Mercurial > repos > rnateam > blockclust

diff blockclust.xml @ 9:171f6015180f draft

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Uploaded
author rnateam
date Thu, 24 Oct 2013 04:18:01 -0400
parents b77328c96ac9
children e1ee289416dd
line wrap: on
line diff
--- a/blockclust.xml	Tue Oct 22 13:32:07 2013 -0400
+++ b/blockclust.xml	Thu Oct 24 04:18:01 2013 -0400
@@ -6,11 +6,10 @@
         <requirement type="package" version="0.1.19 ">samtools</requirement>
         <requirement type="R-module">ggplot2</requirement>
         <requirement type="R-module">ape</requirement>
+        <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement>
     </requirements>
     <!--<version_command> -version</version_command>-->
     <command>
-        #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH
-
         #if str($mode.operation) == "pre":
             #set $outputdir = $tags_bed.extra_files_path
             BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed;
@@ -22,16 +21,16 @@
             #set $reject_bed=list()
             ## prepare annotations
             #if str($mode.reference) == "hg19":
-                $accept_bed.append("$blockclust_data_path/annotations/hg19/hg19.accept.bed")
-                $reject_bed.append("$blockclust_data_path/annotations/hg19/hg19.reject.bed")
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
             #elif str($mode.reference) == "mm10":
-                $accept_bed.append("$blockclust_data_path/annotations/mm10/mm10.accept.bed")
-                $reject_bed.append("$blockclust_data_path/annotations/mm10/mm10.reject.bed")
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
             #elif str($mode.reference) == "dm3":
-                $accept_bed.append("$blockclust_data_path/annotations/dm3/dm3.accept.bed")
-                $reject_bed.append("$blockclust_data_path/annotations/dm3/dm3.reject.bed")
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
             #end if
-            BlockClustPipeLine.pl -m TEST -f SEQUENCE -c $blockclust_data_path/blockclust.config
+            BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config
             -t $mode.input_bbo
             -a #echo ''.join( $accept_bed )
             -r #echo ''.join( $reject_bed )
@@ -43,7 +42,7 @@
     
         #if str($mode.operation) == "post":
             #set $outputdir = $clusters_bed.extra_files_path
-            BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir -rfam $blockclust_data_path/rfam_map.txt;
+            BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt;
             cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
         #end if
     </command>