Mercurial > repos > devteam > sam_pileup
annotate tool-data/fasta_indexes.loc.sample @ 2:37df866ccf1a draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_pileup commit 8301d37348be25a038b3c63b049b1178d05f5003"
author | devteam |
---|---|
date | Thu, 06 Feb 2020 12:11:11 +0000 |
parents | efd77ef84903 |
children |
rev | line source |
---|---|
1
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
2 #to use a directory of Samtools indexed sequences data files. You will need |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
3 #to create these data files and then create a fasta_indexes.loc file |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
4 #similar to this one (store it in this directory) that points to |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
5 #the directories in which those files are stored. The fasta_indexes.loc |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
6 #file has this format (white space characters are TAB characters): |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
7 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
8 # <unique_build_id> <dbkey> <display_name> <file_base_path> |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
9 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
10 #So, for example, if you had hg19 Canonical indexed stored in |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
11 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
12 # /depot/data2/galaxy/hg19/sam/, |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
13 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
14 #then the fasta_indexes.loc entry would look like this: |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
15 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
17 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
18 #and your /depot/data2/galaxy/hg19/sam/ directory |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
19 #would contain hg19canon.fa and hg19canon.fa.fai files. |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
20 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
21 #Your fasta_indexes.loc file should include an entry per line for |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
22 #each index set you have stored. The file in the path does actually |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
23 #exist, but it should never be directly used. Instead, the name serves |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
24 #as a prefix for the index file. For example: |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
25 # |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff
changeset
|
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |