Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
annotate tool-data/picard_index.loc.sample @ 39:ad5d85570342 draft default tip
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 |
| children |
| rev | line source |
|---|---|
|
3
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
2 #to use a directory of Picard dict and associated files. You will need |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
3 #to create these data files and then create a picard_index.loc 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:
diff
changeset
|
4 #similar to this one (store it in this directory) that points to |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
5 #the directories in which those files are stored. The picard_index.loc |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
6 #file has this format (longer white space is the TAB character): |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
7 # |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path> |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
9 # |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
10 #So, for example, if you had hg18 indexed and stored in |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
11 #/depot/data2/galaxy/srma/hg18/, |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
12 #then the srma_index.loc entry would look like this: |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
13 # |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
14 #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
15 # |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
16 #and your /depot/data2/galaxy/srma/hg18/ 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:
diff
changeset
|
17 #would contain the following three files: |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
18 #hg18.fa |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
19 #hg18.dict |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
20 #hg18.fa.fai |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
21 # |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
22 #The dictionary file for each reference (ex. hg18.dict) must be |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
23 #created via Picard (http://picard.sourceforge.net). Note that |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
24 #the dict file does not have the .fa extension although the |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
25 #path list in the loc file does include it. |
|
afd01fcbea26
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
rhpvorderman
parents:
diff
changeset
|
26 # |