annotate tool-data/mosaik_index.loc.sample @ 1:1fea05cdc1a1 draft default tip

Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>.

#This is a sample file distributed with Galaxy that enables tools
#to use a directory of Mosaik indexed sequences data files. You will need
#to create these data files and then create a mosaik_index.loc file 
#similar to this one (store it in this directory) that points to 
#the directories in which those files are stored. The mosaik_index.loc 
#file has this format (longer white space is the TAB character):
#
#<unique_build_id>		<dbkey>		<display_name>		<fasta_file_path>
#
#So, for example, if you had hg18 indexed and stored in 
#/depot/data2/galaxy/mosaik/hg18/
#then the mosaik_index.loc entry would look like this:
#
#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/mosaik/hg18/hg18.fa
#
#and your /depot/data2/galaxy/mosaik/hg18/ directory
#would contain the following files:
#TODO handle mosaik jump tables.
#