Add tutorial to repo (with symlink to datasets folder),

and use as basis for RMW and RM unit tests

CMakeLists.txt

@@ -143,3 +143,9 @@ add_executable(raremetalworker
 target_include_directories(raremetalworker PRIVATE otherLib/eigen-3.2.0)
 target_link_libraries(raremetalworker libraremetal ${LIB_SAVVY} ${LIB_ZSTD})
 target_compile_definitions(raremetalworker PRIVATE VERSION="${PROJECT_VERSION}")
+
+
+if(BUILD_TESTS)
+    enable_testing()
+    add_subdirectory(tests)
+endif()

README.md

@@ -12,16 +12,20 @@ For more information, please see the [RAREMETAL wiki](http://genome.sph.umich.ed
 ## Installation
 1. Clone this repository
 2. Open a terminal and change to the directory containing this README file.
-3. Enter the following sequence of commands to download dependencies and build the code:
+3. Enter the following sequence of commands to download dependencies and build the code (with tests run automatically during build):
 
 ```bash
 cget install -f requirements.txt
 mkdir build && cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake ..
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DBUILD_TESTS=1 ..
 make
 ```
 
-If you encounter problems while building, see the wiki for more information.
+To run unit tests, ensure that you have run cmake with `-DBUILD_TESTS=1` and built at least once, 
+then run `make` or `ctest --verbose`. 
+
+If you encounter problems while building, see the [wiki FAQ](https://genome.sph.umich.edu/wiki/RAREMETAL_FAQ) for 
+more information.
 
 ## Changes
 Newest version: v.4.14.1 released at 07/10/2017

tests/CMakeLists.txt

@@ -0,0 +1,51 @@
+# Test scenarios:
+#   Two tools, many parameters for each
+#       - Raremetalworker
+#       - Raremetal
+
+
+set(RMW_BIN ${CMAKE_BINARY_DIR}/raremetalworker)
+set(RM_BIN ${CMAKE_BINARY_DIR}/raremetal)
+
+
+#### RAREMETAL TUTORIAL
+# Make test assets (inputs) available in build folder
+file(COPY datasets/raremetal_tutorial
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+
+## Prepare the basic directory structure (in the build folder) for tests to run
+# Each test has a base folder with `inputs`, `expected`, and `outputs`
+# For a first-stage analysis, there may be no special inputs. Outputs will be wiped on every test run.
+set(BASE_TEST_FOLDER ${CMAKE_CURRENT_BINARY_DIR}/test_tut_rmw)
+file(MAKE_DIRECTORY ${BASE_TEST_FOLDER})
+file(MAKE_DIRECTORY ${BASE_TEST_FOLDER}/inputs)
+file(MAKE_DIRECTORY ${BASE_TEST_FOLDER}/expected)
+
+file(COPY raremetalworker/tutorial/expected
+     DESTINATION ${BASE_TEST_FOLDER})
+
+add_test(NAME test_tut_rmw
+         COMMAND ${CMAKE_COMMAND}
+            -DRMW_BIN=${RMW_BIN}
+            -DBASE_TEST_FOLDER=${BASE_TEST_FOLDER}
+            -P ${CMAKE_CURRENT_SOURCE_DIR}/raremetalworker/script.cmake)
+
+
+set(BASE_TEST_FOLDER ${CMAKE_CURRENT_BINARY_DIR}/test_tut_rm)
+file(MAKE_DIRECTORY ${BASE_TEST_FOLDER})
+file(MAKE_DIRECTORY ${BASE_TEST_FOLDER}/inputs)
+file(MAKE_DIRECTORY ${BASE_TEST_FOLDER}/expected)
+
+file(COPY raremetal/tutorial/expected
+        DESTINATION ${BASE_TEST_FOLDER})
+file(COPY raremetal/tutorial/expected
+        DESTINATION ${BASE_TEST_FOLDER})
+file(COPY raremetal/tutorial/inputs
+        DESTINATION ${BASE_TEST_FOLDER})
+
+add_test(NAME test_tut_rm
+        COMMAND ${CMAKE_COMMAND}
+        -DRM_BIN=${RM_BIN}
+        -DBASE_TEST_FOLDER=${BASE_TEST_FOLDER}
+        -P ${CMAKE_CURRENT_SOURCE_DIR}/raremetal/script.cmake)

tests/datasets/raremetal_tutorial/command_to_use

@@ -0,0 +1,5 @@
+$yourpath/raremetalworker  --ped example1.ped --dat example1.dat --vcf example1.vcf.gz --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1 
+
+$youpath/raremetalworker  --ped example2.ped --dat example2.dat --vcf example2.vcf.gz --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY2
+
+$yourpath/raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT --hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --labelHits

tests/datasets/raremetal_tutorial/covfiles

@@ -0,0 +1,2 @@
+STUDY1.QT1.singlevar.cov.txt.gz
+STUDY2.QT1.singlevar.cov.txt.gz

tests/datasets/raremetal_tutorial/example1.dat

@@ -0,0 +1,7 @@
+C AGE
+C AGE2
+C SEX
+T QT4
+T QT3
+T QT2
+T QT1