diff --git a/CellRangerArc.deps.zip b/CellRangerArc.deps.zip index 27f33e5..5fd86c4 100644 Binary files a/CellRangerArc.deps.zip and b/CellRangerArc.deps.zip differ diff --git a/README.md b/README.md index a6ae781..f151852 100644 --- a/README.md +++ b/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. diff --git a/tests/validate.sh b/tests/validate.sh index 2d94e8e..85d141b 100755 --- a/tests/validate.sh +++ b/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 diff --git a/validate.sh b/validate.sh index f2ea02d..5ec5d0a 100755 --- a/validate.sh +++ b/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