-build_and_scp_deb python-gflags
-build_and_scp_deb pyvcf
-build_and_scp_deb google-api-python-client
-build_and_scp_deb httplib2
-build_and_scp_deb ws4py
-build_and_scp_deb virtualenv
+for deppkg in python-gflags pyvcf google-api-python-client oauth2client \
+ pyasn1 pyasn1-modules rsa uritemplate httplib2 ws4py virtualenv \
+ pykka apache-libcloud requests six pyexecjs jsonschema; do
+ build_and_scp_deb "$deppkg"
+done
+
+# cwltool from common-workflow-language. We use this in arv-run-pipeline-instance.
+# We use $WORKSPACE/common-workflow-language as the clean directory from which to build the cwltool package
+if [[ ! -d "$WORKSPACE/common-workflow-language" ]]; then
+ mkdir "$WORKSPACE/common-workflow-language"
+ cd "$WORKSPACE"
+ if [[ "$DEBUG" != 0 ]]; then
+ git clone https://github.com/rabix/common-workflow-language.git common-workflow-language
+ else
+ git clone -q https://github.com/rabix/common-workflow-language.git common-workflow-language
+ fi
+fi
+
+cd "$WORKSPACE/common-workflow-language"
+if [[ "$DEBUG" != 0 ]]; then
+ git checkout master
+ git pull
+else
+ git checkout -q master
+ git pull -q
+fi
+
+cd reference
+handle_python_package
+CWLTOOL_VERSION=`git log --first-parent --max-count=1 --format='format:0.1.%ct.%h'`
+
+# Build cwltool package
+cd $WORKSPACE/debs
+
+build_and_scp_deb $WORKSPACE/common-workflow-language/reference cwltool 'Common Workflow Language Working Group' 'python' "$(awk '($1 == "Version:"){print $2}' $WORKSPACE/common-workflow-language/reference/cwltool.egg-info/PKG-INFO)"