Compilation and Installation

Procedure

Run the following command to clear the environment:

yum erase `yum list installed |grep boost|awk {'print $1'}` -y

Run the following command to install dependencies:

yum install -y libcurl libcurl-devel openssl openssl-devel zlib-devel bzip2 bzip2-devel xz-devel

Run the following commands to set environment variables:

export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/path/to/boost/include
export LIBRARY_PATH=$LIBRARY_PATH:/path/to/boost/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/boost/lib

Run the following command to decompress the Delly and HTSlib installation packages:
```
cd /path/to/DELLY && tar -zxf v0.8.5.tar.gz && tar -zxf 1.10.2.tar.gz
```
Run the following command to move the HTSlib source code to the src/htslib directory of the Delly source code:
```
mv htslib-1.10.2/* delly-0.8.5/src/htslib/
```

Run the following commands to modify the Makefile file:

cd /path/to/DELLY/delly-0.8.5
sed -i 's/g++/`which g++`/g' Makefile
sed -i 's/\.\/configure/CC=`which gcc` CXX=`which g++` \.\/configure/g' Makefile
sed -i 's/O3/O3 -std=c++11 -march=armv8.2-a -mtune=tsv110/g' Makefile

Run the following commands to perform compilation:
```
CC=`which gcc` CXX=`which g++` make PARALLEL=1 all
```
PARALLEL=1 indicates that the multi-thread mode is enabled. If this parameter is removed, the multi-thread mode is enabled.
Run the following command to load environment variables:
```
export PATH=/path/to/DELLY/delly-0.8.5/src:$PATH
```

Parent topic: Delly 0.8.5 Porting Guide (CentOS 7.6)