Mercurial > repos > iuc > cnvkit_diagram

annotate tool-data/fasta_indexes.loc.sample @ 2:cd407b016741 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/cnvkit commit bced16a45d19b243a244a093c3b3504b2640d5e0
author iuc
date Mon, 22 Apr 2024 17:46:10 +0000
parents 9d18753f47b4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
2 #to use a directory of Samtools indexed sequences data files. You will need
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
3 #to create these data files and then create a fasta_indexes.loc file
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
5 #the directories in which those files are stored. The fasta_indexes.loc
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
6 #file has this format (white space characters are TAB characters):
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
7 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
9 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
10 #So, for example, if you had hg19 Canonical indexed stored in
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
11 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
12 # /depot/data2/galaxy/hg19/sam/,
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
13 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
14 #then the fasta_indexes.loc entry would look like this:
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
15 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
17 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
18 #and your /depot/data2/galaxy/hg19/sam/ directory
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
19 #would contain hg19canon.fa and hg19canon.fa.fai files.
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
20 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
21 #Your fasta_indexes.loc file should include an entry per line for
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
22 #each index set you have stored. The file in the path does actually
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
23 #exist, but it should never be directly used. Instead, the name serves
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
24 #as a prefix for the index file. For example:
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
25 #
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
9d18753f47b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff changeset
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa