Mercurial > repos > iuc > data_manager_star_index_builder
annotate tool-data/rnastar_index2.loc.sample @ 3:50ca9af6db2e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 4888c06bc87c2b236fae379c4220a23aae036cd6
author | iuc |
---|---|
date | Mon, 15 Jan 2018 15:39:25 -0500 |
parents | f537d3e00eb8 |
children |
rev | line source |
---|---|
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
2 #to use a directory of rna-star indexed sequences data files. You will |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
3 #need to create these data files and then create a rnastar_index2.loc |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
4 #file similar to this one (store it in this directory) that points to |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
5 #the directories in which those files are stored. The rnastar_index2.loc |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
6 #file has this format (longer white space characters are TAB characters): |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
7 # |
2
f537d3e00eb8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 811025ef8d9f60f4b02d66f7218127669fb42e0b
iuc
parents:
1
diff
changeset
|
8 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with-gtf> |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
9 # |
2
f537d3e00eb8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 811025ef8d9f60f4b02d66f7218127669fb42e0b
iuc
parents:
1
diff
changeset
|
10 #The <with-gtf> column should be 1 or 0, indicating whether the index was made |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
11 #with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
12 #respecively. |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
13 # |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
14 #Note that STAR indices can become quite large. Consequently, it is only |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
15 #advisable to create indices with annotations if it's known ahead of time that |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
16 #(A) the annotations won't be frequently updated and (B) the read lengths used |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
17 #will also rarely vary. If either of these is not the case, it's advisable to |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
18 #create indices without annotations and then specify an annotation file and |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
19 #maximum read length (minus 1) when running STAR. |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
20 # |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
21 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
22 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
|
23 |