Building VG on Cent OS 6.6 or 7 and using it

Cent-OS 7

Main task is to get an uptodate gcc on your platform. You can ask a sys admin to do so but building gcc is not to bad

Once you have the new gcc just have it in your path before the existing one. e.g. I have gcc 5.3.0 build and installed into /root/gcc so my path is export PATH="/usr/local/bin:$PATH"

Then you need to make sure VG uses the right glibc/libstc++.so

export LD_PRELOAD="/usr/local/lib64/libstdc++.so"

Make sure you install some basic tools if they are not already installed. You'll need the protobuf and jansson development libraries installed on your server. Additionally, to run the tests, you will need jq, bc and rs.

sudo yum install gcc gcc-c++ glibc-devel make git cmake pkgconfig ncurses-devel bzip2-libs  \
                protobuf-compiler protobuf protobuf-compiler protobuf-devel automake libtool \
                bc rs curl zip redland-devel bison flex gawk \                     

You will need rpm files to install liblzma-dev lzma-dev liblz4-dev libjansson-dev and jq.

# wget http://ftp.tu-chemnitz.de/pub/linux/dag/redhat/el7/en/x86_64/rpmforge/RPMS/lzma-libs-4.32.7-1.el7.rf.x86_64.rpm
# rpm -Uvh lzma-libs-4.32.7-1.el7.rf.x86_64.rpm
# wget http://ftp.tu-chemnitz.de/pub/linux/dag/redhat/el7/en/x86_64/rpmforge/RPMS/lzma-4.32.7-1.el7.rf.x86_64.rpm
# rpm -Uvh lzma-4.32.7-1.el7.rf.x86_64.rpm
# wget http://ftp.tu-chemnitz.de/pub/linux/dag/redhat/el7/en/x86_64/rpmforge/RPMS/lzma-devel-4.32.7-1.el7.rf.x86_64.rpm
# rpm -Uvh lzma-devel-4.32.7-1.el7.rf.x86_64.rpm
# sudo yum install lzma-devel
# sudo yum install lz4
#wget http://springdale.math.ias.edu/data/puias/7/x86_64/os/Addons/Packages/lz4-devel-r131-1.el7.x86_64.rpm
# rpm -Uvh lz4-devel-r131-1.el7.x86_64.rpm
# sudo yum install lz4-devel

For jansson

# wget http://www.digip.org/jansson/releases/jansson-2.7.tar.gz
# tar -zxvf jansson-2.7.tar.gz
# cd jansson-2.7
# ./configure -–prefix=/usr/
# make clean
# make && make install
# ldconfig

For jq

# wget https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64 -O jq
# chmod +x jq
# mv jq /usr/local/bin

Now, obtain the repo and its submodules:

git clone --recursive https://github.com/vgteam/vg.git Then build with make static, and run with ./bin/vg.

Cent-OS 6.6

Warning: this is a major hackatack, using this in production ends badly and quickly...

Cent-OS 6.6 is an old piece of code, but it is what is installed on many a cluster. The first problem is the VG does not compile with the ancient GCC version installed on it.

#Dependencies

GCC

Install a new GCC, but not to new as VG itself is not liked by GCC 5.3.0. i.e. many tests fail on this version.

LibRDF

We need librdf version 2 but that is not available on cent-os 6.6. So build one from source.

Things from yum

yum install ncurses-devel zlib-devel libbsd libbsd-devel samtools jq bzip2-devel

Compiling VG

Use your new gcc, by making sure its first in the path. Make sure the build lib64 is first in your LD_LIBRARY_PATH env. Do the same for raptor2 adding it after GCC libs. Make sure raptor2 is included correctly or just be evil and copy the things into vg/lib and vg/include if you can't be bothered.

XG

XG now depends on DYNAMIC make sure you get it. Also do not build it static. Your base system does not have static pthread or zlib. You will waste hours trying to figure out why libz.so can't be found when its there. Well XG want libz.a.... Hack the makefile to not build static things.

VG

make && make test

Cry for all the failing tests...

Getting rs

rs is a command that is apt-get able on ubuntu/debian but seems to miss a package on fedora/cent-os.

You can get the source at https://www.mirbsd.org/MirOS/dist/mir/rs/ and compile it with

cd rs
gcc -lbsd -Wall -Wextra -Wformat -DUSE_LIBBSD rs.c 

Then your tests should passs