Mercurial > repos > iuc > rgrnastar
comparison tool-data/rnastar_index2.loc.sample @ 3:318b2a9d54dd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
| author | iuc |
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| date | Fri, 21 Apr 2017 07:58:59 -0400 |
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| 2:ace9f5a2b40f | 3:318b2a9d54dd |
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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> <withGTF> | |
| 9 # | |
| 10 #The <with_gtf> column should be 1 or 0, indicating whether the index was made | |
| 11 #with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, | |
| 12 #respecively. | |
| 13 # | |
| 14 #Note that STAR indices can become quite large. Consequently, it is only | |
| 15 #advisable to create indices with annotations if it's known ahead of time that | |
| 16 #(A) the annotations won't be frequently updated and (B) the read lengths used | |
| 17 #will also rarely vary. If either of these is not the case, it's advisable to | |
| 18 #create indices without annotations and then specify an annotation file and | |
| 19 #maximum read length (minus 1) when running STAR. | |
| 20 # | |
| 21 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 | |
| 22 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 | |
| 23 |