Switch to cmake for build

.gitignore

@@ -1,6 +1,20 @@
 .idea
 .DS_Store
-dist
+build
+
+## CMake
+
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Testing
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
 
 ## C
 

CMakeLists.txt

@@ -0,0 +1,62 @@
+cmake_minimum_required(VERSION 3.12)
+project(
+        Mirage
+        VERSION 1.0.0
+        HOMEPAGE_URL https://github.com/TravisWheelerLab/Mirage
+)
+
+set(CMAKE_C_STANDARD 17)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY build)
+
+add_executable(
+        MultiSeqNW
+
+        src/MultiSeqNW.c
+)
+target_link_libraries(MultiSeqNW m)
+install(TARGETS MultiSeqNW RUNTIME)
+
+add_executable(
+        ExonWeaver
+
+        src/ExonWeaver.c
+        src/BasicBio.c
+)
+target_link_libraries(ExonWeaver m)
+install(TARGETS ExonWeaver RUNTIME)
+
+add_executable(
+        FastMap2
+
+        src/FastMap2.c
+        src/BasicBio.c
+)
+target_link_libraries(FastMap2 m)
+install(TARGETS FastMap2 RUNTIME)
+
+# Custom target for handling dependencies, Perl scripts, and shell scripts. We
+# just move all these files to the build directory to aid in distribution and
+# installation. These will be automatically run by the build.
+
+add_custom_target(
+        build-perl ALL
+        COMMAND cp
+                ${CMAKE_SOURCE_DIR}/src/*.pl
+                ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/
+        COMMAND cp
+                ${CMAKE_SOURCE_DIR}/src/*.pm
+                ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/
+)
+
+add_custom_target(
+        build-shell ALL
+        COMMAND cp
+                ${CMAKE_SOURCE_DIR}/src/*.sh
+                ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/
+)
+
+add_custom_target(
+        build-dependencies ALL
+        COMMAND ./install-dependencies.sh
+        VERBATIM
+)

README.md

@@ -5,8 +5,9 @@ Multiple-sequence IsofoRm Alignment tool Guided by Exon boundaries.
 ## Dependencies
 
 Mirage has no build dependencies beyond the C standard library, but it does have
-several runtime dependencies. These are described below. Executables should
-exist somewhere in the user's `PATH`.
+several runtime dependencies. These are listed below. The build process will
+include suitable versions of each in the build output, so there is no need to
+install them manually.
 
 **blat** - <http://www.kentinformatics.com/index.html>
 
@@ -16,20 +17,21 @@ exist somewhere in the user's `PATH`.
 
 **tblastn** - <https://blast.ncbi.nlm.nih.gov/Blast.cgi>
 
-Appropriate versions of these are included in the `dependencies` directory of
-the repository. The `SETUP.pl` script will build and install them.
-
 ## Build
 
-Building Mirage requires a modern C compiler. Use the `CC` environment variable
-to control the compiler used. Set the `WORK_DIR` environment variable to control
-where the binaries end up, the default is `dist`.
+We use CMake to build Mirage. The following commands will place everything
+needed to run Mirage in the `build/` directory.
 
-Then, building is as simple as running `make`.
+```
+cmake .
+make
+```
 
 ## Installation
 
-Once the build is complete, run `make install` to copy binaries. Use the
-`PREFIX` environment variable to control the install location. The default
-location is `/usr/local`.
+ The software can be "installed" simply by adding the `build/` directory to the
+ `PATH`. Optionally, it can be relocated first (for example, to `/opt/`).
+
+## Usage
 
+TODO