galaxy-user November 2010

galaxy-user@lists.galaxyproject.org

50 participants
51 discussions

EC2 User data format
by Rob Syme 16 Nov '10

16 Nov '10

Hi, The wiki is unclear on how the user-data should be formatted when configuring the AMI. >From here <http://bitbucket.org/galaxy/galaxy-central/wiki/cloud> "The user data must follow the following format: cluster_name: <DESIRED CLUSTER NAME> password: <DESIRED Galaxy CloudMan WEB UI PASSWORD> access_key: <YOUR AWS ACCESS KEY> secret_key: <YOUR AWS SECRET KEY>" and then here<http://bitbucket.org/galaxy/galaxy-central/wiki/Cloud/GettingStarted> "User data must follow the following format '<CLUSTER_NAME>|<AWS_ACCESS_KEY>|<AWS_SECRET_KEY>|<Desired Galaxy Cloud Password>' (e.g., galaxy_cloud_cluster|NUEINXSAXCA|NCEW/2OJCCCXLDS|SomePwd)." It's the top format that is correct, isn't it? -r Rob Syme PhD Student ACNFP Curtin University, Western Australia

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Incorporation of Stampy in Galaxy?
by Murilo Sena 15 Nov '10

15 Nov '10

Hi Galaxy Team, do you have any prevision of incorporating this new Illumina short reads mapper called Stampy ( Genome Res. <javascript:AL_get(this, 'jour', 'Genome Res.');> 2010 Oct 27 Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads.) in Galaxy? Has any galaxy user tried this new program? Thanks, Murilo -- Murilo Sena PhD Student Laboratory of Gene Expression in Eukaryotes Departamento de Bioquímica Instituto de Química Universidade de São Paulo Av. Prof. Lineu Prestes 748 sala 1200 05508-000 São Paulo, SP Brasil

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problem with CAPRET Com&Uni function
by Lei, Haiyan (NIH/NIDDK) [F] 15 Nov '10

15 Nov '10

Hi, Does anyone have problem with CAPRET Com&Uni function recently? I submit the jobs, but the status is always "running"? The website problem? Thanks. ------ Haiyan Lei, Ph.D. LMB,NIH/NIDDK Bld 5, Rm b1-04 Bethesda MD 20892 301-594-9864

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SNP_ANNOTATION
by Lakatos, Anita 12 Nov '10

12 Nov '10

Polymorphic variations were retrieved from a sequenced data (aligned to hg18). The output file contains the chr and the position but no (rs number). The tab delimited file with map extension is Chr pos # pos 1 82496 0 82496 1 91549 0 91549 1 98173 0 98173 1 696970 0 696970 Could you please let me know if there is way with galaxy to retrieve the rs number for these SNPs? I am open to any solution! Many thanks for your help, Anita Lakatos ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Re: [galaxy-user] plugging R into galaxy
by Freddy 12 Nov '10

12 Nov '10

The out.data is simply picked up by galaxy: As long as you define your variable capturing the output and also in your tool.xml file. Make sure the output is defined as "data" in the tool.xml file. Initially I thought the same thing, but the piping is not needed with '>', worse, it doesn't work like that. Freddy

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Re: [galaxy-user] Unable to import dataset from history into data library
by Greg Von Kuster 12 Nov '10

12 Nov '10

Gerrit, Renaud and others, We apologize for the inconvenience - it seems that you have uncovered a bug that has been corrected in our development repo, but has not yet made it to our distribution repo. This fix should reach the distribution repo some time next week. Thanks very much for reporting this! On Nov 11, 2010, at 9:34 AM, gerrit wrote: > Hi Greg, > > I did a test and got galaxy as you said: > hg clone http://bitbucket.org/galaxy/galaxy-dist > Installed and same error message was given. > > Then I tried the galaxy-central clone: > hg clone http://bitbucket.org/galaxy/galaxy-central > Installed and now the datasets from the history can be loaded into the data library! > > I've also installed the galaxy-dist on a few pcs at our lab and the same error remains! I do not want to switch to the galaxy-central fork because of the active development that can introduce bugs. There is quite a few researchers using our galaxy server so we need a stable version. > > The galaxy that you're running on http://main.g2.bx.psu.edu/ is a copy of the galaxy-dist, if I'm correct. I would like to reproduce the error, but cannot import any history datasets into a data library folder (do not have permissions). For a test is it possible that you can create a temporary data library for me. You can remove it as soon as I'm done. My user account is gerrit.botha(a)gmail.com. > > Thanks for the help, > Gerrit > > On Wed, Nov 10, 2010 at 4:46 PM, gerrit <gerrit.botha(a)gmail.com> wrote: > Hi Greg, > > It is a long time since I've read the documentation on your site, but since I've started with galaxy I checked it out like this: > > hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist > > > > > The strange thing is then when I run "hg heads" it shows the exact version which you have. > ----------------------- > changeset: 4354:d681ef7538ed > tag: tip > user: Greg Von Kuster <greg(a)bx.psu.edu> > date: Wed Sep 29 12:39:39 2010 -0400 > summary: Fix for rendering hidden widget field values associated with library templates whose fields are displayed on the upload form when importing a dataset from the current history. Added new functional test to cover behavior. > ----------------------- > > I will test a checkout with the other update site. > > Thanks, > Gerrit > > > On Wed, Nov 10, 2010 at 4:22 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello, > > I am not able to reproduce this problem, and in fact, the message being displayed looks like it comes from very old code ( this particular message "Invalid item id..." is no longer in the most recent version of the code. From where are you getting your updates? You should be getting them from here: > > hg clone https://<your account>@bitbucket.org/galaxy/galaxy-dist > > To make sure you are running the latest distribution, go to your Galaxy root directory and type: > > hg heads > > and you should see > > 4354 d681ef7538ed > > > On Nov 10, 2010, at 8:08 AM, gerrit wrote: > >> Dear Galaxy Users, >> >> Since I've updated my Galaxy version I'm unable to import any dataset from my history into my data library. It returns a message of e.g. "Invalid item id (1464) specified". >> >> I then did a complete new test installation to make sure that this problem wasn't because of the update. But the error still remains. I've included a screen shot in which the error is reported. >> >> When I queried the database the dataset id does exist in the history_dataset_association table. >> >> I went through the paster.log file and found the following warning message: Unknown library item type: <class 'galaxy.model. >> HistoryDatasetAssociation'>. Can it be that this class is not loaded or found? >> >> Is anyone experiencing the same problem? >> >> Thanks, >> <import_history_dataset_error.jpg>_______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user > > Greg Von Kuster > Galaxy Development Team > greg(a)bx.psu.edu > > > > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Re: [galaxy-user] Unable to import dataset from history into data library
by Renaud Gaujoux 11 Nov '10

11 Nov '10

Hi, I also get the same error. To reproduce: 1. install a fresh Galaxy from the repository (via: hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist). 2. run the setup.sh script 3. create a user 'test' 4. stop galaxy, make user 'test' admin in universe_wsgi.ini, restart galaxy 5. create a new data library 'Lib' 6. give the user all permission on this data library 7. upload some fasta file 'seq.fas' via: Get Data > Upload File 8. go to Shared Data > Data Libraries > 'Lib' - Add datasets 9. use upload option: import datasets from current history 10. select file 'seq.fas', and hit 'import to library' => Invalid item id (2) specified. The direct import 'Upload files' in 'Upload files to a data library' view works fine. Any help or bug fix is welcome. Thank you. Bests, Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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plugging R into galaxy
by Anthony Ferrari 10 Nov '10

10 Nov '10

Dear galaxy users, My team is involved in the NGS field. We have our own local cluster and we are looking for a workflow management system. Currently we are trying to set up and test galaxy. For our quality control analysis pipeline, R statistical software will be used. So we want to be able to call R scripts from galaxy. I know that it is possible and the xy_plot.xml is a really good example (conditional & when, repeat tags). Also, in this example a <configfile> tag is used. Within this tag you put your R code. And moreover you can add lines beginning with only one '#' which will be interpreted with *cheetah template engine*. This is helpful to create dynamic content of your R code with respect to your submitted parameters. (an old screencast introduces this example) My question is : is there a way to avoid the <configfile> section and to let all the R code be outside the tool's xml config file? If yes, how can we specify an output file in the xml conf that will catch, for instance, a write.table() call in the R script ? Best regards, Anthony

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Unable to import dataset from history into data library
by gerrit 10 Nov '10

10 Nov '10

Dear Galaxy Users, Since I've updated my Galaxy version I'm unable to import any dataset from my history into my data library. It returns a message of e.g. "Invalid item id (1464) specified". I then did a complete new test installation to make sure that this problem wasn't because of the update. But the error still remains. I've included a screen shot in which the error is reported. When I queried the database the dataset id does exist in the history_dataset_association table. I went through the paster.log file and found the following warning message: Unknown library item type: <class 'galaxy.model. HistoryDatasetAssociation'>. Can it be that this class is not loaded or found? Is anyone experiencing the same problem? Thanks,

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Re: [galaxy-user] galaxy-user Digest, Vol 53, Issue 6
by Freddy 10 Nov '10

10 Nov '10

Hi Anthony, You can avoid working with wrappers to run 3 scripts (your R-script, a perl or shell wrapper and the necessary xml file) to make 1 actually run what you want to do. I've struggled with this in the previous digests, which are not so accessible to search-find. simply put in your tool.xml file: <command> R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/<your Rscript.R> --args $inputFile $<any nr of input args> $outputFile </command> This way you can run any R script in galaxy. Unfortunately, (also in one of the previous digests), "warnings" in R are causing an error status, so that once in a while you will need to add to the end of the cmd line in the above: 2>&- to ignore these warnings (but also any error message) My advice is to build and test in shell and galaxy without it and later add it to get to your output file(s). So far this has worked for me. Freddy de Bree Bioinformatics CVI, Lelystad The Netherlands > Date: Tue, 9 Nov 2010 15:20:52 +0100 > From: Anthony Ferrari<ferraria(a)gmail.com> > To: galaxy-user(a)lists.bx.psu.edu > Subject: [galaxy-user] plugging R into galaxy > Message-ID: > <AANLkTikNp+d9E2068H=pXd8_VH1a8cZF+rQ3zTM9rAQD(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear galaxy users, > > My team is involved in the NGS field. We have our own local cluster and we > are looking for a workflow management system. Currently we are trying to set > up and test galaxy. > > For our quality control analysis pipeline, R statistical software will be > used. So we want to be able to call R scripts from galaxy. > > I know that it is possible and the xy_plot.xml is a really good example > (conditional& when, repeat tags). Also, in this example a<configfile> tag > is used. Within this tag you put your R code. And moreover you can add lines > beginning with only one '#' which will be interpreted with *cheetah template > engine*. This is helpful to create dynamic content of your R code with > respect to your submitted parameters. (an old screencast introduces this > example) > > My question is : is there a way to avoid the<configfile> section and to let > all the R code be outside the tool's xml config file? If yes, how can we > specify an output file in the xml conf that will catch, for instance, a > write.table() call in the R script ? > > Best regards, > > Anthony

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galaxy-user November 2010