Rsem On Galaxy

Question: Rsem On Galaxy

6.2 years ago by

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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modified 6.2 years ago by fubar ♦ 1.1k • written 6.2 years ago by Alicia R. Pérez-Porro • 10

6.2 years ago by

fubar ♦ 1.1k

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fubar ♦ 1.1k wrote:

Alicia, Some relevant details usually make it easier for list members to help you - please see http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussi ons Did you load the offending tool from a toolshed or is it a tool wrapper you wrote yourself? If the latter, I have two suggestions: 1) Search paster.log for your tool name and make sure it got correctly loaded when you restarted Galaxy - xml syntax errors like misplaced < characters will break the tool loading process. 2) if the log shows that it loaded, make sure you refresh the tool frame in your browser after restarting Galaxy - eg clicking the "analyse data" tab will get rid of the old cached copy. On Sat, Oct 6, 2012 at 10:02 AM, Alicia R. Pérez-Porro -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ

ADD COMMENT • link written 6.2 years ago by fubar ♦ 1.1k

Hi Alicia, At the moment you have to install the wrapper manually. That is, the current version of the RSEM won't automatically install the rsem binaries for you. We are working on updating the tool from the tool shed. The readme file within the tarball provides instructions on what version of RSEM to install and other details. We ll keep you posted as soon as we update the tool so things will be done for you much like the other newer tools in the tool shed. Thank you for using RSEM and please let me know how it goes. Victor

ADD REPLY • link written 6.2 years ago by Victor Ruotti • 90

Hi there Alicia! To find the tool in the Galaxy tool search, first you have to put your tool files in tools with .xml files then you have to edit tool_conf.xml file. Here's the step by step tutorial: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial Regards, Sachit

ADD REPLY • link written 6.2 years ago by Sachit Adhikari • 320

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