Mercurial > repos > jeremyjliu > region_motif_data_manager
changeset 7:2c918b3a7e8c draft
Uploaded
| author | jeremyjliu |
|---|---|
| date | Thu, 29 Jan 2015 00:00:12 -0500 |
| parents | aa0d1b185070 |
| children | b4c2836d2e4e |
| files | data_manager/data_manager_fetch_motifs.xml tool-data/motif_databases.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 14 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/data_manager_fetch_motifs.xml Wed Jan 28 23:39:30 2015 -0500 +++ b/data_manager/data_manager_fetch_motifs.xml Thu Jan 29 00:00:12 2015 -0500 @@ -15,6 +15,11 @@ <help> **What it does** - UPDATE THIS + Fetches a reference motif database (bgz and tbi files) from Harvard + CBMI source and populates the "motif_databases" data table. + + **TO DO** + Ability to add motif database from local file, as the last step in + a MEME pipeline. </help> </tool>
--- a/tool-data/motif_databases.loc.sample Wed Jan 28 23:39:30 2015 -0500 +++ b/tool-data/motif_databases.loc.sample Thu Jan 29 00:00:12 2015 -0500 @@ -1,7 +1,9 @@ -# -#<value> <display_name> <file_path> +# This file lists the locations and values of all the motif databases bgz +# and tbi files. This file has the format (white space characters are TAB +# characters) +# <value> <display_name> <file_path> # -#So, motif_databases.loc could look something like this: +# So, motif_databases.loc could look something like this: # -#test Test Pouya Subset (hg19) /<path_to_galaxy>/tool-data/motifs/pouya_test_motifs.bed.bgz -# +# test_bgz Test Pouya Subset (hg19) BGZ /<path_to_galaxy>/tool-data/motifs/pouya_test_motifs.bed.bgz +# test_tbi Test Pouya Subset (hg19) TBI /<path_to_galaxy>/tool-data/motifs/pouya_test_motifs.bed.bgz.tbi
--- a/tool_data_table_conf.xml.sample Wed Jan 28 23:39:30 2015 -0500 +++ b/tool_data_table_conf.xml.sample Thu Jan 29 00:00:12 2015 -0500 @@ -1,5 +1,5 @@ <tables> - <!-- Locations of all fasta files under genome directory --> + <!-- Locations of all motif database files under genome directory --> <table name="motif_databases" comment_char="#"> <columns>value, name, path</columns> <file path="tool-data/motif_databases.loc" />