Mercurial > repos > iuc > bcftools_isec

annotate tool-data/fasta_indexes.loc.sample @ 23:39bca000353d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 10:04:43 +0000
parents cfc3a6940b18
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
2 #to use a directory of Samtools indexed sequences data files. You will need
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
3 #to create these data files and then create a fasta_indexes.loc file
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
5 #the directories in which those files are stored. The fasta_indexes.loc
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
6 #file has this format (white space characters are TAB characters):
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
7 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
9 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
10 #So, for example, if you had hg19 Canonical indexed stored in
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
11 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
12 # /depot/data2/galaxy/hg19/sam/,
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
13 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
14 #then the fasta_indexes.loc entry would look like this:
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
15 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
17 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
18 #and your /depot/data2/galaxy/hg19/sam/ directory
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
19 #would contain hg19canon.fa and hg19canon.fa.fai files.
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
20 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
21 #Your fasta_indexes.loc file should include an entry per line for
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
22 #each index set you have stored. The file in the path does actually
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
23 #exist, but it should never be directly used. Instead, the name serves
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
24 #as a prefix for the index file. For example:
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
25 #
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa