annotate sam_fa_indices.loc.sample @ 1:046c7983e2ff

Uploaded sam_fa_indices.loc.sample
author devteam
date Mon, 02 Jul 2012 17:55:37 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
2 #to use a directory of Samtools indexed sequences data files. You will need
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
3 #to create these data files and then create a sam_fa_indices.loc file
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
5 #the directories in which those files are stored. The sam_fa_indices.loc
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
6 #file has this format (white space characters are TAB characters):
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
7 #
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
8 #index <seq> <location>
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
9 #
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
10 #So, for example, if you had hg18 indexed stored in
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
11 #/depot/data2/galaxy/sam/,
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
12 #then the sam_fa_indices.loc entry would look like this:
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
13 #
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
14 #index hg18 /depot/data2/galaxy/sam/hg18.fa
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
15 #
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
16 #and your /depot/data2/galaxy/sam/ directory
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
17 #would contain hg18.fa and hg18.fa.fai files:
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
18 #
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
21 #
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
22 #Your sam_fa_indices.loc file should include an entry per line for
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
23 #each index set you have stored. The file in the path does actually
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
24 #exist, but it should never be directly used. Instead, the name serves
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
25 #as a prefix for the index file. For example:
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
26 #
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
27 #index hg18 /depot/data2/galaxy/sam/hg18.fa
046c7983e2ff Uploaded sam_fa_indices.loc.sample
devteam
parents:
diff changeset
28 #index hg19 /depot/data2/galaxy/sam/hg19.fa