d0aad7f66c2fee0fa9366c3b3caf4d761750c055
braney
  Tue Aug 17 10:27:07 2021 -0700
first version of Gencode genes (knownGene version) for mm39

diff --git src/hg/utils/otto/knownGene/buildBioCyc.sh src/hg/utils/otto/knownGene/buildBioCyc.sh
new file mode 100755
index 0000000..98361b8
--- /dev/null
+++ src/hg/utils/otto/knownGene/buildBioCyc.sh
@@ -0,0 +1,17 @@
+#!/bin/sh -ex
+cd $dir
+{
+# need to request download from website
+
+mkdir $dir/bioCyc
+cd $dir/bioCyc
+
+grep -E -v "^#" $bioCycDir/genes.col  > genes.tab
+grep -E -v "^#" $bioCycDir/pathways.col  | awk -F'\t' '{if (140 == NF) { printf "%s\t\t\n", $0; } else { print $0}}' > pathways.tab
+
+kgBioCyc1 -noEnsembl genes.tab pathways.tab $tempDb bioCycPathway.tab bioCycMapDesc.tab
+hgLoadSqlTab $tempDb bioCycPathway ~/kent/src/hg/lib/bioCycPathway.sql ./bioCycPathway.tab
+hgLoadSqlTab $tempDb bioCycMapDesc ~/kent/src/hg/lib/bioCycMapDesc.sql ./bioCycMapDesc.tab
+echo "BuildBioCyc successfully finished"
+} > doBioCyc.log < /dev/null 2>&1
+