Mercurial > repos > iuc > rgrnastar
annotate tool-data/rnastar_index2x_versioned.loc.sample @ 31:53255f6eecfc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57d05675396f0b44265fb4dbc8f9f891c6073219
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2024 06:50:18 +0000 |
| parents | 4074fc1940e2 |
| children |
| rev | line source |
|---|---|
|
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
2 #to use a directory of rna-star indexed sequences data files. |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
3 #You will need to create these data files and then create a |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
4 #rnastar_index2x_versioned.loc file similar to this one (store it in this |
|
21
4074fc1940e2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents:
15
diff
changeset
|
5 #directory) that points to the directories in which those files are stored. |
|
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
6 #The rnastar_index2x_versioned.loc file has this format (longer white space |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
7 #characters are TAB characters): |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
8 # |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
9 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
10 # |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
11 #The <with_gene_model> column should be 1 or 0, indicating whether the index |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
12 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
13 #or not. |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
14 # |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
15 #The <version> column indicates the STAR version that introduced the format of |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
16 #the index, i.e., the oldest STAR version that could make use of the index. |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
17 # |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
18 #Note that STAR indices can become quite large. Consequently, it is only |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
19 #advisable to create indices with annotations if it's known ahead of time that |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
20 #(A) the annotations won't be frequently updated and (B) the read lengths used |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
21 #will also rarely vary. If either of these is not the case, it's advisable to |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
22 #create indices without annotations and then specify an annotation file and |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
23 #maximum read length (minus 1) when running STAR. |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
24 # |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
25 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
26 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
diff
changeset
|
27 |