[galaxy-user] BWA question on Mac OS X 10.7.2
Hi, I have tried to install BWA on my MacPro. Once installed, I typed the command make and it did not work. When installing BWA to a Linux machine, it worked fine. How do I get around this problem? Thanks, CWC ___ 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] Galaxy local install problems understanding where to put mouse ref seq data to populate ref genome in BWA
Hello, I am still having problems understanding how to install mm9 mouse ref genome into our own install of Galaxy. When I try to map with BWA for Illumina the drop down for select ref genome is not populated with anything. How do you grab the mm9 ref file and how do you convert it so that Galaxy local "sees" it? How do you build the index and how do you prepare the loc file? Our install does not contain a folder tool-data/shared/ucsc/builds.txt. Sorry but I am not a programmer, just a bench scientist. Thanks in advance, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way # Salt Lake City, UT 84108 ___ 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] BWA install problem
Hi, I am trying to run Galaxy locally and downloaded BWA but I can't get it to run. Do I have to use 0.5.6 or can I use 0.5.9? The make command does not work with ver. 0.5.9. Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way # Salt Lake City, UT 84108 ___ 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] customizing mm9 mouse reference genome and then using that as the ref genome when uploading Illumina data
I would like to filter out the mm9 mouse build ref genome to only show MspI sites, and then use that as my "Genome" when uploading my Illumina data. Anyone have a protocol for that? Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way # Salt Lake City, UT 84108 ___ 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/
