- galaxy-dev - lists.galaxyproject.org

Interested in speaking with other institutions deploying Galaxy locally?
by Ann Black-Ziegelbein 05 Jul '12

05 Jul '12

Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein

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Looking for recommendations: How to run galaxy workflows in batch
by Dave Lin 05 Jul '12

05 Jul '12

Hi All, I'm looking to batch process 40 large data sets with the same galaxy workflow. This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin 2) command-line 3) web-service Thanks in advance for any pointers. Dave

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Liftover tool installation woes
by Kwon SoonJae 05 Jul '12

05 Jul '12

Hi Everyone, I installed a local instance of galaxy and some tools using the command line, and for some reason liftover will work in the command line but won't work in galaxy. Here's what I've done so far: - Downloaded liftover standalone executable from the tool-dependencies page in the Gwiki. - Changed permissions on liftover executable to make it usable in the command prompt (terminal, macosx) -> otherwise I get permission denied. - Copied executable over to /usr/local/bin likewise to use in command prompt and in Galaxy. - Modified liftover.loc to include all the conversion types and directories of chain.gz files I downloaded to use with the tool (I believe liftover can make use of both .chain and .chain.gz files). After that I tried to run liftover in Galaxy and it didn't work, giving me some error that said hg19ToMm9 mapping is currently not available. It seems to work fine using the command line though. Since my goal is to setup galaxy locally, I really want to get this working correctly. Can anyone guide me through what's gone wrong? Also, there must be a better way of installing all these tools than manually downloading every single one and using the command line, surely? I had to type out the format of liftover.loc file manually for around 130 chain files... I'm convinced there has to be a better way. Thanks in advance, SJ

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Display with IGV local
by Chebbi Mohamed Amine 05 Jul '12

05 Jul '12

HI Galaxy-team ! I 'am trying to display BAM files whith the * local* IGV. However D*isplay with IGV "local*" use the already running copy of IGV on the server machine. So I need evry time to run manually igv by the command above: java -Xmx750m -jar igv.jar Is there any way to do this automatically I guess that I have to configure bam.xml file to call "java -Xmx750m -jar igv.jar" command , when cliking on D*isplay with IGV local*. ? Thanks for help Regards Amine

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Adding the tag in tool xml file
by sshashi 05 Jul '12

05 Jul '12

Hi, is it possible to add the tag in tool_xml_file ? how can i add new tag in tool_xml_file ? if anyone is working on this , guide me .... Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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conflicting migration files
by Langhorst, Brad 04 Jul '12

04 Jul '12

When I merged brad chapmans code into galaxy-central two 0099 migration files are created. I got things working by moving the ngs lims one to 0104 , but now i think i'll be in for a problem when a new 104 is created... What's the right way to solve this? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

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Question about compressed files
by Ciara Ledero 04 Jul '12

04 Jul '12

Hi all, My colleague tried to upload via filesystem path a file with an approximate size of 2GB. It was a compressed file (filename.fq.gz). No error was reported, so I thought everything went fine, but when he tried running a tool, the uploaded file did not show in the input dropdown. But when he tried again, this time using an uncompressed file, every thing worked well. Now to my question: by default, can Galaxy accept and use compressed files? Or do I have to change something in its configuration just to do so? Thanks for the help! CL

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Byte-range support for IGV ?
by Chebbi Mohamed Amine 04 Jul '12

04 Jul '12

HELLO ! I just updated our local galaxy instance and just wanted to try the new IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message : "HTTP and FTP access to BAM files require byte-range support" Has anyone encountred the same probleme? Thanks in advances Regards Amine

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how to add new Xml tag in tool xml file
by sshashi 04 Jul '12

04 Jul '12

Hi, I am using my local instance of galaxy . I want to create a tag which will open an new window in galaxy. How can i create a new tag in tool_xml_file ? for this any modification is required in any file of galaxy ? Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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how to create a new tag in tool_xml_file of galaxy
by sshashi 04 Jul '12

04 Jul '12

Hi, I am using my local instance of galaxy . I want to create a tag which will open an new window in galaxy. How can i create a new tag in tool_xml_file ? for this any modification is required in any file of galaxy ? Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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