Mercurial > repos > jjohnson > defuse
changeset 35:a004033614d4
Change for extra_files_path
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 13 Oct 2014 15:42:10 -0500 |
| parents | 3099cec648e7 |
| children | 4353f776dfa3 |
| files | create_reference_dataset.xml defuse.xml |
| diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/create_reference_dataset.xml Tue Oct 15 17:02:23 2013 -0500 +++ b/create_reference_dataset.xml Mon Oct 13 15:42:10 2014 -0500 @@ -149,7 +149,7 @@ ncbi_prefix = $genome.ncbi_prefix # Directory where you want your dataset -dataset_directory = $config_txt.extra_files_path +dataset_directory = $config_txt.dataset.extra_files_path #raw # Input genome and gene models @@ -247,7 +247,7 @@ ## copy config to output cp $defuse_config $config_txt ## make a data_dir and ln -s the input fastq -mkdir -p $config_txt.extra_files_path +mkdir -p $config_txt.dataset.extra_files_path ## create_reference_dataset.pl perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config </configfile>
--- a/defuse.xml Tue Oct 15 17:02:23 2013 -0500 +++ b/defuse.xml Mon Oct 13 15:42:10 2014 -0500 @@ -574,8 +574,8 @@ ln -s $right_pairendreads data_dir/reads_2.fastq ## ln to output_dir in from_work_dir #if $defuse_out.__str__ != 'None': -mkdir -p $defuse_out.extra_files_path -ln -s $defuse_out.extra_files_path output_dir +mkdir -p $defuse_out.dataset.extra_files_path +ln -s $defuse_out.dataset.extra_files_path output_dir #else mkdir -p output_dir #end if @@ -603,7 +603,7 @@ then echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out - pushd $defuse_out.extra_files_path + pushd $defuse_out.dataset.extra_files_path for f in `find -L . -maxdepth 1 -type f`; do fn=`basename ${ds}f`; echo '${lt}li${gt}${lt}a href="'${ds}fn'"${gt}'${ds}fn'${lt}/a${gt}${lt}/li${gt}' ${gt}${gt} $defuse_out; done @@ -616,8 +616,8 @@ #if $fusion_reads.__str__ != 'None': if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ] then - mkdir -p $fusion_reads.extra_files_path - results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path + mkdir -p $fusion_reads.dataset.extra_files_path + results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path fi #end if </configfile>