Mercurial > repos > iuc > rgrnastar
annotate tool-data/rnastar_index2x_versioned.loc.sample @ 16:e132e7d02a3e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b"
| author | iuc |
|---|---|
| date | Fri, 04 Dec 2020 22:05:07 +0000 |
| parents | 5ec75f5dae3c |
| children | 4074fc1940e2 |
| rev | line source |
|---|---|
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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1 #This is a sample file distributed with Galaxy that enables tools |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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2 #to use a directory of rna-star indexed sequences data files. |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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3 #You will need to create these data files and then create a |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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4 #rnastar_index2x_versioned.loc file similar to this one (store it in this |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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5 directory) that points to the directories in which those files are stored. |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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6 #The rnastar_index2x_versioned.loc file has this format (longer white space |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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7 #characters are TAB characters): |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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8 # |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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9 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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10 # |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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11 #The <with_gene_model> column should be 1 or 0, indicating whether the index |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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12 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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13 #or not. |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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14 # |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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15 #The <version> column indicates the STAR version that introduced the format of |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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16 #the index, i.e., the oldest STAR version that could make use of the index. |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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17 # |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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18 #Note that STAR indices can become quite large. Consequently, it is only |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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19 #advisable to create indices with annotations if it's known ahead of time that |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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20 #(A) the annotations won't be frequently updated and (B) the read lengths used |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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21 #will also rarely vary. If either of these is not the case, it's advisable to |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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22 #create indices without annotations and then specify an annotation file and |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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23 #maximum read length (minus 1) when running STAR. |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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24 # |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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25 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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26 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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27 |