Build instructions

Author: pjotrp

Diff for: .gitignore

@@ -1,5 +1,4 @@
 *~
-Makefile
 .Rhistory
 .*swp
 .nfs*
@@ -123,3 +122,7 @@ bin/
 obj/
 include/
 build/
+*.aux
+*.log
+*.synctex.gz
+

Diff for: Makefile

@@ -1,11 +1,13 @@
+# Convenience Makefile invokes cmake. See also the README
+
 VCF_LIB_LOCAL:=$(shell pwd)
 BUILD_DIR:=$(VCF_LIB_LOCAL)/build
 BIN_DIR:=$(VCF_LIB_LOCAL)/bin
 LIB_DIR:=$(VCF_LIB_LOCAL)/lib
 INC_DIR:=$(VCF_LIB_LOCAL)/include
 CMAKE_FLAGS?=
 
-all: 
+all:
 	if [ ! -d $(BUILD_DIR) ]; then mkdir -p $(BUILD_DIR); fi
 	cd $(BUILD_DIR); \
 		cmake $(CMAKE_FLAGS) -DCMAKE_INSTALL_PREFIX=$(VCF_LIB_LOCAL) $(VCF_LIB_LOCAL); \

Diff for: README.md

@@ -35,21 +35,31 @@ conda install -c conda-forge -c bioconda -c defaults vcflib
 brew install brewsci/bio/vcflib
 ```
 
-### source
-```
+### build from source
+
+VCFLIB uses the cmake build system, after a recursive checkout
+of the sources make the files in the ./build directory with:
+
+```sh
 git clone --recursive https://github.com/vcflib/vcflib.git
 cd vcflib
-make -j
+mkdir -p build && cd build
+cmake ..
+make
 ```
-Executables are built into the `./bin` directory in the repository.
-A number of shell, perl, python3, and R scripts already reside there.
-This makes installation easy, as users can add vcflib/bin
-to their path, or copy the contained executables to a directory already in their path.
 
+and to run the tests
+
+```sh
+cd test
+make
+```
+
+Executables are built into the `./build` directory in the repository.
 
 ## using the C++ library
 
-```
+```make
 # Put this in your Makefile
 
 VCFLIB_DIR = /path/to/vcflib