Add new png

htdocs/ucsc/.gitignore

@@ -8,3 +8,4 @@
 !*/*/*.html
 !*/*/*/*.pl
 !*/*/*/*/*.pl
+!*/*/*/*/*.sh

htdocs/ucsc/epdHub/hg19/bigWIG/scripts/make_fantom_tracks.sh

+#!/usr/bin/bash
+
+awk 'BEGIN {FS=OFS="\t"}
+     NR > 1 && $1 !~ /allSamples/ {print $1}
+    ' /export/data/mga/hg19/fantom5/fantom5.txt |
+./make_merge_table.pl > merge_table.txt
+
+mkdir -p sgatmp
+
+# SGA files are written to the "sgatmp" directory
+(./merge_files.pl < merge_table.txt; echo "Merging done." | mailx Philipp.Bucher@sib.swiss) > log 2>&1 &
+wait
+
+NAMES1=$(ls sgatmp/*.sga | sed -n '1,140p' | sed 's%sgatmp/\(.*\).sga$%\1%')
+NAMES2=$(ls sgatmp/*.sga | sed -n '141,280p' | sed 's%sgatmp/\(.*\).sga$%\1%')
+NAMES3=$(ls sgatmp/*.sga | sed -n '281,420p' | sed 's%sgatmp/\(.*\).sga$%\1%')
+NAMES4=$(ls sgatmp/*.sga | sed -n '421,$p' | sed 's%sgatmp/\(.*\).sga$%\1%')
+(for I in $NAMES1; do
+    echo "Processing $I..."
+    ./make_fantom_bw.sh $I sgatmp bigWig
+done) > log1 2>&1 &
+(for I in $NAMES4; do
+    echo "Processing $I..."
+    ./make_fantom_bw.sh $I sgatmp bigWig
+done) > log4 2>&1 &
+(for I in $NAMES3; do
+    echo "Processing $I..."
+    ./make_fantom_bw.sh $I sgatmp bigWig
+done) > log3 2>&1 &
+(for I in $NAMES2; do
+    echo "Processing $I..."
+    ./make_fantom_bw.sh $I sgatmp bigWig
+done) > log2 2>&1 &
+wait
+
+ls bigWig/*.bw | grep -v 'all_fantom' | sed 's/.bw$//' | sed 's/.*\///' | ./write_tracks.pl > trackDb.txt
+