Mercurial > repos > wolma > rnastar_index_builder

annotate tool-data/rnastar_index2_versioned.loc.sample @ 4:039890bdcb62 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 93138516106c74b1ccc70d2d946e6eaa29c7c1a3-dirty
author wolma
date Wed, 16 Oct 2019 03:33:53 -0400
parents 6127cd38980b
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6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
wolma
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1 #This is a sample file distributed with Galaxy that enables tools
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
wolma
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2 #to use a directory of rna-star indexed sequences data files. You will
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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3 #need to create these data files and then create a rnastar_index2.loc
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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4 #file similar to this one (store it in this directory) that points to
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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5 #the directories in which those files are stored. The rnastar_index2.loc
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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6 #file has this format (longer white space characters are TAB characters):
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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7 #
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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8 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version>
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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9 #
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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10 #The <with_gene_model> column should be 1 or 0, indicating whether the index
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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11 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
wolma
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12 #or not.
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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13 #
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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14 #The <version> column indicates the STAR version that introduced the format of
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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15 #the index, i.e., the oldest STAR version that could make use of the index.
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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16 #
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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17 #Note that STAR indices can become quite large. Consequently, it is only
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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18 #advisable to create indices with annotations if it's known ahead of time that
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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19 #(A) the annotations won't be frequently updated and (B) the read lengths used
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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20 #will also rarely vary. If either of these is not the case, it's advisable to
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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21 #create indices without annotations and then specify an annotation file and
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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22 #maximum read length (minus 1) when running STAR.
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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23 #
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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24 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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25 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a
6127cd38980b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty
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