comparison tool-data/rnastar_index2.loc.sample @ 1:cdc4d8a998e1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
author iuc
date Fri, 21 Apr 2017 12:36:31 -0400
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children f537d3e00eb8
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0:e4b87a00b1df 1:cdc4d8a998e1
1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of rna-star indexed sequences data files. You will
3 #need to create these data files and then create a rnastar_index2.loc
4 #file similar to this one (store it in this directory) that points to
5 #the directories in which those files are stored. The rnastar_index2.loc
6 #file has this format (longer white space characters are TAB characters):
7 #
8 #<unique_build_id> <dbkey> <display_name> <file_base_path> <withGTF>
9 #
10 #The <with_gtf> column should be 1 or 0, indicating whether the index was made
11 #with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not,
12 #respecively.
13 #
14 #Note that STAR indices can become quite large. Consequently, it is only
15 #advisable to create indices with annotations if it's known ahead of time that
16 #(A) the annotations won't be frequently updated and (B) the read lengths used
17 #will also rarely vary. If either of these is not the case, it's advisable to
18 #create indices without annotations and then specify an annotation file and
19 #maximum read length (minus 1) when running STAR.
20 #
21 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0
22 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
23