[galaxy-dev] Help with Send output to Galaxy function
Hi, I am trying to connect my local database/webpages to my local galaxy server. But I have a hard to implement send output to galaxy function. Right now I have a sending page to send a form to galaxy and it looks like everything goes well. From the variable json_params(data_source.py), I can see that all parameters have been received by galaxy. But the problem is that how I get my parameters from my getfile.php file(This is used in the Galaxy_URL too, the callback function)? I tried to print out $_POST, $_GET, $_REQUEST, nothing shows up. I did see some output from $_Server. I am using php. Please help! Best, Huayan ___ 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] allow users for specifying the number of CPUs
Jens, The obvious way to temporarily solve this is by adding an additional select in your tool xml having a low default core setting where users can select more cores...this is however not user specific unless you let another wrapper deal with that. This solution we use for the blast wrappers currently. Cheers Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Keilwagen, Jens Verzonden: dinsdag 9 juli 2013 17:29 Aan: galaxy-...@bx.psu.edu Onderwerp: [galaxy-dev] allow users for specifying the number of CPUs Hi guys, we are currently trying to integrate CLC Bios short read assembler into our local Galaxy version. So far everything went smoothly. However, the command line tool allows for specifying the number of CPU that should be used for computation. We are wondering, whether it is also possible to enable Galaxy users also to specify the number of CPUs. Thanks for any help. Best regards, Jens ___ 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] Tool Error: Failure Preparing Job
Unicode isn't handled nicely yet AFAIK so UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 23: ordinal not in range(128) might mean a http://www.fileformat.info/info/unicode/char/2013/index.htm - overtyping these in an ascii text editor will remove them but this is a wart for sure IMHO. You can follow our progress at fixing this on the trello card at https://trello.com/c/couxOih6 On Mon, Jul 8, 2013 at 6:28 PM, Venice Margarette Juanillas venicemargarettejuanil...@gmail.com wrote: Hi all, I'm working on a local Galaxy instance and I want to integrate TASSEL's GLM pipeline into it. But when I run the tool, it prompts: tool error An error occurred running this job:* failure preparing job* This is how the log looks like: galaxy.jobs.handler INFO 2013-07-08 16:00:47,648 (73) Job dispatched galaxy.jobs.runners.local DEBUG 2013-07-08 16:00:47,735 Local runner: starting job 73 galaxy.jobs.runners.local ERROR 2013-07-08 16:00:47,939 failure running job 73 Traceback (most recent call last): File /storage/irri-gsl-galaxy/lib/galaxy/jobs/runners/local.py, line 72, in run_job job_wrapper.prepare() File /storage/irri-gsl-galaxy/lib/galaxy/jobs/__init__.py, line 184, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /storage/irri-gsl-galaxy/lib/galaxy/tools/__init__.py, line 2435, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /storage/irri-gsl-galaxy/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 23: ordinal not in range(128) galaxy.datatypes.metadata DEBUG 2013-07-08 16:00:48,206 Cleaning up external metadata files 127.0.0.1 - - [08/Jul/2013:16:00:50 +0800] GET /api/histories/846c4efa2e1f970a HTTP/1.1 200 - http://localhost:8081/history?status=doneshow_deleted=Falsefilename=Nonedataset_id=b89568d7c4cc60f1; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0 I figured the problem is that UnicodeEncodeError but I don't have an idea how to fix this or where to begin. I do hope you can help me. Thanks and Best Regards, Venice Margarette B. Juanillas ___ 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] Configuring the time of permanently deleting data sets.
Ricardo, You can configure galaxy such that it will allow users to permanently delete and purge datasets from their own histories. After deleting by pressing the cross...select 'include deleted datasets' from the history menu. There you can undelete but also purge immediately from disk. So if they are in a hurry or need the space within their quota they can do it like that... see scrndmp. [cid:image001.png@01CE7D4B.F292A8C0] Hope this helped, Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Perez, Ricardo Verzonden: dinsdag 2 juli 2013 7:09 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Configuring the time of permanently deleting data sets. Dear all, I am currently trying to find a way to decrease the time the users need to wait to permanently delete their data sets. In galaxy I read the following Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted.; I am wondering where can I configure this option in my local instance of galaxy. I have looked for such an option in the universe_wsgi.ini file but I have not found it. I would greatly appreciate if someone can point me to the right direction to modify this. Thank you all, --Ricardo Perez ___ 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/ inline: image001.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] remove already selected options from selection menu
Hi, I am working on a tool that allows to filter on a selected set of contrasts. The contrast names are read from the second column of a history item. In order to allow selection of individual filters for each contrast, I am using the repeat tag. Now I would like to make sure that the user selects each contrast at max one time. Can I use the filter ... to remove the contrasts that have already been chosen from the selection? Or is there a more elegant way? repeat name=contrasts title=Contrast min=1 max=3 param name=contrast type=select label=Contrast to filter on multiple=false options from_dataset=edgercont column name=name index=1/ column name=value index=1/ /options /param param name=lfc type=float label=Linear fold-change value=2.0 / param name=pval type=float label=p-value cutoff value=0.001 / /repeat Thanks for your help in advance Tim ___ 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] no metadata for tools in toolshed
Hi, I grabbed some xml files from Hannons website for his fastx toolkit (improved over galaxys default version). Then I created a repository, uploaded the xml files, but the toolshed complains that it could not find the tools for creating metadata in the xml files. Could somebody please tell me what the problem is with these files? They look like valid tool.xml files to me. http://toolshed.g2.bx.psu.edu/view/idot/fastx_toolkit2 http://i...@toolshed.g2.bx.psu.edu/repos/idot/fastx_toolkit2 thank you very much, ido ___ 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] remove already selected options from selection menu
On Wed, Jul 10, 2013 at 11:23 AM, Tim-Christoph Roloff tim.rol...@fmi.ch wrote: Hi, I am working on a tool that allows to filter on a selected set of contrasts. The contrast names are read from the second column of a history item. In order to allow selection of individual filters for each contrast, I am using the repeat tag. Now I would like to make sure that the user selects each contrast at max one time. Can I use the filter ... to remove the contrasts that have already been chosen from the selection? Or is there a more elegant way? repeat name=contrasts title=Contrast min=1 max=3 param name=contrast type=select label=Contrast to filter on multiple=false options from_dataset=edgercont column name=name index=1/ column name=value index=1/ /options /param param name=lfc type=float label=Linear fold-change value=2.0 / param name=pval type=float label=p-value cutoff value=0.001 / /repeat Thanks for your help in advance Tim Would a multi-select column picker work instead? Note that would not give you any control of the order of the selected rows. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] no metadata for tools in toolshed
On Wed, Jul 10, 2013 at 11:26 AM, Ido Tamir ta...@imp.ac.at wrote: Hi, I grabbed some xml files from Hannons website for his fastx toolkit (improved over galaxys default version). Then I created a repository, uploaded the xml files, but the toolshed complains that it could not find the tools for creating metadata in the xml files. Could somebody please tell me what the problem is with these files? They look like valid tool.xml files to me. http://toolshed.g2.bx.psu.edu/view/idot/fastx_toolkit2 http://i...@toolshed.g2.bx.psu.edu/repos/idot/fastx_toolkit2 thank you very much, ido Hi Ido, For future reference, there is a Test Tool Shed which is a great place to upload unfinished tools for basic sanity testing before publishing them on the Main Tool Shed, see: http://testtoolshed.g2.bx.psu.edu/ (Note - it is a good idea to register with the same username on both the main and test toolsheds, i.e. idot in your case.) As to the immediate problem, I don't recall experiencing that myself. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] queue system
Is it possible to create a queue system for separate jobs. I have a module which roughly consumes all CPUs on our machine and if another user decides to run the same module with other data it should wait till all other runs are finished to prevent overloading. Is there a setting for this? Jasper Koehorst Wageningen UR ___ 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] remove already selected options from selection menu
Hi Peter, I thought about that but the user is expected to choose individual fold-change and p-value for each of the selected contrasts. I currently don't see how I would be able to connect the selected items in the multi-select column picker with these values. Any suggestions on that? Thanks Tim On 07/10/2013 12:30 PM, Peter Cock wrote: On Wed, Jul 10, 2013 at 11:23 AM, Tim-Christoph Roloff tim.rol...@fmi.ch wrote: Hi, I am working on a tool that allows to filter on a selected set of contrasts. The contrast names are read from the second column of a history item. In order to allow selection of individual filters for each contrast, I am using the repeat tag. Now I would like to make sure that the user selects each contrast at max one time. Can I use the filter ... to remove the contrasts that have already been chosen from the selection? Or is there a more elegant way? repeat name=contrasts title=Contrast min=1 max=3 param name=contrast type=select label=Contrast to filter on multiple=false options from_dataset=edgercont column name=name index=1/ column name=value index=1/ /options /param param name=lfc type=float label=Linear fold-change value=2.0 / param name=pval type=float label=p-value cutoff value=0.001 / /repeat Thanks for your help in advance Tim Would a multi-select column picker work instead? Note that would not give you any control of the order of the selected rows. Peter -- Dr. Tim-Ch. Roloff Handschin Head Functional Genomics Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel Switzerland Tel: +41 61 697 7709 Fax: +41 61 697 3976 ___ 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] remove already selected options from selection menu
On Wed, Jul 10, 2013 at 12:39 PM, Tim-Christoph Roloff tim.rol...@fmi.ch wrote: Hi Peter, I thought about that but the user is expected to choose individual fold-change and p-value for each of the selected contrasts. I currently don't see how I would be able to connect the selected items in the multi-select column picker with these values. Any suggestions on that? Thanks Tim I see what you mean - the repeat block does seem the best bet in that case. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] queue system
You have two options: (1) set the number of workers in the LocalJobRunner; (2) Galaxy can use many different computing clusters, all of which have queuing systems that you can control. See this page for more details on both options: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Local Good luck, J. On Jul 10, 2013, at 7:18 AM, Jasper Jan Koehorst wrote: Is it possible to create a queue system for separate jobs. I have a module which roughly consumes all CPUs on our machine and if another user decides to run the same module with other data it should wait till all other runs are finished to prevent overloading. Is there a setting for this? Jasper Koehorst Wageningen UR ___ 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/
[galaxy-dev] NFS noac option
Hi All, I've setup the Galaxy application on a standard NFS mount without the 'noac' option and then the galaxy datasets on a enabled 'noac' NFS mount. I updated the universe configuration to reflect the updated locations. The performance however to the 'noac' mount is really poor, something like 700kb/sec on a 1GB interface. Is this the only option available or have alternatives been recommended to improve the speed ? Regards Timothy Carr University of Cape Town ___ 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] Setting up reference genomes for GATK Genotyper
Hi, A follow up to my own question. When I setup up the Galaxy instance from Cloudman the GATK tools were not included automatically. Something most have gone wrong during the upgrade process from Mercurial. Based on Dan Blankenberg's advice, I was able to got the GATK tools to show up in Galaxy by doing some hand editing of configuration files. But I have no reference genome. Should the reference genome been part of the initial installation if it had gone cleanly? Or including any reference genome for GATK tools supposed to be a manual post-installation process. Either way, I would be appreciative of pointers on how I can include the reference genomes for the GATK tools in Galaxy. Thanks Marco On Mon, Jul 8, 2013 at 12:43 PM, Marco Ocana moc...@broadinstitute.orgwrote: Hi, I am running an instance of Galaxy that I setup using Cloudman. We are trying to use the GATK Unified Genotyper, but we are missing the reference genomes. I saw in your website instructions on how to setup reference genomes for some other tools, but not for the Unified Genotyper. Where can I find instructions on how to setup reference genomes for this tool? Thanks 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool unit tests using composite datatypes
On Tue, Apr 30, 2013 at 4:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Apr 25, 2013 at 3:36 PM, Peter Cock p.j.a.c...@googlemail.com wrote: OK, I've updated to the latest galaxy-central default branch. Here's the slightly revised test for ncbi_makeblastdb.xml, ... In the absence of any fresh feedback, I've filed an issue on Trello for this to make sure it gets tracked: https://trello.com/card/basic-composite-datatypes-not-working-as-test-outputs/506338ce32ae458f6d15e4b3/819 Composite datatypes like HTML seem to work (with a primary file). Basic composite datatypes seem not to work (with no primary file). Regards, Peter Hi guys, Has anything changed in this area of the test framework since April? 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] datatype display_data function
Hello everyone, I had been using an old galaxy build, downloaded in 2010, on my local server and now I am updating it to latest build. I had made some changes as per our need. Along with the output file I have added a piece of code which was making us able to download the stderr file as well in case. I had made those changes inside the display function of lib/galaxy/webapps/galaxy/controllers/dataset.py file. But galaxy have gone through significant changes. Now the display function of lib/galaxy/webapps/galaxy/controllers/dataset.py calls display_data function. def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, chunk=None, **kwd): ... return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd) display_data function is present in lib/galaxy/datatypes/data.py as well as in lib/galaxy/datatypes/tabular.py The code which I had changed in previous galaxy is present in /data.py but the display function is calling the display_data function of .../tabular.py always. How will I make it able to call display_data function of /data.py Please tell me the solution of the above problem or is there any better way to download some more file like stdout, stderr apart from the regular output file. Any help would be really appreciated. P.S. I am creating stderr and stdout file inside database/user_directory Thanks Himanshu ___ 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] trouble with share string
After 1 year of using the same share string at the launch page * https://biocloudcentral.herokuapp.com/launch, *the program no longer loads my application; I. The instance loads, but my galaxyData folder is empty. I am not sure if the problem has occurred because Galaxy has moved something or whether I have deleted something critical. Any ideas? Thanks ___ 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] datatype display_data function
On Wed, Jul 10, 2013 at 1:38 PM, Himanshu Gupta himanshucs...@gmail.com wrote: Hello everyone, I had been using an old galaxy build, downloaded in 2010, on my local server and now I am updating it to latest build. I had made some changes as per our need. Along with the output file I have added a piece of code which was making us able to download the stderr file as well in case. I had made those changes inside the display function of lib/galaxy/webapps/galaxy/controllers/dataset.py file. But galaxy have gone through significant changes. Now the display function of lib/galaxy/webapps/galaxy/controllers/dataset.py calls display_data function. def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, chunk=None, **kwd): ... return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd) display_data function is present in lib/galaxy/datatypes/data.py as well as in lib/galaxy/datatypes/tabular.py The code which I had changed in previous galaxy is present in /data.py but the display function is calling the display_data function of .../tabular.py always. How will I make it able to call display_data function of /data.py Please tell me the solution of the above problem or is there any better way to download some more file like stdout, stderr apart from the regular output file. Any help would be really appreciated. P.S. I am creating stderr and stdout file inside database/user_directory Thanks Himanshu Galaxy now saves stdout and stderr on its own (unless it is very large, in which case that start and end only are kept), and this can be viewed via the i information icon on each history entry. Maybe that is enough and you can abandon your old modification? 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Server Processes Dying?
Hi, Ross, I appreciate you taking the time to answer my inquiry. I did know about the options that technically should not be set on a production server (i.e. debug), although I have to admit I did not fully understand the implications of this (i.e. your Galaxy process may run out of memory if it's serving large files.). I think what probably happened is that this setting was turned on at some point to troubleshoot a problem, however it was never subsequently disabled. I am going to start by disabling the developer settings as you specified, and then depending on the result of this, considering upgrading to a newer version of Galaxy. Again, I want to express my gratitude for you taking the time to respond to my email. I'll try to remember to post back to the mailing list to report my findings. Dan On Mon, Jul 8, 2013 at 3:33 AM, Ross ross.laza...@gmail.com wrote: Hi Dan, That's old code. Updating will probably help. Logging level just takes disk space, but just in case you haven't followed http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance leaving debug = True uncommented used to fill all available server process RAM eventually AFAIK. If not already done, try # Debug enables access to various config options useful for development and # debugging: use_lint, use_profile, use_printdebug and use_interactive. It # also causes the files used by PBS/SGE (submission script, output, and error) # to remain on disk after the job is complete. Debug mode is disabled if # commented, but is uncommented by default in the sample config. # debug = True Hope this helps? On Mon, Jul 8, 2013 at 4:26 PM, Dan Sullivan dansulli...@gmail.comwrote: Hi, Galaxy Developers, I have what I'm hoping is a fairly simple inquiry for the Galaxy community; basically, our production Galaxy server processes appear to be dying off over time. Our production Galaxy instance implements apache web scaling features so I have a number of server processes, for example my apache Apache configuration has: BalancerMember http://127.0.0.1:8080 BalancerMember http://127.0.0.1:8081 BalancerMember http://127.0.0.1:8082 BalancerMember http://127.0.0.1:8083 BalancerMember http://127.0.0.1:8084 BalancerMember http://127.0.0.1:8085 Nothing unconventional as I understand it. Similarly, my galaxy config has matching [server:ws3], [server:ws2] configuration blocks for each of these processes. When I restart Galaxy, everything is all fine and good. I'll see a server listening on each one of these ports (if I do something like lsof -i TCP -P, for example). What appears to be happening, is that for whatever reason, these server processes seem to die off over time (i.e eventually nothing is listening on ports 8080-8085). This process can take days, and at the time when no servers are available, Apache will begin throwing 503 service unavailable errors. I am fairly confident this process is gradual, for example I just checked now and the Galaxy was still available, however one server had died (the one on TCP port 8082). I do do have a single separate job manager and two job handlers; at this point I believe this problem to be related to the servers only (i.e. the job manager and job handlers do not app! ear to be crashing). Now, I believe that late last week I might have 'caught' the last server process dying, just by coincidence, although I am not 100% certain. Here is the Traceback as it occurred: galaxy.jobs.runners.pbs DEBUG 2013-07-02 08:47:12,011 (6822/39485.sc01) PBS job state changed from Q to R galaxy.jobs.runners.pbs DEBUG 2013-07-02 08:54:36,565 (6822/39485.sc01) PBS job state changed from R to C galaxy.jobs.runners.pbs DEBUG 2013-07-02 08:54:36,566 (6822/39485.sc01) PBS job has completed successfully galaxy.jobs DEBUG 2013-07-02 08:54:36,685 Tool did not define exit code or stdio handling; checking stderr for success galaxy.datatypes.metadata DEBUG 2013-07-02 08:54:36,812 loading metadata from file for: HistoryDatasetAssociation 6046 galaxy.jobs DEBUG 2013-07-02 08:54:38,153 job 6822 ended galaxy.jobs.runners.pbs DEBUG 2013-07-02 08:54:49,130 (6812/39473.sc01) PBS job state changed from R to E galaxy.jobs.runners.pbs DEBUG 2013-07-02 08:54:52,267 (6812/39473.sc01) PBS job state changed from E to C galaxy.jobs.runners.pbs ERROR 2013-07-02 08:54:52,267 (6812/39473.sc01) PBS job failed: Unknown error: -11 galaxy.jobs.runners ERROR 2013-07-02 08:54:52,267 (unknown) Unhandled exception calling fail_job Traceback (most recent call last): File /group/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 58, in run_next method(arg) File /group/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py, line 560, in fail_job if pbs_job_state.stop_job: AttributeError: 'AsynchronousJobState' object has no attribute 'stop_job' Now, I have some questions regarding this issue; 1) It
[galaxy-dev] Tool availability
Hi, Are any of the following tools available in galaxy? 1) IDRhttp://www.uwencode.org/software/hotspot 2) Hotspot https://sites.google.com/site/anshulkundaje/projects/idr 3) Wiggler https://code.google.com/p/align2rawsignal/ 4) PhantomPeakQualTools Regards, Vijayalakshmi. ___ 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] Help with Send output to Galaxy function
Hi Huayan, Your external website should accept a parameter GALAXY_URL and use this value as e.g. the content of the form action=xxx attribute (use a sensible default when not starting at Galaxy and this value is not provided). Your webpage should post back to GALAXY_URL with a parameter named URL which contains the url from which Galaxy will fetch the incoming data (e.g. similar to 'wget URL'). You'll also need to define a new datasource tool xml for your resource, see GALAXY_ROOT/tools/data_source for a large number of examples. See http://wiki.galaxyproject.org/Admin/Internals/Data%20Sources for more information. Thanks for using Galaxy, Dan On Jul 10, 2013, at 2:24 AM, Huayan Gao wrote: Hi, I am trying to connect my local database/webpages to my local galaxy server. But I have a hard to implement send output to galaxy function. Right now I have a sending page to send a form to galaxy and it looks like everything goes well. From the variable json_params(data_source.py), I can see that all parameters have been received by galaxy. But the problem is that how I get my parameters from my getfile.php file(This is used in the Galaxy_URL too, the callback function)? I tried to print out $_POST, $_GET, $_REQUEST, nothing shows up. I did see some output from $_Server. I am using php. Please help! Best, Huayan ___ 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/
[galaxy-dev] problem with python output
Hi,
I am trying to integrate a tool into galaxy. The tool runs in two parts -
1) Computes correlation and provides an ouput 'txt' file (Java) 2)
Takes the previously ouput txt file and outputs a 'pdf' file. (Python)
I am having trouble with the second tool. If I provide a sample 'txt' file
as input, it's working fine. But if I run it in galaxy, it is not working
(for some reason it is not reading the 'txt' file from the previous
output). Below is the code.
#!/usr/bin/python
import sys, os
import numpy as np
import matplotlib.pyplot as plt
input_file = sys.argv[1]
output_file = sys.argv[2]
print 'Number of arguments:', len(sys.argv), 'arguments.'
print 'Argument List:', str(sys.argv)
txt_in = input_file + '.txt'
mydata = np.loadtxt(txt_in)
plt.figure(1)
plt.plot(mydata[:,0],mydata[:,1],label = Feature);
plt.plot(mydata[:,0],mydata[:,2], label = Variance);
plt.xlabel('Distance from feature(bp)');
plt.ylabel('Score');
plt.title(sys.argv[1]);
plt.legend(loc=best)
pdf_out = output_file + '.pdf'
plt.savefig(pdf_out)
data = file(pdf_out, 'rb').read()
fp = open(output_file, 'wb')
fp.write(data)
fp.close()
os.remove(txt_in)
os.remove(pdf_out)
Below is the xml code.
tool id=archtex_massdata_extraction name=Extract mass data
description for the given BAM file /description
command java -jar Extraction.jar
$input_bam_file $ref_filename $ref_filetype $output1
/command
command interpreter=python plot.py $output1$out_file1
/command
inputs
param name=input_bam_file type=data format=BAM label=Input BAM
file help=Choose an input BAM file/
param name=ref_filename type=data format=gen,txt,gtf,bed
label=Reference/Coordination
file help=Choose a reference file/
param name=ref_filetype type=select label=Choose the reference file
type
option value=customCustom/option
option value=refgenerefGene/option
option value=GFFGFF/option
option value=bedBED/option
/param
/inputs
outputs
data name=output1 format=txt /
data name=out_file1 format=pdf /
/outputs
/tool
I am forcing the input to be 'tx't and the output to be 'pdf' in the python
script. When I run the code, it is not showing any errors but it's not
showing any output either. I am able to download the first output 'txt'
file but there is no download button option in the right pane of galaxy for
the second part.
Any help is appreciated!
Thanks,
VJ.
___
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] problem with python output
On Wed, Jul 10, 2013 at 8:03 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi VJ, you only can have one command tag in a tool, afaik. You can try to write it with cheetah and concatenate several shell commands with or you can extend your python script to call your java tool at first step. Cheers, Bjoern Also this part will break - Galaxy is telling you the filename, if you add .txt to it then it no longer points to a file on disk: input_file = sys.argv[1] ... txt_in = input_file + '.txt' Likewise Galaxy has told you which output filename to use, if you add .pdf to it Galaxy won't find it: output_file = sys.argv[2] .. pdf_out = output_file + '.pdf' The tool should just use the filenames Galaxy tells it (and they will end in .dat regardless of the datatype). 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] problem with python output
Apologies if my previous suggestion confused you :
http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp4660463p4660464.html
You may first generate the pdf :
input_file = sys.argv[1]
output_file = sys.argv[2]
#txt_in = options.exp_data # + '.txt' ## NOT REQUIRED
mydata = np.loadtxt(input_file)
plt.figure(1)
plt.plot(mydata[:,0],mydata[:,1],label = Feature);
plt.plot(mydata[:,0],mydata[:,2], label = Variance);
plt.xlabel('Distance from feature(bp)');
plt.ylabel('Score');
plt.title(sys.argv[1]);
plt.legend(loc=best)
pdf_out = output_file + '.pdf'
plt.savefig(pdf_out)
## Write back to the output file
## You can do a shutil.move too [http://docs.python.org/2/library/shutil.html]
## like this : shutil.move(pdf_out,output_file)
data = file(output_file, 'rb').read()
fp = open(output_file, 'wb')
fp.write(data)
fp.close()
I tried it locally and it worked. But this is under the assumptio that
I am passing your python code the input-file from the Galaxy interface
itself . I just created a CSV and ran the tool. The CSV was simple
enough :
0 1 2
2 3 6
Saket
On 11 July 2013 00:19, vijayalakshmi v...@buffalo.edu wrote:
Hi,
I am trying to integrate a tool into galaxy. The tool runs in two parts -
1) Computes correlation and provides an ouput 'txt' file (Java) 2)
Takes the previously ouput txt file and outputs a 'pdf' file. (Python)
I am having trouble with the second tool. If I provide a sample 'txt' file
as input, it's working fine. But if I run it in galaxy, it is not working
(for some reason it is not reading the 'txt' file from the previous output).
Below is the code.
#!/usr/bin/python
import sys, os
import numpy as np
import matplotlib.pyplot as plt
input_file = sys.argv[1]
output_file = sys.argv[2]
print 'Number of arguments:', len(sys.argv), 'arguments.'
print 'Argument List:', str(sys.argv)
txt_in = input_file + '.txt'
mydata = np.loadtxt(txt_in)
plt.figure(1)
plt.plot(mydata[:,0],mydata[:,1],label = Feature);
plt.plot(mydata[:,0],mydata[:,2], label = Variance);
plt.xlabel('Distance from feature(bp)');
plt.ylabel('Score');
plt.title(sys.argv[1]);
plt.legend(loc=best)
pdf_out = output_file + '.pdf'
plt.savefig(pdf_out)
data = file(pdf_out, 'rb').read()
fp = open(output_file, 'wb')
fp.write(data)
fp.close()
os.remove(txt_in)
os.remove(pdf_out)
Below is the xml code.
tool id=archtex_massdata_extraction name=Extract mass data
description for the given BAM file /description
command java -jar Extraction.jar
$input_bam_file $ref_filename $ref_filetype $output1
/command
command interpreter=python plot.py $output1$out_file1
/command
inputs
param name=input_bam_file type=data format=BAM label=Input BAM file
help=Choose an input BAM file/
param name=ref_filename type=data format=gen,txt,gtf,bed
label=Reference/Coordination file help=Choose a reference file/
param name=ref_filetype type=select label=Choose the reference file
type
option value=customCustom/option
option value=refgenerefGene/option
option value=GFFGFF/option
option value=bedBED/option
/param
/inputs
outputs
data name=output1 format=txt /
data name=out_file1 format=pdf /
/outputs
/tool
I am forcing the input to be 'tx't and the output to be 'pdf' in the python
script. When I run the code, it is not showing any errors but it's not
showing any output either. I am able to download the first output 'txt' file
but there is no download button option in the right pane of galaxy for the
second part.
Any help is appreciated!
Thanks,
VJ.
___
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] problem with python output
On 11 July 2013 04:31, Saket Choudhary sake...@gmail.com wrote:
Apologies if my previous suggestion confused you :
http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp4660463p4660464.html
You may first generate the pdf :
input_file = sys.argv[1]
output_file = sys.argv[2]
#txt_in = options.exp_data # + '.txt' ## NOT REQUIRED
mydata = np.loadtxt(input_file)
plt.figure(1)
plt.plot(mydata[:,0],mydata[:,1],label = Feature);
plt.plot(mydata[:,0],mydata[:,2], label = Variance);
plt.xlabel('Distance from feature(bp)');
plt.ylabel('Score');
plt.title(sys.argv[1]);
plt.legend(loc=best)
pdf_out = output_file + '.pdf'
plt.savefig(pdf_out)
## Write back to the output file
## You can do a shutil.move too [http://docs.python.org/2/library/shutil.html]
## like this : shutil.move(pdf_out,output_file)
data = file(output_file, 'rb').read()
Sorry the above line should be
data = file(pdf_file, 'rb').read()
fp = open(output_file, 'wb')
fp.write(data)
fp.close()
I tried it locally and it worked. But this is under the assumptio that
I am passing your python code the input-file from the Galaxy interface
itself . I just created a CSV and ran the tool. The CSV was simple
enough :
0 1 2
2 3 6
Saket
On 11 July 2013 00:19, vijayalakshmi v...@buffalo.edu wrote:
Hi,
I am trying to integrate a tool into galaxy. The tool runs in two parts -
1) Computes correlation and provides an ouput 'txt' file (Java) 2)
Takes the previously ouput txt file and outputs a 'pdf' file. (Python)
I am having trouble with the second tool. If I provide a sample 'txt' file
as input, it's working fine. But if I run it in galaxy, it is not working
(for some reason it is not reading the 'txt' file from the previous output).
Below is the code.
#!/usr/bin/python
import sys, os
import numpy as np
import matplotlib.pyplot as plt
input_file = sys.argv[1]
output_file = sys.argv[2]
print 'Number of arguments:', len(sys.argv), 'arguments.'
print 'Argument List:', str(sys.argv)
txt_in = input_file + '.txt'
mydata = np.loadtxt(txt_in)
plt.figure(1)
plt.plot(mydata[:,0],mydata[:,1],label = Feature);
plt.plot(mydata[:,0],mydata[:,2], label = Variance);
plt.xlabel('Distance from feature(bp)');
plt.ylabel('Score');
plt.title(sys.argv[1]);
plt.legend(loc=best)
pdf_out = output_file + '.pdf'
plt.savefig(pdf_out)
data = file(pdf_out, 'rb').read()
fp = open(output_file, 'wb')
fp.write(data)
fp.close()
os.remove(txt_in)
os.remove(pdf_out)
Below is the xml code.
tool id=archtex_massdata_extraction name=Extract mass data
description for the given BAM file /description
command java -jar Extraction.jar
$input_bam_file $ref_filename $ref_filetype $output1
/command
command interpreter=python plot.py $output1$out_file1
/command
inputs
param name=input_bam_file type=data format=BAM label=Input BAM file
help=Choose an input BAM file/
param name=ref_filename type=data format=gen,txt,gtf,bed
label=Reference/Coordination file help=Choose a reference file/
param name=ref_filetype type=select label=Choose the reference file
type
option value=customCustom/option
option value=refgenerefGene/option
option value=GFFGFF/option
option value=bedBED/option
/param
/inputs
outputs
data name=output1 format=txt /
data name=out_file1 format=pdf /
/outputs
/tool
I am forcing the input to be 'tx't and the output to be 'pdf' in the python
script. When I run the code, it is not showing any errors but it's not
showing any output either. I am able to download the first output 'txt' file
but there is no download button option in the right pane of galaxy for the
second part.
Any help is appreciated!
Thanks,
VJ.
___
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/
