Mercurial > repos > rhpvorderman > data_manager_select_index_by_path

annotate tool-data/all_fasta.loc.sample @ 39:ad5d85570342 draft default tip

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planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit a9b8c9549044fb951570d9c6cf88107d98800afb
author rhpvorderman
date Wed, 25 Jul 2018 10:34:49 -0400
parents afd01fcbea26
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
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afd01fcbea26 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
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2 #under the "genome" directory (a directory that contains a directory
afd01fcbea26 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents: 0
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3 #for each build). The script extract_fasta.py will generate the file
afd01fcbea26 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents: 0
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4 #all_fasta.loc. This file has the format (white space characters are
afd01fcbea26 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents: 0
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5 #TAB characters):
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288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
6 #
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
8 #
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
10 #
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
14 #
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
17 #such as with hg19 above.
288819f540fd planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 3ffb01380e2fe315bf3fe88f97781a83595b3fff
rhpvorderman
parents:
diff changeset
18 #