comparison tool-data/rnastar_index2x_versioned.loc.sample @ 7:6c6c6df09e64 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
author iuc
date Wed, 05 Aug 2020 09:38:12 -0400
parents
children c520a52b5174
comparison
equal deleted inserted replaced
6:64deddb6a8ec 7:6c6c6df09e64
1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of rna-star indexed sequences data files.
3 #You will need to create these data files and then create a
4 #rnastar_index2x_versioned.loc file similar to this one (store it in this
5 directory) that points to the directories in which those files are stored.
6 #The rnastar_index2x_versioned.loc file has this format (longer white space
7 #characters are TAB characters):
8 #
9 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version>
10 #
11 #The <with_gene_model> column should be 1 or 0, indicating whether the index
12 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
13 #or not.
14 #
15 #The <version> column indicates the STAR version that introduced the format of
16 #the index, i.e., the oldest STAR version that could make use of the index.
17 #
18 #Note that STAR indices can become quite large. Consequently, it is only
19 #advisable to create indices with annotations if it's known ahead of time that
20 #(A) the annotations won't be frequently updated and (B) the read lengths used
21 #will also rarely vary. If either of these is not the case, it's advisable to
22 #create indices without annotations and then specify an annotation file and
23 #maximum read length (minus 1) when running STAR.
24 #
25 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a
26 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a
27