comparison tool-data/rnastar_index2_versioned.loc.sample @ 10:d82339e37e8e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
author iuc
date Thu, 15 Aug 2019 01:54:13 -0400
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9:0a563fd2f22e 10:d82339e37e8e
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> <with_gene_model> <version>
9 #
10 #The <with_gene_model> column should be 1 or 0, indicating whether the index
11 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
12 #or not.
13 #
14 #The <version> column indicates the STAR version that introduced the format of
15 #the index, i.e., the oldest STAR version that could make use of the index.
16 #
17 #Note that STAR indices can become quite large. Consequently, it is only
18 #advisable to create indices with annotations if it's known ahead of time that
19 #(A) the annotations won't be frequently updated and (B) the read lengths used
20 #will also rarely vary. If either of these is not the case, it's advisable to
21 #create indices without annotations and then specify an annotation file and
22 #maximum read length (minus 1) when running STAR.
23 #
24 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a
25 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a
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