Hi David,
tha BAM file is compressed in the BGZF format and is not uncompressed by default. So I would try the following:
- write your own datatype http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes - write a sniffer similar to the BAM sniffer https://bitbucket.org/galaxy/galaxy-central/src/8fc56b85e0a5353ffd6790685a4a...
Thanks to the wonderful toolshed it is also possible to include datatypes in your repo. http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
Hopefully that will work out! Bjoern
Hello,
I have a tool that needs a directory containing a bunch of files as an input : mytool -d $directory -p param1 -o $output ...
I thought the best approach would be to use a Zip file that I would temporally uncompress in a bash wrapper. But when I upload the zip file, galaxy unzip it.
What would you recommend to accomplish such a task ? I want that tool to be installable from a toolshed, so I don't want to modify the upload.py script or any other files.
Thanks,
David ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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