Ensure RADAR uses temporary directory for sorting

Avoid out of disk space errors when using global temporary directory. Thanks to Moiz Bootwalla https://groups.google.com/d/msg/biovalidation/I21KymcawwY/SedbQMazDQAJ
chapmanb · Jan 31, 2017 · f0f11b7 · f0f11b7
1 parent 3f27d3e
commit f0f11b7
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/ggd-recipes/GRCh37/RADAR.yaml b/ggd-recipes/GRCh37/RADAR.yaml
@@ -15,9 +15,11 @@ recipe:
         TAB=$'\t'
         mkdir -p editing
         cd editing
+        TMPDIR=`pwd`/tmpsort
+        mkdir -p $TMPDIR
         remap_url=http://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh37_UCSC2ensembl.txt
         wget --no-check-certificate -qO- $remap_url | awk '{if($1!=$2) print "s/^"$1"/"$2"/g"}' > remap.sed
-        wget --no-check-certificate -qO- $url | sed -f remap.sed | awk 'BEGIN{OFS="\t"} {print $1,$2,$2+1,$3,$4,$5,$6,$7,$8,$9,$10,$11}' | sed "s/position${TAB}position/start${TAB}end/" | sed "s/chromosome/#chromosome/" | sort -k1,1 -k2,2n | bgzip > RADAR.bed.gz
+        wget --no-check-certificate -qO- $url | sed -f remap.sed | awk 'BEGIN{OFS="\t"} {print $1,$2,$2+1,$3,$4,$5,$6,$7,$8,$9,$10,$11}' | sed "s/position${TAB}position/start${TAB}end/" | sed "s/chromosome/#chromosome/" | sort -T $TMPDIR -k1,1 -k2,2n | bgzip > RADAR.bed.gz
         tabix RADAR.bed.gz
         rm remap.sed
         cd ../

diff --git a/ggd-recipes/hg19/RADAR.yaml b/ggd-recipes/hg19/RADAR.yaml
@@ -13,7 +13,9 @@ recipe:
         TAB=$'\t'
         mkdir -p editing
         cd editing
-        wget --no-check-certificate -qO- $url | awk 'BEGIN{OFS="\t"} {print $1,$2,$2+1,$3,$4,$5,$6,$7,$8,$9,$10,$11}' | sed "s/position${TAB}position/start${TAB}end/" | sed "s/chromosome/#chromosome/" | sort -k1,1 -k2,2n | bgzip > RADAR.bed.gz
+        TMPDIR=`pwd`/tmpsort
+        mkdir -p $TMPDIR
+        wget --no-check-certificate -qO- $url | awk 'BEGIN{OFS="\t"} {print $1,$2,$2+1,$3,$4,$5,$6,$7,$8,$9,$10,$11}' | sed "s/position${TAB}position/start${TAB}end/" | sed "s/chromosome/#chromosome/" | sort -T $TMPDIR -k1,1 -k2,2n | bgzip > RADAR.bed.gz
         tabix RADAR.bed.gz
         cd ../
     recipe_outfiles: