Minor update

README.md

@@ -2,6 +2,10 @@
 
 WDLized Cell Ranger ARC Pipeline
 
+## License
+
+The code is available to everyone under the standard [MIT license](./LICENSE). However, the code internally uses 10x software for certain things, so please make sure that you read and agree to [10x End User Software License](https://www.10xgenomics.com/end-user-software-license-agreement).
+
 ## Setup
 
 The pipeline is a part of SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/). For setup, please refer to [this page](https://github.com/hisplan/scing). All the instructions below is given under the assumption that you have already configured SCING in your environment.

tests/validate.sh

@@ -1,5 +1,11 @@
 #!/usr/bin/env bash
 
+if [ -z $SCING_HOME ]
+then
+    echo "Environment variable 'SCING_HOME' not defined."
+    exit 1
+fi
+
 #hack: get dependency set up
 ln -s ../modules/ modules
 
@@ -10,7 +16,7 @@ do
 
     echo "Validating ${module_name}..."
 
-    java -jar ~/Applications/womtool.jar \
+    java -jar ${SCING_HOME}/devtools/womtool.jar \
         validate \
         test.${module_name}.wdl \
         --inputs test.${module_name}.inputs.json

validate.sh

@@ -1,6 +1,12 @@
 #!/usr/bin/env bash
 
-java -jar ~/Applications/womtool.jar \
+if [ -z $SCING_HOME ]
+then
+    echo "Environment variable 'SCING_HOME' not defined."
+    exit 1
+fi
+
+java -jar ${SCING_HOME}/devtools/womtool.jar \
     validate \
     CellRangerArc.wdl \
     --inputs ./configs/template.inputs.json