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annotate tool-data/all_fasta.loc.sample @ 24:33c3ddea63c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 09721a12bdd393441b162056316241aba3895a4f
author iuc
date Sun, 18 Feb 2018 15:07:08 -0500
parents b73962f8fcbf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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1 #This file lists the locations and dbkeys of all the fasta files
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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2 #under the "genome" directory (a directory that contains a directory
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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3 #for each build). The script extract_fasta.py will generate the file
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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5 #TAB characters):
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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6 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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8 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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9 #So, all_fasta.loc could look something like this:
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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10 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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14 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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17 #such as with hg19 above.
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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18 #