galaxy-dev February 2012

galaxy-dev@lists.galaxyproject.org

96 participants
162 discussions

corrupted binary file
by Yingwei HU 26 Feb '12

26 Feb '12

Dear all, I found one of my binary files was corrupted after its uploading through "Get data'. I used editplus to check its hex code and found some "0D" is changed to "0A" and also one byte is lost. May I ask how to solve this problem? Thank you for your help. Best Regards, HU Yingwei

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different number output files generated based on user parameter
by Victor Ruotti 25 Feb '12

25 Feb '12

Thank you Shaun. That worked really good! One final question. What is the best way to generate output files dynamically by galaxy. That is if the user sets a parameter, say create bam file. Then the output file gets generated. If the same parameter is false or no, then galaxy does not generate this file. We tried using the when tags and the conditional tags inside the output tags with no luck. Thanks again and looking forward to your response. Victor On Feb 24, 2012, at 4:16 AM, SHAUN WEBB wrote: > > > > Hi Victor, > > this is how I have implemented this: > > <param name="sample" type="text" format="txt" label="Sample label" /> > > <data format="tabular" name="filename" label="${sample}.genes-results" /> > > Shaun > > > > > Quoting VICTOR M RUOTTI wisc-mail <ruotti(a)wisc.edu> on Thu, 23 Feb 2012 13:06:23 -0600: > >> Hi Peter,Thanks for the quick feedback. >> Sorry if I wasn't clear. >> Yes, I asking on how to set the labels for a file so instead of >> <data format="tabular" name="filename" label="genes-results"/> >> we can have a variable that comes from the interface set by the user so it can be like this? >> Say the user set the name from a text box to be "S" >> We can have S saved as $prefix, something like below. >> <data format="tabular" name="$prefix.filename" label="$prefix.genes-results"/> >> >> >> The files then will be labeled: >> S.genes-results >> They still be called dataset_547.dat but labeled based on the user's input? >> >> >> Victor >> >> >> On 02/23/12, Peter Cock >> wrote: >>> On Thu, Feb 23, 2012 at 5:46 PM, Victor Ruotti <ruotti(a)wisc.edu> wrote: >>> > Hi, >>> > I hope someone can help me on how to implement this into a wrapper. >>> >>> This kind of question is normally redirected to the galaxy-dev list. >>> >>> > We would like to add an option so the user can set a sample name >>> > which then be used for the prefix of the output files names. >>> >>> You have no control over the file names at all - Galaxy will assign >>> something like database/files/000/dataset_547.dat automatically. >>> The user never sees the file names anyway. >>> >>> Are you asking about how to control the description/caption shown >>> to the user in Galaxy? >>> >>> Peter >> >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > >

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cannot startup the local instance of tool shed
by JIE CHEN 24 Feb '12

24 Feb '12

Hello everyone, I'm a new to Galaxy and the tool sheds. Right now i am learning it by reading the tutorial and have a problem: when i try to start my local tool shed by typing the command "%sh run_community.sh" within the galaxy installation directory, nothing happens. It just terminate itself immediately without any error message. It's quite different from when i start up a local galaxy instance. What i did: 1)Modify the community_wsgi.ini so that it has the right connection to my own MySQL server. 2)in cmd prompt, cd to the installation directory 3)in cmd prompt, sh run_community.sh Thanks a lot. Any help is appreciated. Tyler

2 1

Issues importing a shared workflow
by Iry Witham 24 Feb '12

24 Feb '12

I have a Galaxy user who has created a workflow from a history and share it with me. However, when I attempt to view and import the workflow I get the following error: The owner of this workflow has disabled imports via this link. You can return to the previous page<http://galaxy/u/anuj/w/workflow-constructed-from-history-chipseqworkflowwit…> How do I fix this issue? Are there settings that need to be modified on the users side? Thanks Iry Witham Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org

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Re: [galaxy-dev] galaxy-dev Digest, Vol 68, Issue 31
by Hariprasadreddy Kosgi 24 Feb '12

24 Feb '12

unsubsacrb On Thu, Feb 23, 2012 at 12:00 PM, <galaxy-dev-request(a)lists.bx.psu.edu>wrote: > Send galaxy-dev mailing list submissions to > galaxy-dev(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-dev > or, via email, send a message with subject or body 'help' to > galaxy-dev-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-dev-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-dev digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to > the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread > you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: Error 500 when trying to execute a workflow with the API > (Anthonius deBoer) > 2. Re: Error 500 when trying to execute a workflow with the API > (dannonbaker(a)me.com) > 3. Re: Splitting large jobs over multiple nodes/CPUs? (Peter Cock) > 4. Re: Splitting large jobs over multiple nodes/CPUs? > (dannonbaker(a)me.com) > 5. FastX tools (Borrone, James) > 6. snpEff: html report is not displaying after update > (Jennifer Jackson) > 7. R scripts for DESeq (Jennifer Jackson) > 8. limited tool shed browse (David Hoover) > 9. Re: FastX tools (Peter Cock) > 10. Re: limited tool shed browse (Greg Von Kuster) > 11. Re: R scripts for DESeq (Vipin TS) > 12. Re: limited tool shed browse (David Hoover) > 13. Re: limited tool shed browse (Greg Von Kuster) > 14. Re: How to learn about new tools in the official Tool Shed > (Jennifer Jackson) > 15. Re: R scripts for DESeq (Liusong Yang) > 16. Re: R scripts for DESeq (Greg Von Kuster) > 17. Re: uploads stuck in history (Bossers, Alex) > 18. Re: R scripts for DESeq (Christian Cole) > 19. Re: R scripts for DESeq (Vipin TS) > 20. Re: Splitting large jobs over multiple nodes/CPUs? (Peter Cock) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Feb 2012 18:09:40 +0000 (GMT) > From: Anthonius deBoer <thondeboer(a)me.com> > To: Dannon Baker <dannonbaker(a)me.com> > Cc: Galaxy-dev <galaxy-dev(a)lists.bx.psu.edu> > Subject: Re: [galaxy-dev] Error 500 when trying to execute a workflow > with the API > Message-ID: <ddf015a9-c563-e45d-cb06-af4780110d91(a)me.com> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Huh? I have many string inputs to some particular workflow steps...Those > are parameters etc that need to be entered or chosen from a dropdown..How > would we deal with those kinds of entries into a workflow in the API? Or do > all of them have to be pre-set? > > Thanks > > Thon? > > On Feb 21, 2012, at 04:21 PM, Dannon Baker <dannonbaker(a)me.com> wrote: > > > There is no string input. If the string you're looking for is, say, the > name of a dataset what you'd do is make separate calls to the history and > workflow API. > > > > For example, if you had a history "My important history", and a dataset > "My input dataset", and no knowledge of the id's (as you shouldn't' have to > have, externally), it'd be three separate calls. One to list histories, > then you would programmatically grab the one you want ("My important > history") and the ID associated with it. Then you'd make a call to grab the > contents of that history, from which you could extract the id of the > dataset you had the name of. And from there you know how to execute a > workflow with that id (hda, in this case). > > > > -Dannon > > > > > > > > > > On Feb 21, 2012, at 7:13 PM, thondeboer(a)me.com wrote: > > > > > One more question... > > > How do I pass a string value to one of the workflow input steps? > > > Is there an equivalent of ldda and hda, maybe "str".. > > > > > > So 38=str="Some value" > > > > > > Where could I find a list of the expected dataset sources? > > > > > > Thanks > > > > > > Thon > > > > > > On Feb 21, 2012, at 03:46 PM, Dannon Baker <dannonbaker(a)me.com> wrote: > > > > > >> Hi Thon, > > >> > > >> You have the right idea about what's going wrong here. Galaxy is > trying to pull up a library dataset with the ID you specify, but it doesn't > exist. > > >> > > >> In this context, src refers to the 'type' of dataset input id, more > specifically whether it's from a history or library. 'hda' indicates that > the dataset is from a history, and 'ldda' is what you'll most likely use in > the case of a library dataset. If you browse the history and library API > functionality, you'll see other methods for explicitly grabbing these ids. > > >> > > >> My hunch is that you have an id from a history and that you should > swap ldda to hda and give it another shot. Definitely let me know if you > run into more issues, though, and I'll help figure out what's going on. > > >> > > >> -Dannon > > >> > > >> On Feb 21, 2012, at 6:22 PM, thondeboer(a)me.com wrote: > > >> > > >> > Hi, > > >> > > > >> > I tried to run a workflow with the API, but get an Error 500 when I > try to run the WF...The paster.log shows the following error... > > >> > > > >> > $ workflow_execute.py 92cc01ed93dc0f0fc91e3ded35497c0a > http://srp106:8080/api/workflows ebfb8f50c6abde6d 'TEST the API' > '1=ldda=7c5ebce002fc9d5c' > > >> > > > >> > > > >> > Paster.log > > >> > galaxy.web.framework ERROR 2012-02-21 14:36:33,067 Uncaught > exception in exposed API method: > > >> > Traceback (most recent call last): > > >> > File > "/home/tdeboer/code/galaxy-central/lib/galaxy/web/framework/__init__.py", > line 145, in decorator > > >> > return simplejson.dumps( func( self, trans, *args, **kwargs ), > indent=4, sort_keys=True ) > > >> > File > "/home/tdeboer/code/galaxy-central/lib/galaxy/web/api/workflows.py", line > 123, in create > > >> > hda = ldda.to_history_dataset_association(history, > add_to_history=add_to_history) > > >> > AttributeError: 'NoneType' object has no attribute > 'to_history_dataset_association' > > >> > 172.16.108.6 - - [21/Feb/2012:14:36:32 -0700] "POST > /api/workflows?key=92cc01ed93dc0f0fc91e3ded35497c0a HTTP/1.1" 500 - "-" > "Python-urllib/2.6" > > >> > > > >> > > > >> > Any ideas? > > >> > > > >> > Also...I had a hard time finding out what I should use for the > dataset source parameter "src" in "step=src=dataset_id" and just tried > ldda, but would hope there is a little info on what this hda and ldda is? > > >> > > > >> > Thanks, > > >> > > > >> > Thon > > >> > ___________________________________________________________ > > >> > 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/ > > >> > > >> One > > >

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unsubscrb
by Hariprasadreddy Kosgi 24 Feb '12

24 Feb '12

1 0

KeyError: 'datatypes_config'
by Sarah Diehl 24 Feb '12

24 Feb '12

Hi all, I just updated our Galaxy from the latest dist to the latest central release. When I had previously updatet to the dist release, the emboss datatypes were installed as a shed tool. However when restarting the server after the update the datatypes_conf.xml in the emboss shed directory got deleted. After some back and forth I ended up with the following error, which I can't seem to resolve. galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File "/galaxy/galaxy_server/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/galaxy/galaxy_server/lib/galaxy/app.py", line 58, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/galaxy/galaxy_server/lib/galaxy/tool_shed/__init__.py", line 21, in load_proprietary_datatypes datatypes_config = metadata[ 'datatypes_config' ] KeyError: 'datatypes_config' Any help would be greatly appreciated! Thanks! Sarah

2 2

Running galaxy in a cluster as if it was local
by Daniel Sobral 24 Feb '12

24 Feb '12

Hi, We're trying to setup a galaxy server, but where we want some of the tools to run on a cluster. This cluster is supporting mosix so at the moment we cannot use any of the drmaa stuff available (or can we?). The way we're setting it up at the moment is to run the command we want to run on the cluster through a remote mosix run. This works (almost) fine if we do it for specific command line tools (e.g. samtools). But now I've tried to run the whole python wrapper instead of only the command-line tool. In this case the problem we have is that the libraries on the end of the compute node are not set in the environment, since the environment is set only on the machine running the frontend. Is there any way I can set up the PYTHONPATH or other environment variables so that this would work in the compute node? Thanks, Daniel

2 1

Splitting large jobs over multiple nodes/CPUs?
by Peter Cock 23 Feb '12

23 Feb '12

Hi all, The comments on this issue suggest that the Galaxy team is/were working on splitting large jobs over multiple nodes/CPUs: https://bitbucket.org/galaxy/galaxy-central/issue/79/split-large-jobs Is there any relevant page on the wiki I should be aware of? Specifically I am hoping for a general framework where one of the tool inputs can be marked as "embarrassingly parallel" meaning it can be subdivided easily (e.g. multiple sequences in FASTA or FASTQ format, multiple annotations in BED format, multiple lines in tabular format) and the outputs can all be easily combined (e.g. by concatenation in the same order as the input was split). Thanks, Peter

5 22

How to learn about new tools in the official Tool Shed
by Sarah Diehl 22 Feb '12

22 Feb '12

Hello, one quick question: is there a way to get news about new tools in the Tool Shed? I saw that I can subscribe to get news about already existing tools, but how about newly created ones? I would also be fine with some subscription to any changes in the Tool Shed in general. Best regards, Sarah

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galaxy-dev February 2012