Mercurial > repos > yating-l > ucsc_blat
changeset 14:413230d715d2 draft
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
| author | yating-l |
|---|---|
| date | Fri, 12 May 2017 12:16:12 -0400 |
| parents | 42f1509f3d5a |
| children | c8f6fe46ba91 |
| files | tool-data/fasta_blat_database.loc.sample tool-data/tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 36 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_blat_database.loc.sample Fri May 12 12:16:12 2017 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Fri May 12 12:16:12 2017 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Location of blat database files --> + <table name="fasta_blat_database" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_blat_database.loc" /> + </table> +</tables> \ No newline at end of file