Mercurial > repos > chrisw > monorail_test
changeset 20:f158bf75c44c draft
Uploaded
| author | chrisw |
|---|---|
| date | Wed, 13 Nov 2019 23:55:04 +0000 |
| parents | 20bc706870bd |
| children | 1ec6238425ac |
| files | tool-data/monorail_index.loc.sample tool-data/rnastar_index2.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 25 insertions(+), 25 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/monorail_index.loc.sample Wed Nov 13 23:55:04 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
--- a/tool-data/rnastar_index2.loc.sample Wed Nov 13 21:32:51 2019 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -#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
--- a/tool_data_table_conf.xml.sample Wed Nov 13 21:32:51 2019 +0000 +++ b/tool_data_table_conf.xml.sample Wed Nov 13 23:55:04 2019 +0000 @@ -1,6 +1,6 @@ <tables> - <table name="rnastar_index2" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, path, with-gtf</columns> - <file path="tool-data/rnastar_index2.loc" /> + <table name="monorail_index" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/monorail_index.loc" /> </table> </tables>