User: Jelle Scholtalbers

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Germany
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2 years, 1 month ago
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Posts by Jelle Scholtalbers

<prev • 36 results • page 1 of 4 • next >
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Answer: A: local galaxy ftp_upload_site
... The host entry in the config file of Galaxy only refers to the location the Galaxy web process(http) will be listening on. Galaxy itself does not provide any FTP server functionality. You will have to setup a FTP server if you want this capability. Have a look a this documentation https://wiki.gala ...
written 2.3 years ago by Jelle Scholtalbers360
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Answer: A: How can I choose tools/section order?
... Hi Christ, you will need to edit the integrated_tool_panel.xml as described here: https://wiki.galaxyproject.org/GalaxyToolPanel "A new file named integrated_tool_panel.xml has been introduced to define the arrangement for displaying these loaded items in your Galaxy tool panel" Cheers, Jelle ...
written 2.4 years ago by Jelle Scholtalbers360
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Comment: C: Fastq.gz files in shared Data Libraries
... We are basically doing the same thing on our instance. The issue is ofcourse that with each tool update you will have to add the support for fastq.gz again. I'm not sure if it helps, but maybe upvoting this ticket might highlight the need for this: https://trello.com/c/3RkTDnIn/345-666-support-gzip ...
written 2.4 years ago by Jelle Scholtalbers360
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Comment: C: Memory requirement? Picard missing tool dependencies
... Hi Marc, often you can just install that particular dependency by clicking on the respective dependency that is listed by the installed tool, otherwise reinstalling or repairing often also helps. In addition, in the main toolshed, there seems to be one picard package, which is updated and maintained ...
written 2.5 years ago by Jelle Scholtalbers360
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Answer: A: local galaxy in Windows OS
... No, you cannot have a fully functional Galaxy installation natively on a windows pc (its unsupported and many tools will just not work). However, you do have a few other options: https://wiki.galaxyproject.org/BigPicture/Choices In addition, to keep it local, you could run a linux(like ubuntu) or b ...
written 2.7 years ago by Jelle Scholtalbers360
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Answer: A: Need help with "Cufflinks" tool
... (According to the specific tool xml - https://toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/file/5346d5eea8b1/cufflinks_wrapper.xml) You will have to set "Set advanced Cufflinks options:" to "yes" and then you should be able to specify "Maximum number of fragments per locus" which sets the --max-b ...
written 2.9 years ago by Jelle Scholtalbers360
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Comment: C: Custom toolshed tool: job memory requirements
... ow, this might indeed be the solution for the error stated... However, I'm actually more referring to an error similar to "PBS: job killed: mem job total 4131052 kb exceeded limit 1048576 kb". (sorry for the confusion). I updated the question. ...
written 3.1 years ago by Jelle Scholtalbers360
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Custom toolshed tool: job memory requirements
... Is it possible to add job requirements to (toolshed) tools? For example, if a tool minimally requires >4gb of ram, ("java -Xmx4g") this will most of the time run fine on a non-cluster enabled galaxy instance. However, when using a cluster this might fail with "PBS: job killed: mem job total 4131 ...
toolshed written 3.1 years ago by Jelle Scholtalbers360 • updated 3.1 years ago by jmchilton1.0k
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Comment: C: Installing Galaxy With Apache ...
... Hi Neil, I'm certainly not an apache expert so I might be giving you the wrong advise, but try adding the following: LoadModule proxy_module modules/mod_proxy.so LoadModule proxy_http_module modules/mod_proxy_http.so If above fails, try to go back to the simplest configuration mentioned on the gal ...
written 5.3 years ago by Jelle Scholtalbers360
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Answer: A: Installing Galaxy With Apache ...
... Hi Neil, with your current apache configuration, you should probably see Galaxy at http://yourip/galaxy This is due to your Rewriterule /galaxy and for that you have also set proxy_prefix = /galaxy in your universe_wsgi.ini You should probably remove the empty galaxy directory under /var/www Furth ...
written 5.3 years ago by Jelle Scholtalbers360

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