Re: [galaxy-user] Regarding .exe file
Shambhavi, Any tool that can be run from the command line, whether it be a .exe, .sh, .pl, .ph, etc, can be installed in Galaxy. All this is explained on the wiki. The best page to start would be: http://wiki.g2.bx.psu.edu/Admin/Tools Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 14/11/2011 04:47, Shambhavi Srivastava shambhavi.srivast...@gmail.com wrote: Dear Galaxy users, Is it possible to install .exe files in galaxy?If yes then how? Thanx, Shambhavi ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] GATK wrapper in Galaxy
Hello all, I am trying to run through the GATK pipeline on the Galaxy Test page. I have a question related to the UnifiedGenotyper wrapper page. At the bottom of the page, I choose the Advanced tab for Basic or Advanced Analysis options. After the automatically refreshed, I choose the Annotation Types that I was interested in. Then below that are options for Annotation Interfaces/Groups: What are these options used for? I have looked all over the web, on the GATK wiki and at the GATK QA page (located at getsatisaction.com) without any luck. Are these options important? The description located at the bottom of the page lists: Group - One or more classes/groups of annotations to apply to variant calls. What type of group or class is Standard, Experiments or WorkInProgress? Does class refer to a Java class in a similar way that annotations are arguments? Any clarification would be very helpful. Thanks, Mike ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
