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fastq and index file upload problems
by Shawn Starkenburg 28 Jan '11

28 Jan '11

I'm trying to create a RNA-Seq Workflow with Bowtie/Tophat and Cufflinks using a newly assembled genome (not public). I created the genome index files via Bowtie locally but Galaxy will not accept the .ebwt index files (n=4)--"Inappropriate content" error. Second, for some reason, the Illumina fastq files will not load on the web version or my local version either. (FYI, I successfully ran these same files through our local command line version of Tophat and Cufflinks without problems) Please advise. Thanks, Shawn

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How insert gene IDs?
by Asuncion Lago 25 Jan '11

25 Jan '11

Hi, I have used the RNAseq tools to calculate the FPKMs values, now I would like to know how I can link this values with the gene name or the Flybase ID in my particular case. I have been trying in different ways without success. Could you help me, please? A El 17/12/10 16:57, "galaxy-user-bounces(a)lists.bx.psu.edu" <galaxy-user-bounces(a)lists.bx.psu.edu> escribió: > Your mail to 'galaxy-user' with the subject > > Upload problem > > Is being held until the list moderator can review it for approval. > > The reason it is being held: > > Post by non-member to a members-only list > > Either the message will get posted to the list, or you will receive > notification of the moderator's decision. If you would like to cancel > this posting, please visit the following URL: > > > http://lists.bx.psu.edu/confirm/galaxy-user/6682d97aabcbfc0d3b720c1e020e8c6… > 76e27d > ------ Fin del mensaje reenviado

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Unsubscribe
by Ralf JAUCH 24 Jan '11

24 Jan '11

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Fw: NGS RNA-seq
by vasu punj 24 Jan '11

24 Jan '11

Thanks Jeremy, The issue mentioned by Slim is also related to the same issue as of Matteo. In the end out put files either dont have geneIDS or has multiple enteries of particular gene. Any suggestion? --- On Mon, 1/24/11, Slim Sassi <ssassi(a)CCIB.MGH.HARVARD.EDU> wrote: From: Slim Sassi <ssassi(a)CCIB.MGH.HARVARD.EDU> Subject: [galaxy-user] NGS RNA-seq To: galaxy-user(a)bx.psu.edu Date: Monday, January 24, 2011, 7:47 AM Hello, I have followed the steps described by Jeremy in his exercise (http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise) to analyze RNA-seq data and all of the steps seemed to go ok except that at the end the gene IDs were missing, so for example the file CDS diff file had nothing in it. All the steps seemed to be executed correctly with proper mapping to various places in the mouse genome. Please help Thanks Slim Slim O. Sassi, PhD Research Fellow Center for Computational and Integrative Biology, Massachusetts General Hospital Department of Genetics, Harvard Medical School 185 Cambridge Street CCIB- CPZN 7-7228 Simches Research Center Boston MA 02114 Phone: (617) 726-5971 Fax: (617) 643-3328 ssassi(a)ccib.mgh.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

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Re: [galaxy-user] "interval" attribute for Input?
by Sonali Amonkar 24 Jan '11

24 Jan '11

Hi, What I am trying is, A) to write an exec_after_process for tool1(Scatterer tool). This tool1 gives multiple outputs(in the form of files names generated by Galaxy). ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ scatterer_postprocess.py def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): print "Collected Dataset[Primary] is %s"% param_dict.get('__collected_datasets__')['primary']['output1']; Output: Collected Dataset[Primary] is {'output2': <galaxy.model.HistoryDatasetAssociation object at 0xb0648ac>, 'output3': <galaxy.model.HistoryDatasetAssociation object at 0xb15170c>, 'output4': <galaxy.model.HistoryDatasetAssociation object at 0xaf499ac>} ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ I could see these values successfully. Next, B) I wanted to view these multiple values in the exec_prejob hook of tool2(Gatherer) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ gatherer_prejob.py def exec_before_job(inp_data, out_data, param_dict, tool): print "******************* collected dataset is %s"% param_dict.get('__collected_datasets__')['primary']['output1']; Output: TypeError: Error in 'Gather' hook 'exec_before_job', original message: exec_before_job() got multiple values for keyword argument 'inp_data' ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ I am not very savy with Python for now. Can someone point me out to any possible resolution to this issue. The reason I am writing these hooks is to read the multiple inputs in tool2 thrown out by tool1. Thank you for your time. Regards, Sonali Amonkar From: Sonali Amonkar Sent: Friday, January 21, 2011 8:16 PM To: 'galaxy-dev(a)lists.bx.psu.edu' Subject: "interval" attribute for Input? Hi, Currently I am building a workflow which splits a file into multiple chunks and then recreates it back into one. Following the document on https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput, I wrote the following code. The following is my Splitter tool: <tool id="sc" name="sc" version = "1.0.0" force_history_refresh="True"> <description> My tool 1 </description> <requirements/> <command>java -cp /Splitter1.jar /Common.jar SplitterModule $input $output1 $output1.id $__new_file_path__</command> <inputs> <param format="txt" name="input" type="data" label="reads"> <label>Reads</label> </param> </inputs> <outputs> <data format="interval" name="output1" metadata_source="input"/> </outputs> <help> </help> </tool> The following is my Integrator tool: <tool id="gt" name="gt" version = "1.0.0"> <description> My Tool 2 </description> <requirements/> <command> java -cp Integrator1.jar:Common.jar IntegratorModule $input $output </command> <inputs> <param format="interval" name="input" type="data" label="pp"> <label>File Name</label> </param> </inputs> <outputs> <data format="text" name="output"/> </outputs> <help> This tool reads the reads.pp.txt file and creates smaller sized batches of it. </help> </tool> When I try to connect and run the workflow, this is what happens: 1. The files with the names generated from the parameters are created in the tmp folder temporarily 2. Then these are removed and converted to .dat files and placed in database/files/000 folder with the galaxy generated numbers file names.(eg. dataset_89.dat) 3. However, when I check the parameters in the IntegratorModule program, I receive new dataset files generated by Galaxy and NOT the ones which were created and should have been passed from the Splitter module Is there a format I need to follow when writing the Integrator Module's input parameters? Any pointer to any document which mentions this will be helpful. Thank you for your time. Warm Regards, Sonali Amonkar From: Sonali Amonkar Sent: Tuesday, January 18, 2011 3:23 PM To: galaxy-user(a)lists.bx.psu.edu Subject: "interval" attribute for Input? Hi, Currently I am building a workflow which splits a file, say File 1 into chunks of files say File1.0, File1.1, File1.2. I used the interval attribute to have multiple outputs and got the chunks created successfully. <data format="interval" name="output" metadata_source="input"/> However, now I want to connect another tool to this, which Reads multiple inputs(interval). I could not find any documentation for Input interval type. Is this supported? If yes then where can I find the syntax? Warm Regards, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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NGS RNA-seq
by Slim Sassi 24 Jan '11

24 Jan '11

Hello, I have followed the steps described by Jeremy in his exercise (http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise) to analyze RNA-seq data and all of the steps seemed to go ok except that at the end the gene IDs were missing, so for example the file CDS diff file had nothing in it. All the steps seemed to be executed correctly with proper mapping to various places in the mouse genome. Please help Thanks Slim Slim O. Sassi, PhD Research Fellow Center for Computational and Integrative Biology, Massachusetts General Hospital Department of Genetics, Harvard Medical School 185 Cambridge Street CCIB- CPZN 7-7228 Simches Research Center Boston MA 02114 Phone: (617) 726-5971 Fax: (617) 643-3328 ssassi(a)ccib.mgh.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Run tools/Workflow from command line
by Sonali Amonkar 24 Jan '11

24 Jan '11

Hi, 1. Does Galaxy provide command line execution of Workflows / tools? 2. Does Galaxy provide API of its own, which can be imported as a library in another program and used for executing certain workflows? Thanks for your time. Regards, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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An update to Galaxy CloudMan
by Enis Afgan 24 Jan '11

24 Jan '11

We'd like to announce an update to Galaxy CloudMan - a completely standalone version Galaxy on Amazon's cloud. The new version has been released that brings a number of improvements to the core functionality of CloudMan and expands the number of tools available within Galaxy CloudMan to match that of Galaxy Main. The new AMI ID is: ami-9a7485f3; complete instructions on how to use Galaxy CloudMan are available at usegalaxy.org/cloud. Some of the specific improvements now available include the following: - number of Galaxy tools available on the cloud mirrors that of Galaxy Main - the size of tool index files has grown from 40GB to 600GB - autoscale the size of your cluster (i.e., the size of your cloud cluster automatically adjusts to the amount of your workload) - termination of instances happens in parallel - automated update of CloudMan source code - ability to terminate and/or delete a cluster directly from the CloudMan web interface - tagging of cloud resources with cluster name - overall greater reliability and several bugs fixed - still built on top of the CloudBioLinux AMI so all of the NERC BioLinux tools are available at command line and also allowing CloudMan UI to extend usage scenarios for BioLinux tools in terms of cluster composition (full code changes available at https://bitbucket.org/galaxy/cloudman/changesets)

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file upload
by Thomas, Huw [hbt] 21 Jan '11

21 Jan '11

I have recently been attempting to upload some large data files to the galaxy portal but have had varying success. The file size range from around 1GB to around 3.5GB. On previous attempts the files of around 1GB have successfully uploaded in a matter of minutes (approx 40 mins), but I have been unable to successfully upload the largest file of 3 GB despite leaving the file in the "uploading" stage for more than 2 days, and re-attempting several times. Could you please tell me whether there is anything I can do to remedy this and in particular how long you would expect a file of around 1-3GB should take to upload to your server. Regards Huw Thomas (University of Liverpool)

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SNPs identity
by Elena Shumay 21 Jan '11

21 Jan '11

hi, is there a quick way to add an allele directionality (i.e., C->T) to the SNPs in a given region? thank you! best regards, elena

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