Mercurial > repos > jjohnson > arriba_get_filters

annotate tool-data/arriba_indexes.loc.sample @ 0:463dd21dc267 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author jjohnson
date Fri, 11 Feb 2022 19:08:51 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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1 #This is a sample file distributed with Galaxy that enables tools
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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2 #to use a directory of Ariba data files.
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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3 #The Arriba script download_references.sh retrieves a genome assembly fasta
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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4 #and a related GTF annotation file, then builds a STAR index.
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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5 #You will need to create these data files and then create a
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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6 #arriba_indexes.loc similar to this one (store it in this
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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7 #directory) that points to the directories in which those files are stored.
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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8 #The arriba_indexes.loc file has this format (longer white space
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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9 #characters are TAB characters):
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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10 #
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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11 #<unique_build_id> <display_name> <genome_fasta_path> <genome_gtf_path> <STAR_index_path>
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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12 #
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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13 #Note that STAR indices can become quite large.
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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14 #
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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15 #<unique_build_id> <display_name> <genome_fasta_path> <genome_gtf_path> <STAR_index_path>
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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/
463dd21dc267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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