Mercurial > repos > jjohnson > arriba

annotate tool-data/arriba_indexes.loc.sample @ 12:73fd7703a743 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit fe2e3c7429c5bea23690a27b5889b502984ad58a"
author jjohnson
date Tue, 26 Apr 2022 20:35:35 +0000
parents 8c4c97fd0555
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
parents:
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1 #This is a sample file distributed with Galaxy that enables tools
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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2 #to use a directory of Ariba data files.
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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3 #The Arriba script download_references.sh retrieves a genome assembly fasta
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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4 #and a related GTF annotation file, then builds a STAR index.
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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5 #You will need to create these data files and then create a
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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6 #arriba_indexes.loc similar to this one (store it in this
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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7 #directory) that points to the directories in which those files are stored.
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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8 #The arriba_indexes.loc file has this format (longer white space
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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9 #characters are TAB characters):
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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10 #
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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11 #<unique_build_id> <display_name> <genome_fasta_path> <genome_gtf_path> <STAR_index_path>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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12 #
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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13 #Note that STAR indices can become quite large.
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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14 #
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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15 #<unique_build_id> <display_name> <genome_fasta_path> <genome_gtf_path> <STAR_index_path>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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16 #GRCh38+ENSEMBL93 GRCh38+ENSEMBL93 /depot/GRCh38+ENSEMBL93/genome.fa /depot/GRCh38+ENSEMBL93/genome.gtf /depot/GRCh38+ENSEMBL93/STAR_index/
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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