Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?
Hi Ed You can use the variable $userEmail in the 'command' tag of the tool definition file Regards, Hans On 05/06/2011 03:56 AM, Edward Kirton wrote: is there a variable i can use in the tool config xml file? thanks! ed ___ 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] Uploading Binary Files into Galaxy
Hi In your_galaxy_root_path/lib/galaxy/datatypes/binary.py try adding the extension of your suffix array file type in the unsniffable_binary_formats array. It would be a good idea to add a class for this file type here too and make sure the datatypes_conf.xml file refers to it. Hope that helps L-A darren.culle...@csiro.au wrote: Hi Everyone, I have encountered a problem and I don’t know how to fix it. We have built a Galaxy instance on a couple of machines here and have built the XML files to use a couple of tools in Galaxy. The input of one of these is a Suffix Array (a binary file). Unfortunately, when I try and upload the Suffix Array, I get the following error message: /The uploaded binary file contains inappropriate content/ My gut feeling is that it is related to Galaxy trying to preview the file and not being able to determine the type. Is there any way around this? I can provide the file and the tool if you need to investigate it further. Thanks, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.culle...@csiro.au mailto:darren.culle...@csiro.au ___ 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] Uploading Binary Files into Galaxy
Hi Darren I assume, you have created a new data type https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes You can now disable the 'sniffing' by adding the data type to the following line: unsniffable_binary_formats = [ 'ab1', 'scf' ] in: ~/galaxy-dist/lib/galaxy/datatypes/binary.py I hope this helps Regards, Hans On 05/06/2011 03:59 AM, darren.culle...@csiro.au wrote: Hi Everyone, I have encountered a problem and I don't know how to fix it. We have built a Galaxy instance on a couple of machines here and have built the XML files to use a couple of tools in Galaxy. The input of one of these is a Suffix Array (a binary file). Unfortunately, when I try and upload the Suffix Array, I get the following error message: The uploaded binary file contains inappropriate content My gut feeling is that it is related to Galaxy trying to preview the file and not being able to determine the type. Is there any way around this? I can provide the file and the tool if you need to investigate it further. Thanks, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.culle...@csiro.aumailto:darren.culle...@csiro.au ___ 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] quick question: how can i supply the user's email address to a tool?
On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Ed You can use the variable $userEmail in the 'command' tag of the tool definition file Regards, Hans That should probably be listed on the wiki, https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Are there any other similar variables worth knowing about? 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] options from file
Hi, I have created a tool that will fetch sequences for selected IDs from a tabular file containing multiple IDs and additional info. I want the tool config to scan the first column of the tab file for IDs and provide the user with a selection box where they can select a single ID or multiple IDs and get output for all selected. The following method does this: param name=tabfile type=data format=tabular label=ID File/ param name=selection type=select multiple=true accept_default=true label=ID options from_dataset=tabfile column name=name index=0/ column name=value index=0/ /options /param The issue is, if the top file in my history is a SAM file containing ~30,000 IDs in the first column the tool initially attempts to load these all in to the selection box and effectively crashes my local instance. I only want to use this on tab files that ill have ~100 IDs at most. I have got around this by creating a new datatype indexfile as a class of Tabular in tabular.py: class IndexFile( Tabular ): file_ext = 'indexfile' def sniff( self, filename ): return False And changing the input file to: param name=tabfile type=data format=tabular label=ID File/ This means I must first set the tabular file to type indexfile, then it will be the only dataset shown under tabfile. Selecting options from a file is really useful, I was wondering if there is a better workaround for this or if a similar indexfile datatype could be included in Galaxy. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] options from file
On Fri, May 6, 2011 at 10:17 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote: Hi, I have created a tool that will fetch sequences for selected IDs from a tabular file containing multiple IDs and additional info. I want the tool config to scan the first column of the tab file for IDs and provide the user with a selection box where they can select a single ID or multiple IDs and get output for all selected. The following method does this: param name=tabfile type=data format=tabular label=ID File/ param name=selection type=select multiple=true accept_default=true label=ID options from_dataset=tabfile column name=name index=0/ column name=value index=0/ /options /param The issue is, if the top file in my history is a SAM file containing ~30,000 IDs in the first column the tool initially attempts to load these all in to the selection box and effectively crashes my local instance. I only want to use this on tab files that ill have ~100 IDs at most. Maybe the options from_dataset=tabfile tag could have a max setting? e.g. options from_dataset=tabfile max=100 could load just the first 100 entries in the tabular file. That seems much more general than the new filetype idea. It could have a default max value which should useful. Thinking of the example of a tabular file of gene IDs for an organism, you might well want 20 to 30 thousand entries. Since Galaxy puts a search function on the selection, the UI should be OK. Its just the performance we need to worry about. 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] typo in galaxy-dist/tool_conf.xml?
Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution downloaded yesterday tool file=indels/indel_table.xml / should be tool file=indels/indel_table.xml / ? Marina -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ___ 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] Restoring galaxy database return few empty tables.
Vipin TS wrote: Dear Galaxy Team, I am switching our Galaxy production service to a new machine, We are using Postgres as database server. The existing database belongs to postgres version 8.3 and I took my instance's dump using postgres version 8.4. I am able to restore my database on postgres 8.4, Except few tables were empty and with few strange error message left on log file. I am not sure how many tables are empty, but I found table called 'job' returns 0 rows. Original job table returns me 40733 rows. excerpts from error log: ERROR: insert or update on table history_dataset_association_annotation_association violates foreign key constraint history_dataset_association_a_history_dataset_association__fkey DETAIL: Key (history_dataset_association_id)=(284985) is not present in table history_dataset_association. STATEMENT: ALTER TABLE ONLY history_dataset_association_annotation_association ADD CONSTRAINT history_dataset_association_a_history_dataset_association__fkey FOREIGN KEY (history_dataset_association_id) REFERENCES history_dataset_association(id); ERROR: insert or update on table history_dataset_association_tag_association violates foreign key constraint history_dataset_association_t_history_dataset_association__fkey DETAIL: Key (history_dataset_association_id)=(387932) is not present in table history_dataset_association. STATEMENT: ALTER TABLE ONLY history_dataset_association_tag_association In my knowledge we didn't do any manual transactions on Galaxy database and Could anyone let me know something wrong at my end. I'm sure this has been covered somewhere but I haven't been able to find it on the Wiki or by searching the archives. Hi Vipin, When restoring, I generally use the --disable-triggers, which instructs Postgres to ignore foreign key constraints. --nate Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany ___ 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 downloading file from local Galaxy
Marco Moretto wrote: Hi all, I successfully installed a Galaxy instance locally. I use Galaxy with Apache. Every time I try to download a file from history (like Options - Export to file) the browser (Firefox 3.6) reply with the error /tmp/lFeL6erm.asc.part could not be saved, because the source file could not be read.. I can correctly view the file content with the Display data in browser button. Thank you for any help. Hi Marco, Does this also happen with the single history item floppy disk icon? Are you using the sendfile module for Apache (described in the ApacheProxy page in our wiki)? Thanks, --nate --- Marco ___ 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] Workflow steps stuck in job queue - since cleanup_datasets.py
Liisa Koski wrote: Hi, Yesterday I ran the cleanup_datasets.py scripts as follows.. Deleting Userless Histories python cleanup_datasets.py universe_wsgi.ini -d 10 -1 Purging Deleted Histories python cleanup_datasets.py universe_wsgi.ini -d 10 -2 -r Purging Deleted Datasets python cleanup_datasets.py universe_wsgi.ini -d 10 -3 -r Purging Library Folders python cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r Purging Libraries python cleanup_datasets.py universe_wsgi.ini -d 10 -4 -r Deleting Datasets / Purging Dataset Instances python cleanup_datasets.py universe_wsgi.ini -d 10 -6 -r This morning I noticed a number of workflows were either stuck at a certain step (ie..job running) or the step was grey (waiting in queue) but our cluster has free nodes. If I start a new workflow...it completes fine...just the 19 histories that were running yesterday are stuck. Did I do something wrong with the cleanup. Is there a way to restart these stuck histories without having to restart the entire workflow? Hi Liisa, I don't think cleanup would've been related. If you have enable_job_recovery = True in your configuration, since you're using a cluster you can restart the Galaxy job runner process and it should resume those jobs and finish them. --nate Thanks in advance, Liisa ___ 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] Question on setting metadata on upload via API
Duddy, John wrote: I'm looking at extending the metadata fields for one of the supported file types. The files can get VERY large, and since I'm creating those files, I'd like to save as metadata some of the information I have on the contents. Specifically, I'd like to tag the files with information about the sample as well as the byte offsets in the file for every millionth record (to facilitate fast file splitting). I saw the sample script for uploading a file to a library via the API. It looks to me like the most direct approach would be to modify LibrariesController.create() to handle arbitrary key-value pairs to be set on the data file. However, that might not support things like having metadata values be arrays. So, does my understanding of the problem and the areas involved seem reasonable? Is there something already out there that does what I need? I saw the set_metadata.py script, but that looks like it is meant to operate directly on the files, which might not make a running instance of Galaxy too happy. Is there an API version of that (or something in one of the web controllers I can repurpose to my needs)? Hi John, Galaxy will still set its own required metadata elements (determined by the file type) on upload, but if you create additional optional metadata elements and don't set them in your datatype's set_meta(), you could then set them after the job runs with a call to the API. Editing metadata via the API is not yet implemented, but shouldn't be too difficult to add. This does mean you'd have to get the newly created dataset ID and make second call to the API. If that's not feasible it could probably be incorporated at creation time, but would be trickier since the upload code doesn't account for the possibility that metadata exists prior to running the upload tool itself. --nate Thanks! John Duddy Illumina, Inc. ___ 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] typo in galaxy-dist/tool_conf.xml?
Marina Gourtovaia wrote: Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution downloaded yesterday tool file=indels/indel_table.xml / should be tool file=indels/indel_table.xml / ? Hi Marina, Indeed, thanks for catching this. It has been fixed and will go out in the next stable release (probably next week). --nate Marina -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ___ 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 downloading file from local Galaxy
Hi Nate, thanks for answering. I performed some tests stealing PCs from my collegues and actually it was a problem of my profile data. I experienced these problems with both Chromium and Firefox on my machine, but with others it works, so I decided to simply clean up my profile data and now it works also for me. Still don't know on what it could depend but in the end it doesn't really matter. The trick works. Thanks a lot. --- Marco On 6 May 2011 16:37, Nate Coraor n...@bx.psu.edu wrote: Marco Moretto wrote: Hi all, I successfully installed a Galaxy instance locally. I use Galaxy with Apache. Every time I try to download a file from history (like Options - Export to file) the browser (Firefox 3.6) reply with the error /tmp/lFeL6erm.asc.part could not be saved, because the source file could not be read.. I can correctly view the file content with the Display data in browser button. Thank you for any help. Hi Marco, Does this also happen with the single history item floppy disk icon? Are you using the sendfile module for Apache (described in the ApacheProxy page in our wiki)? Thanks, --nate --- Marco ___ 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] Automatically sending an email to users you've shared a history with
Hello Leandro, On the main Galaxy site, an automatic email function is not currently possible (but the suggestion is a good one!). If you are running your own instance, this is something that could likely be written up and added in (and shared with other user's through the tool shed). For searches, Google is the only way to search the entire archives. Nabble at GMOD is another search tool, although the contents are based on the most recent list activity (perhaps desirable, as Galaxy in under continual change as more features are added and improved). http://gmod.827538.n3.nabble.com/Galaxy-f829901.html Hopefully this helps, Best, Jen Galaxy team On 4/13/11 2:41 AM, Leandro Hermida wrote: Hi all, Can Galaxy be configured to automatically send an email to users you have shared a history with (with appropriate link to Galaxy history URL included)? I tried to search the mail list history and could not find, which bring another question, is Google the only way to search the galaxy mailing list archive? regards, Leandro ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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] Bowtie why it does not take the 1_sequence.txt nor for bowtie nor the Convert
Hello Olivier, The first place to start is to change the metadata for the history items so that the filetype is .fastq. Do this by clicking on the pencil icon for each dataset, change the filetype, and save. Or, rename the files before transfer. If there are still problems, double check the actual fastq file format first - if the data are large (over 2G) consider using direct FTP to reduce the chance of file corruption during transfer (instructions are on the Upload form). Also please feel free to share a link to your history containing the problem data and we can try to offer advice. (Options - Share or Publish). You can send the share link back directly to me. Apologies for the delay in reply, Best, Jen Galaxy team On 4/14/11 9:24 AM, Olivier Schaad wrote: Dear Sir I try to use Bowtie mapping in galaxy , I import my Illumina s_1_sequence.txt , then I try to use the convert my userName is my email 21: FASTQ Groomer on data 9 An error occurred running this job: /There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have/ but I do have for all the files an error I upload the data using URL http://home.adm.unige.ch/~prnfg/HowardRiezman/wt(RH%20448)%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-1B%20erg3%209f-10A-1B%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-9D%20erg3%2013f-9D-9D%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-13B%20erg3%2013f-9D-13B%20%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/erg3%20RH%205702%20erg3%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-3A%20erg3%209f-10A-3A%20s_1_sequence.txt Could you advice me ? Best regards ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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/
