Mercurial > repos > iuc > data_manager_star_index_builder
comparison tool-data/rnastar_index2x_versioned.loc.sample @ 7:6c6c6df09e64 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
| author | iuc |
|---|---|
| date | Wed, 05 Aug 2020 09:38:12 -0400 |
| parents | |
| children | c520a52b5174 |
comparison
equal
deleted
inserted
replaced
| 6:64deddb6a8ec | 7:6c6c6df09e64 |
|---|---|
| 1 #This is a sample file distributed with Galaxy that enables tools | |
| 2 #to use a directory of rna-star indexed sequences data files. | |
| 3 #You will need to create these data files and then create a | |
| 4 #rnastar_index2x_versioned.loc file similar to this one (store it in this | |
| 5 directory) that points to the directories in which those files are stored. | |
| 6 #The rnastar_index2x_versioned.loc file has this format (longer white space | |
| 7 #characters are TAB characters): | |
| 8 # | |
| 9 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> | |
| 10 # | |
| 11 #The <with_gene_model> column should be 1 or 0, indicating whether the index | |
| 12 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) | |
| 13 #or not. | |
| 14 # | |
| 15 #The <version> column indicates the STAR version that introduced the format of | |
| 16 #the index, i.e., the oldest STAR version that could make use of the index. | |
| 17 # | |
| 18 #Note that STAR indices can become quite large. Consequently, it is only | |
| 19 #advisable to create indices with annotations if it's known ahead of time that | |
| 20 #(A) the annotations won't be frequently updated and (B) the read lengths used | |
| 21 #will also rarely vary. If either of these is not the case, it's advisable to | |
| 22 #create indices without annotations and then specify an annotation file and | |
| 23 #maximum read length (minus 1) when running STAR. | |
| 24 # | |
| 25 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a | |
| 26 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a | |
| 27 |