docs: demo fixup

README.md

@@ -143,19 +143,12 @@ All internal paths used in the workflow are relative.
 ### Demo / Build Verification 
 
 To help verify a successful installation, Manta includes a small demo data
-set and test script. After completing the installation steps above, run the
-demo as follows:
+set and test script. After completing the installation steps above, the
+demo can be run as follows:
 
-    ${MANTA_INSTALL_PATH}/bin/runMantaWorkflowDemo.bash
+    bash ${MANTA_INSTALL_PATH}/bin/runMantaWorkflowDemo.bash
 
-The demo data includes aligned reads near the breakends of an HCC1954 somatic translocation
-([COSMIC] id: COST16011). The demo script runs Manta on these regions and verifies that the
-somatic translocation is called as expected. Data, expected results and additional details 
-can be found in the Manta installation demo directory:
-
-    ${MANTA_INSTALL_PATH}/share/demo/manta
-
-[COSMIC]:http://cancer.sanger.ac.uk/cosmic
+See [the demo README](src/demo/README.md) for additional information on the test script and data.
 
 Data analysis and Interpretation
 --------------------------------
@@ -187,7 +180,7 @@ target for the makefile:
 There is no installation for the documentation outside of the build directory,
 the root doxygen page after completing this target will be:
 
-    ${MANTA_BUILD_DIR}/c++/doxygen/html/index.html
+    ${MANTA_BUILD_PATH}/c++/doxygen/html/index.html
 
 #### Improving build time
 

src/demo/CMakeLists.txt

@@ -19,7 +19,7 @@
 include ("${THIS_GLOBALS_CMAKE}")
 
 set (THIS_MANTADEMODIR "${THIS_DEMODIR}/manta")
-install(FILES "README.txt" DESTINATION ${THIS_MANTADEMODIR})
+install(FILES "README.md" DESTINATION ${THIS_MANTADEMODIR})
 install(DIRECTORY "expectedResults" DESTINATION ${THIS_MANTADEMODIR})
 
 install(FILES "runMantaWorkflowDemo.bash"  DESTINATION ${THIS_BINDIR} PERMISSIONS ${THIS_EXECUTABLE_PERMISSIONS})

src/demo/README.md

@@ -0,0 +1,23 @@
+Manta Workflow Demo
+-------------------
+
+This directory contains a small dateset which can be used to verify
+correct installation and demonstrate basic elements of the
+workflow. To run the demonstration, run the demo script found in the
+installation bin directory:
+
+```
+bash ${MANTA_INSTALL_PATH}/bin/runMantaWorkflowDemo.bash
+```
+
+This script creates a `MantaDemoAnalysis` directory under the current
+working directory, runs Manta on a small demo dataset, and compares
+the somatic structural variant output to an expected result.
+
+The demo data contain reads from HCC1954/HCC1954BL mapped in the
+vicinity of somatic translocation breakends corresponding to COSMIC
+variant [COST16011][1]. The demo sequencing data is extracted from
+[TCGA Benchmark 4][2].
+
+[1]:http://grch37-cancer.sanger.ac.uk/cosmic/rearrangement/overview?id=16011
+[2]:https://cghub.ucsc.edu/datasets/benchmark_download.html