Mercurial > repos > chrisw > monorail_test
changeset 25:d780661251a1 draft
Uploaded
author | chrisw |
---|---|
date | Thu, 14 Nov 2019 06:11:06 +0000 |
parents | d16b3dc144d8 |
children | 2b6bfe0e2127 |
files | tool-data/monorail_index.loc.sample tool_data_table_conf.xml.sample |
diffstat | 2 files changed, 28 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/monorail_index.loc.sample Thu Nov 14 06:11:06 2019 +0000 @@ -0,0 +1,22 @@ +#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> <withGTF> +# +#The <with_gtf> column should be 1 or 0, indicating whether the index was made +#with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, +#respecively. +# +#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 +#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 14 06:11:06 2019 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="monorail_index" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/monorail_index.loc" /> + </table> +</tables>