Streamlining linking to dependencies in build process

README.md

@@ -32,32 +32,32 @@ Note that this script is quite experimental, and your system is different from m
 Installation
 ------------
 
-WiggleTools requires three main dependencies: LibBigWig, HTSLib and GSL (GNU scientific) libraries. 
-
-They themselves require:
-* [zlib](http://www.zlib.net/)
-* [libcurl](https://curl.haxx.se/download.html)
+WiggleTools requires three main dependencies: [LibBigWig](https://github.com/dpryan79/libBigWig), [HTSLib](https://github.com/samtools/htslib) and [GSL (GNU scientific)](https://www.gnu.org/software/gsl/) libraries. They themselves require [zlib](http://www.zlib.net/) and [libcurl](https://curl.haxx.se/download.html).
 
 **Installing LibBigWig**
 
 ```
 git clone https://github.com/dpryan79/libBigWig.git
 cd libBigWig
-make
-setenv LIBBIGWIG_SRC $PWD
-# or, if you use bash...
-export LIBIGWIG_SRC=$PWD
+make install
 ```
 
 **Installing the htslib library**
 
 ```
 git clone https://github.com/samtools/htslib.git
 cd htslib 
+make install
+```
+
+**Installing the GSL library**
+```
+wget ftp://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz 
+tar -xvzpf gsl-latest.tar.gz
+cd gsl*
+./configure
 make
-setenv HTSLIB_SRC $PWD
-# or, if you use bash...
-export HTSLIB_SRC=$PWD
+make install
 ```
 
 Obtaining WiggleTools

src/Makefile

@@ -1,9 +1,9 @@
 CFLAGS=-g -Wall -O3 -std=gnu99
 LIBDIR=../lib
 BINDIR=../bin
-INC=-I${HTSLIB_SRC}/htslib -I${LIBBIGWIG_SRC}
-LIB_PATHS=-L${LIBBIGWIG_SRC} -L${HTSLIB_SRC} -L${LIBDIR}
-LIBS= -lwiggletools ${LIBBIGWIG_SRC}/libBigWig.a -lcurl -lhts -lgsl  -lgslcblas -lz -lpthread -lm
+INC=
+LIB_PATHS=-L${LIBDIR}
+LIBS= -lwiggletools -lBigWig -lcurl -lhts -lgsl  -lgslcblas -lz -lpthread -lm
 OPTS=-D_PBGZF_USE
 
 default: lib bin

src/bamReader.c

@@ -13,8 +13,8 @@
 // limitations under the License.
 
 #include <string.h>
-#include "sam.h"
-#include "hts.h"
+#include "htslib/sam.h"
+#include "htslib/hts.h"
 #include "wiggleIterator.h"
 #include "bufferedReader.h"
 #include "fib.h"

src/bcfReader.c

@@ -14,7 +14,7 @@
 
 #include <string.h>
 #include <zlib.h>
-#include "vcf.h"
+#include "htslib/vcf.h"
 #include "wiggleIterator.h"
 #include "bufferedReader.h"