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Frames issue with tool shed README links?
by Peter Cock 10 Oct '13

10 Oct '13

Consider the following sequence: 1. Goto http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan 2. The README file explains this is for InterProScan 4, and has a link to http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5 for Bjoern's InterProScan 45 wrapper. 3. Click the link for InterProScan 5. 4. Notice the link opened within the frame, and you now have a nested tool shed menu. 5. Click on the link to InterPro itself, http://www.ebi.ac.uk/interpro/interproscan.html 6. Notice the double nested frame remains, and now the InterPro page is squeezed into the bottom left. ----- This isn't specific to these repositories, e.g. 1. Goto http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go 2. The README file introduction refers to the tool being available on the main tool shed, "It is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go " 3. Click on that link 4. Observe a double nested tool shed interface, with the Test Tool Shed at the top, and the Main Tool Shed nested within. ----- Suggested fix: All links within Tool Shed README files should be modified to open full frame by adding target="_top" to them. Peter

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UCSC Main table browser invalid link
by Gonsky, Rivkah, Ph.D 10 Oct '13

10 Oct '13

Link doesn't work Rivkah Gonsky Inflammatory Bowel and Immunobiology Research Institute Davis 4063 8700 Beverly Blvd Los Angeles, CA 90048 310-423-7624 gonsky(a)cshs.org<mailto:gonsky@cshs.org> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation.

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Dealing with cluster job preemption
by Sytchev, Ilya 10 Oct '13

10 Oct '13

Hi, Our Galaxy instance is configured to use LSF. The problem is that sometimes our jobs get preempted (stopped and re-queued to let higher-priority jobs run) and Galaxy thinks that those jobs have failed. Is there any way around that by any chance? Thanks, Ilya

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FASTQ converter not working
by James Tarver 10 Oct '13

10 Oct '13

So I have used Galaxy to convert >50 different FASTQ files into FASTA with no problems before over the past year. The sequencer and FASTQ file format have been identical, however, yesterday when I tired to use the the FASTQ to FASTA converter I couldn't get it to recognise my files. The drop down 'FASTQ Library to convert:' tab was empty and unable to select the dataset to convert I then switched histories to one where this action had already been done to repeat it and make sure it was nothing odd with the file I uploaded. However, again the tab was empty and I was unable to select the file to convert. Suggestions? JT

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Visualizations broken after Aug. 12 update
by Liisa Koski 10 Oct '13

10 Oct '13

Hello, We recently updated to the Aug.12 distribution. I u commented the visualizations_config_directory = config/visualizations in the universe file and when I restarted and tried to view past Trackster Visualizations none of my tracks load. I get the error displayed in the track itself: Cannot display dataset due to an error. View error. Try again. When I click on View error I get pop up with this for my gff3 track: Input error: Cannot split into blocks. Found interval with fewer than 12 columns. needLargeMem: trying to allocate 0 bytes (limit: 17179869184) With this for my BAM track: grep: /Galaxy/galaxy_dist/database/files/016/dataset_16392.dat: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) All tracks in all published Visualizations are no longer loading. I do not see any errors in the log files. I have also updated my datatypes.conf file by copying over datatypes.conf.sample Any help would be much appreciated. Thanks in advance, Liisa

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unable to import run or save-to-file published workflow after galaxy upgrade
by Jennifer Jackson 09 Oct '13

09 Oct '13

Hi Alan, I do not personally know the solution for this, but am moving it over to the mailing list for local installs so that our dev team or community can help provide some feedback. Thanks! Jen Galaxy team -------- Original Message -------- Subject: [galaxy-user] unable to import run or save-to-file published workflow after galaxy upgrade Date: Tue, 8 Oct 2013 23:44:32 +0000 From: McCulloch, Alan <alan.mcculloch(a)agresearch.co.nz> To: galaxy-user(a)lists.bx.psu.edu <galaxy-user(a)lists.bx.psu.edu> dear all, we've just upgraded our Galaxy server (Galaxy revision 7148:17d57db9a7c0, upgraded to revision 10422:a886bc3ae924 ), and have found that an NGS training workflow that one of us set up and published is no longer accessible - we now get a stack trace when we try to run it (screenshot attached) ; if we try to save to file, we "get page not found" from the browser, but no errors reported in web logs, or Galaxy log as far as we can see Is there any way we can recover the workflow ? How to avoid this happening in future upgrades ? This time it is not a major problem, however we would not want this to happen to production workflows. Should we save-to-file on all workflows as a precaution before an upgrade ? (Would that help ? ) The workflow included steps as below. Grateful for any suggestions. Cheers Alan McC First Part : checking GC content .Upload the sampling.fasta file or get it from the shared data in Galaxy. .Use geecee from EMBOSS .Remove beginning (Text manipulation), first line .Convert as tabular (Text manipulation) or cut (Text manipulation) .Histogram (Graph/Display Data)on col2 .Compute data (Text manipulation) (data4 convert; col2>0.2) .Count data (statistics on col3) If it is worth it we can remove the sequences which have a too low GC content 3 Second part : sequence length .Compute Sequence length (FASTA manipulation) .Summary Statistics (Statistics)on col2 .Filter by length(FASTA manipulation) ; 800 .Line/world/character count(Text manipulation) .Blastn against fungi db : yeast, only one hit to show (advanced options ) .Count the lines to know how many sequences have a hit . (Text manipulation) 4 Bonus track : removing sequences with low GC content .Select (filter and sort) on data 6 where matching = True .FASTA-to-Tabular (FASTA manipulation) the input file sampling.fasta (2 col for the title) .Join two datasets(Join, Subtract and Group) on the columns c1 .Tabular-to-FASTA (fasta manipulation) of the previous results. .You can see how many sequences you took away (click on the dataset name in History) and it should correspond to the number of True in Count . 5

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Filter and Sort Errors
by Mersee Madison-Villar 09 Oct '13

09 Oct '13

Hello... I have tried to filter my data to contain only those results with e-values of less than 0.05. I am given output...however, this only goes to 0.001. When I sort these same data, I see results between 0.001 and 0.05. However, even if I try to filter off of the sorted results, I still get only values <= 0.001. Can this be fixed? My user information is under the email account "mjmv(a)brandeis.edu". M -- M.J. Madison-Villar, PhD NSF Funded Postdoctoral Research Fellow Mueller Lab Research Group Colorado State University, Fort Collins, CO Fax: (781) 316-0249

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Intergrate custom script with multiple outputs
by UMD Bioinformatics 09 Oct '13

09 Oct '13

Hello, I'm trying to incorporate a python tool that can accommodate multiple input files and the number of output files cannot be determined prior to running the tool. I've been though the help section at http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_… but I'm not getting any results. The tool isn't even running and creating the proper output in the tool directory. I've felt with the naming convention requited by Galaxy and the tool works from the command line. I know that the issue isn't with my local Galaxy install because a generic tool I've installed that produces multiple outputs works fine. I've attached my code and the XML file. Any help would be appreciated. Cheers Ian

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Launching CloudMan in Other AWS Regions than US East
by Ryota Yamanaka 09 Oct '13

09 Oct '13

Dear Galaxy Team, We would like to benchmark CloudMan with NGS data in Tokyo, and we are wondering if it is possible to launch it at AWS's Tokyo DC in order to facilitate large-size data transfer and low-latency response. However, CloudMan AMI is currently available only at Virginia DC according to Wiki: > ... set your AWS Region to US East (Virginia). This is the only > region Galaxy CloudMan is fully supported in at this time ... http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted 1) Do you plan to clone CloudMan AMI to other regions outside the US in the near future? 2) Or, is there any way we can build CloudMan in such regions, with or without your support? Sincerely, Ryota Yamanaka Genome Science, RCAST, The University of Tokyo

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2 RNAseq files in Main queue 1 week to map w/Top hat
by Theresa Stueve 09 Oct '13

09 Oct '13

Greetings, I have had two RNAseq files in queue to map with Top hat in Galaxy Main since last Thursday (History began Sept 19). I got word that NGS was stalled, my jobs were mistakenly believed to be moving afterwards when they weren't- but are now under review again. It has been a week now and the 2 mapping jobs are still waiting to run. Can you tell me whether I should delete the jobs and re-run them as new? Is there a problem with my trimmed dataset? My concern is that these jobs are still "believed to be moving" as was indicated by one of your galaxy stewards, but are actually still stalled in space. One week is a long tme to wait for local jobs, no? thank you very much for your help https://main.g2.bx.psu.edu/u/trstueve/h/rnaseqjegcsc3wkrun130924-1 <https://main.g2.bx.psu.edu/history/sharing#> Theresa Ryan Stueve 510-225-8894 (text better than voicemail for quick response) -- Theresa Ryan Stueve 510-225-8894 (text better than voicemail for quick response)

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