Mercurial > repos > iuc > rgrnastar
comparison tool-data/rnastar_index2_versioned.loc.sample @ 10:d82339e37e8e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
| author | iuc |
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| date | Thu, 15 Aug 2019 01:54:13 -0400 |
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| 9:0a563fd2f22e | 10:d82339e37e8e |
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| 1 #This is a sample file distributed with Galaxy that enables tools | |
| 2 #to use a directory of rna-star indexed sequences data files. You will | |
| 3 #need to create these data files and then create a rnastar_index2.loc | |
| 4 #file similar to this one (store it in this directory) that points to | |
| 5 #the directories in which those files are stored. The rnastar_index2.loc | |
| 6 #file has this format (longer white space characters are TAB characters): | |
| 7 # | |
| 8 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> | |
| 9 # | |
| 10 #The <with_gene_model> column should be 1 or 0, indicating whether the index | |
| 11 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) | |
| 12 #or not. | |
| 13 # | |
| 14 #The <version> column indicates the STAR version that introduced the format of | |
| 15 #the index, i.e., the oldest STAR version that could make use of the index. | |
| 16 # | |
| 17 #Note that STAR indices can become quite large. Consequently, it is only | |
| 18 #advisable to create indices with annotations if it's known ahead of time that | |
| 19 #(A) the annotations won't be frequently updated and (B) the read lengths used | |
| 20 #will also rarely vary. If either of these is not the case, it's advisable to | |
| 21 #create indices without annotations and then specify an annotation file and | |
| 22 #maximum read length (minus 1) when running STAR. | |
| 23 # | |
| 24 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a | |
| 25 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a | |
| 26 |