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annotate tool-data/all_fasta.loc.sample @ 18:bb74e17e47d7 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 02087ce2966cf8b4aac9197a41171e7f986c11d1"
author bgruening
date Tue, 01 Oct 2019 12:43:53 -0400
parents fcadce4d9a06
children
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fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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1 #This file lists the locations and dbkeys of all the fasta files
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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2 #under the "genome" directory (a directory that contains a directory
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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3 #for each build). The script extract_fasta.py will generate the file
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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5 #TAB characters):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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6 #
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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8 #
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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9 #So, all_fasta.loc could look something like this:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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10 #
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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14 #
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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15 #Your all_fasta.loc file should contain an entry for each individual
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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17 #such as with hg19 above.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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18 #
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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19 #Arabidopsis_thaliana Arabidopsis_thaliana_TAIR10 Arabidopsis_thaliana: TAIR 10 /export/home1/users/biocomp/chbernar/galaxy_testing/tool-data/from_personal_data/Fasta/TAIR10.fa