October 2012 - galaxy-user - lists.galaxyproject.org

Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error
by Joel Rosenberg 08 Oct '12

08 Oct '12

So I'm trying to install the recently migrated ncbi_blast_plus tool from the Tool Shed to my local galaxy instance running in EC2 and am getting errors at the installation step. After clicking "Install to local Galaxy" I immediately get: "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" and an HTTP 500 error code is returned. Chrome tells me the URL it's attempting to request is: http://toolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c… I tried the same process for other non-blast related tools that appeared to be simple (no 3rd party binary dependencies) and got the same server error. I restarted galaxy with its log level set to DEBUG and wasn't illuminated further, but that doesn't surprise me since my browser's requesting data from the public toolshed, not my server. I just performed a mercurial update in my cluster, too. Any ideas?

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please restore my account
by Du, Jianguang 08 Oct '12

08 Oct '12

Dear Sir or Madam, I had onpened multiple accounts at Galaxy Main, I did not know that it is against policy. I noticed this policy when I found that all the accounts are blocked. Would you please restore the account with email address jiandu(a)iupui.edu<mailto:jiandu@iupui.edu>? If you are not responsible for account management, would you please forward this email to Galaxy adminstrator, or give me the right email address of Galaxy adminstrator (I could not find the email address of Galaxy adminstator)? Thanks. Jianguang

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Are tools must be installed in local machine?
by Sachit Adhikari 08 Oct '12

08 Oct '12

Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are those tools must be installed in order to work in Galaxy. For example: I am using Debian machine(Don't have tophat and bowtie installed). Will tophat and bowtie work in my local galaxy? Thanks

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cuffdiff fold change
by i b 08 Oct '12

08 Oct '12

HI all, just a quick question about cuffdiff: when I write the imputs files, for example sample1 (untreated) and sample2(treated), does it make any difference the order? E.g., the order in which i insert the relative tophat samples? I compared 3 samples (a, b, c) each of then against a non trated sample (x), but i realised that in cuffdiff i gave in one case first the tophat of sample a and than sample x than when i ran a new cuffdiff i gave first sample x and then sample b or c....is the test statistic goign to be different?The log2fold change has the same number, just + or - depending on the order thanks, ib

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RSEM on Galaxy
by Alicia R. Pérez-Porro 05 Oct '12

05 Oct '12

Hi all, Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open "my" galaxy in my computer. I checked and rsem folder is inside the tool folder. Any suggestions? Thanks, Alicia. -- Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/ Department of Marine Ecology Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St. Francesc 14 17300 Blanes, Girona, SPAIN phone: +34 972 336 101 fax: +34 972 337 806 www.ceab.csic.es

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Galaxy October 5, 2012 Distribution & News Brief
by Jennifer Jackson 05 Oct '12

05 Oct '12

*Galaxy October 5, 2012 Distribution & News Brief* /http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05/ /* Highlights:* http://wiki.g2.bx.psu.edu/News / ** * *BWA <http://bio-bwa.sourceforge.net/>* tool wrappers /migrated <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#BWA_Migration_to_Tool_Sh…>/ to the *Galaxy Main Tool Shed <http://toolshed.g2.bx.psu.edu/>*. * *Tool Factory* paper has been /E Published <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Galaxy_Tool_Factory_Pape…>/ in PubMed <http://www.ncbi.nlm.nih.gov/pubmed> at *PMID: 23024011 <http://www.ncbi.nlm.nih.gov/pubmed/23024011>*. * The *Tool Shed Wiki <http://wiki.g2.bx.psu.edu/Tool%20Shed>* wiki has been re-written with a new, cleaner presentation. And check out all the /new features <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Tool_Shed>/! * Accessible *tool versions* in the UI and *new exit code features* enable /clearer experimental tracking and ease reproducibility <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Tools>/. * Release also includes *Visualization <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Visualization_framework>* updates, a new admin tool for /PostgreSQL <http://www.postgresql.org>/ *Dataset cleanup <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Dataset_Cleanup>*, and improvements in *API <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#AP>* , *Workflow <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Workflows>*, and *Security <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Security_Fixes>* components. http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist * new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist * upgrade:* $ hg pull -u -r b5bda7a5c345 ** * Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team http://galaxyproject.org

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Datasets Disappear following import of additional datasets
by Josh Romney 04 Oct '12

04 Oct '12

Galaxy, I am able to upload fastqsanger files via FTP and import them to my various histories without a problem. When I import additional files from the Shared Data library CloudMap into my various histories, my fastqsanger files disappear 'they are no longer visible in the history panel'. The amount of disk usage suggests that my files are still there and the saved histories page shows that there are six datasets even though only five are visible. Any help would be appreciated. Josh

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Fastq-groomer help
by Kshama Aswath 04 Oct '12

04 Oct '12

Hello: I have this 20GB data that I have uploaded onto my history and trying to get it run thr groomer. Just the first data set was uploaded yesterday and ran groomer on it and it was not done this morning. The message indicated taht it is still waiting to be run !!! I have 57 data sets to run and would appreciate if you could inform me about how long it may take to even get started or any other suggestion to get my job done will help. Thanks so much, user name :genenart Kshama. -- Kshama Aswath Graduate Student-(PhD) Bioinformatics and computational Biology Prince Williams Campus George Mason University Manasses,VA-20110

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Trim Galore Galaxy Integration
by Sachit Adhikari 04 Oct '12

04 Oct '12

Hello. I would like to integrate this great tool "Trim Galore" in the local Galaxy. Has anyone did this before? If so, please provide me with the wrapper and .xml file? How can I integrate it? Best wishes, Sachit

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Trim Galore Galaxy Integration
by Sachit Adhikari 04 Oct '12

04 Oct '12

Hello. I would like to integrate this great tool "Trim Galore" in the local Galaxy. How can I do that? Thanks in advance.

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