Mercurial > repos > greg > ideas
changeset 6:8c6de654737b draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 10 Aug 2017 12:46:17 -0400 |
| parents | 4b0f64ae5923 |
| children | 00b59afd9fbd |
| files | ideas.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/ideas.xml Thu Aug 10 12:41:43 2017 -0400 +++ b/ideas.xml Thu Aug 10 12:46:17 2017 -0400 @@ -9,7 +9,8 @@ </requirements> <command><![CDATA[ #import os -mkdir -p tmp && +#set tmp_dir = ($os.path.join($os.getcwd(), 'tmp') +mkdir -p $tmp_dir && ############################################## ## Create the config file and prepare the data ############################################## @@ -53,16 +54,16 @@ ## Build the R matrix from the prepMat output ############################################## #set r_matrix_input = None -#for f in $os.listdir('tmp'): +#for f in $os.listdir($tmp_dir): #if f.endswith('.bed.gz'): - #set r_matrix_input = $os.path.join('tmp', f) + #set r_matrix_input = $os.path.join($tmp_dir, $f) #end if #end for #assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty." && Rscript '$__tool_directory__/build_matrix.R' -i $r_matrix_input -o '%s.input' % $f --w 'tmp' +-w $tmp_dir ############################################## ## Run IDEAS on the R matrix ##############################################