Mercurial > repos > big-tiandm > mirplant2
changeset 53:f5a2e8308836 draft default tip
Uploaded
| author | big-tiandm |
|---|---|
| date | Mon, 08 Dec 2014 01:51:16 -0500 |
| parents | 8b8c356e6db5 |
| children | |
| files | tool-data/rfam_bowtie_indices.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 42 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rfam_bowtie_indices.loc.sample Mon Dec 08 01:51:16 2014 -0500 @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, +#then the bowtie_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +#
--- a/tool_data_table_conf.xml.sample Fri Dec 05 01:28:46 2014 -0500 +++ b/tool_data_table_conf.xml.sample Mon Dec 08 01:51:16 2014 -0500 @@ -5,4 +5,9 @@ <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie_indices.loc" /> </table> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="rfam_bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/rfam_bowtie_indices.loc" /> + </table> </tables>