Mercurial > repos > jjohnson > arriba

comparison test-data/arriba_indexes.loc @ 9:8c4c97fd0555 draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
author jjohnson
date Wed, 13 Oct 2021 18:45:16 +0000
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8:1a56888ddb7d 9:8c4c97fd0555
1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of Ariba data files.
3 #The Arriba script download_references.sh retrieves a genome assembly fasta
4 #and a related GTF annotation file, then builds a STAR index.
5 #You will need to create these data files and then create a
6 #arriba_indexes.loc similar to this one (store it in this
7 #directory) that points to the directories in which those files are stored.
8 #The arriba_indexes.loc file has this format (longer white space
9 #characters are TAB characters):
10 #
11 #<unique_build_id> <display_name> <genome_fasta_path> <genome_gtf_path> <STAR_index_path>
12 #
13 #Note that STAR indices can become quite large.
14 #
15 #<unique_build_id> <display_name> <genome_fasta_path> <genome_gtf_path> <STAR_index_path>
16 #GRCh38+ENSEMBL93 GRCh38+ENSEMBL93 /depot/GRCh38+ENSEMBL93/genome.fa /depot/GRCh38+ENSEMBL93/genome.gtf /depot/GRCh38+ENSEMBL93/STAR_index/
17 GRCh38+ENSEMBL93 GRCh38+ENSEMBL93 ${__HERE__}/test-cache/genome.fasta ${__HERE__}/test-cache/genome.gtf ${__HERE__}/test-cache/STAR_index/
18