'gmap' in the tool_shed_repository table. docutils WARNING 2012-02-09 12:51:47,238 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.docutils WARNING 2012-02-09 12:51:47,332 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.galaxy.tools DEBUG 2012-02-09 12:51:47,391 Reloading section: GMAP galaxy.tools DEBUG 2012-02-09 12:51:47,413 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_iit_store/2.0.0, version: 2.0.0. docutils WARNING 2012-02-09 12:51:47,445 string:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.galaxy.tools DEBUG 2012-02-09 12:51:47,462 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gsnap/2.0.1, version: 2.0.1. galaxy.tools DEBUG 2012-02-09 12:51:47,482 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_snpindex/2.0.0, version: 2.0.0. galaxy.tools DEBUG 2012-02-09 12:51:47,501 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_build/2.0.0, version: 2.0.0. galaxy.tools DEBUG 2012-02-09
Re: [galaxy-dev] generate dynamic select list based on other input dataset
Dear all, I'm still stuck with the problem to dynamically generate an option list extracted from a user-selectable input dataset. Does anybody have experience here, or is this not possible at all? Have a nice weekend, Holger On 02/07/2012 09:58 PM, Holger Klein wrote: Dear all, I have a working module which generates wig files for genomic annotation from a single column of a bigger input data matrix (Input A). In the current state, the user has to input the column name (Input B) from which to calculate the values in the wig file. Now I'd like to modify the xml in such a way, that depending on the input dataset (Input A) a dynamic list for Input B is generated. I found Hans-Rudolf Hotz' hints from some time ago on this list and thought that the following would be a good start: param name = InputB label = InputBName format = data type = select help = Use tickboxes to select model display = radio dynamic_options = getInputBOptions($InputA) / code file=getInputBOptionsFromInputA.py getInputBOptionsFromInputA.py contains a single function def getInputBOptions($InputA): ## parse Input A ## create list InputBOptions return(InputBOptions) Using this approach I get an invalid syntax message when trying to even open the module - in any case I have the feeling that something is still missing here. Did anybody solve a similar problem already and could give me a hint on how to solve that? Cheers, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___ 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] Error with large BAM files?
Hello, I'm very new to Galaxy development. What we've got is a tool we've created that will use our own API/web services in order to use BAM files in our database as the data source in Galaxy. I got it to work on a very tiny BAM file, but now that that is working, I tried it on a larger one and am seeing the following error: An error occurred running this job: Unable to fetch https://[address to method calling web service]: 'ascii' codec can't decode byte 0xc2 in position 25686: ordinal not in range(128) As far as I can tell from Google, it appears this error has to do with python expecting ascii, but I'm calling Galaxy with the following code: String MimeType = application/octet-stream; BufferedOutputStream out = new BufferedOutputStream(response.getOutputStream()); byte[] result = [call to my web service]; response.setContentType(MimeType); response.setHeader(Content-Disposition,attachment;filename=GalaxyResponse); out.write(result, 0, result.length); Is there anything wrong with this? Or is there some other code I might need to modify, such as in data_source.py? Any help is appreciated, thanks! Brian Luerman Intrepid Bioinformatics (502) 212-2699 http://intrepidbio.com/ ___ 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/
