[galaxy-dev] missing .fa files in rsync datacache indexes

2012-09-25 Thread Kevin Y
Hi, Thanks for providing the indexes via rsync:: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration We've, noticed that despite soft links pointing to it, there are no .fa files for example in hg19/seq/ However there are 2bit files. Would you guys recommend we convert them from 2bit to fasta?

Re: [galaxy-dev] missing .fa files in rsync datacache indexes

2012-09-25 Thread Kevin Y
to fasta shouldn't cause any problems. --Dave B. On 9/25/12 03:20:14.000, Kevin Y wrote: Hi, Thanks for providing the indexes via rsync:: http://wiki.g2.bx.psu.edu/**Admin/Data%20Integrationhttp://wiki.g2.bx.psu.edu/Admin/Data%20Integration We've, noticed that despite soft links pointing

Re: [galaxy-dev] missing .fa files in rsync datacache indexes

2012-09-26 Thread Kevin Y
the (approximately) four times larger files when 2bit is available. --Dave B. On 9/25/12 20:55:31.000, Kevin Y wrote: Thanks Dave, A question before we go ahead, why are they missing in the first place? Does the main galaxy not actually need them? are the tools moving away from fa? Cheers

[galaxy-dev] Gencode Partition (version 1.0.0)

2012-10-14 Thread Kevin Y
Hi, We are trying to debug our local instance of Gencode Partition (version 1.0.0) We seem to missing this configuation file encode_feature_partitions/partition_list.txt The link given in the tool is behind a login wall and I can't get through:

[galaxy-dev] language inside command tag set

2012-11-05 Thread Kevin Y
Hi, I'm looking for documentation on what I can do inside the command tag for tools. I know of things like #if str( $input ) == 'yes': Do stuff #end if can I do for loops? What should I google? I can't find anything on the wiki. Thanks, Kevin.

[galaxy-dev] How to make toolshed tool to create dummy env.sh

2012-11-11 Thread Kevin Y
Hi dev list, What is the simplest xml I can put into a tool_dependencies.xml for it to create a dummy env.sh in tool-dependency/tool/version/ /awef234243/env.sh And will this be sourced each time. Or does the dependency need to be some sort of successfully install status for it to be

Re: [galaxy-dev] How to make toolshed tool to create dummy env.sh

2012-11-12 Thread Kevin Y
in the installed repository is executed in the Galaxy instance in case this is what you're looking for. http://wiki.galaxyproject.org/ToolShedToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time Greg Von Kuster On Nov 12, 2012, at 1:51 AM, Kevin Y