Mercurial > repos > chrisw > data_manager_monorail_index_fetcher
changeset 12:b456cb342e9e draft
Uploaded
| author | chrisw |
|---|---|
| date | Wed, 13 Nov 2019 22:17:12 +0000 |
| parents | 11daa95fdc3e |
| children | 32f5ba11ad99 |
| files | data_manager_monorail_index/data_manager_conf.xml data_manager_monorail_index/tool-data/monorail_index.loc.sample data_manager_monorail_index/tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 30 insertions(+), 4 deletions(-) [+] |
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--- a/data_manager_monorail_index/data_manager_conf.xml Wed Nov 13 21:12:37 2019 +0000 +++ b/data_manager_monorail_index/data_manager_conf.xml Wed Nov 13 22:17:12 2019 +0000 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.0" ncoding="utf-8" ?> <data_managers> <data_manager tool_file="data_manager/monorail_index_fetcher.xml" id="monorail_index_fetcher" version="1.0.0"> <data_table name="monorail_index">
--- a/data_manager_monorail_index/tool-data/monorail_index.loc.sample Wed Nov 13 21:12:37 2019 +0000 +++ b/data_manager_monorail_index/tool-data/monorail_index.loc.sample Wed Nov 13 22:17:12 2019 +0000 @@ -0,0 +1,26 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of rna-star indexed sequences data files. You will +#need to create these data files and then create a rnastar_index2.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The rnastar_index2.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> +# +#The <with_gene_model> column should be 1 or 0, indicating whether the index +#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) +#or not. +# +#The <version> column indicates the STAR version that introduced the format of +#the index, i.e., the oldest STAR version that could make use of the index. +# +#Note that STAR indices can become quite large. Consequently, it is only +#advisable to create indices with annotations if it's known ahead of time that +#(A) the annotations won't be frequently updated and (B) the read lengths used +#will also rarely vary. If either of these is not the case, it's advisable to +#create indices without annotations and then specify an annotation file and +#maximum read length (minus 1) when running STAR. +# +#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a +#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a +
--- a/data_manager_monorail_index/tool_data_table_conf.xml.sample Wed Nov 13 21:12:37 2019 +0000 +++ b/data_manager_monorail_index/tool_data_table_conf.xml.sample Wed Nov 13 22:17:12 2019 +0000 @@ -1,8 +1,8 @@ <?xml version="1.0"?> <tables> <!-- Locations of gene annotation data --> - <table name="gene_annotation" comment_char="#"> + <table name="monorail_index" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/gene_annotation.loc" /> + <file path="tool-data/monorail_index.loc" /> </table> -</tables> \ No newline at end of file +</tables>