Installation

Supported platform

x86-64 Linux

Tested Linux distributions

If you successfully run SeqMule on other platforms or distributions, please email me.

CentOS release 7.2.1511 (Core) via Docker 1.12.6 (build 3a094bd/1.12.6)
CentOS release 6.6 (Final)
CentOS release 6.5 (Final)
Amazon Linux AMI release 2015.03
Ubuntu 12.04LTS
RHEL5.4

Many thanks to Amet Umerov.

Prerequisites

perl, make, cmake, gcc, g++ (4.4.7 or 4.6.3), curses.h, R, unzip, automake, autoconf, git, gzip, tar, java

Download and Install

Stable releases of SeqMule can be downloaded https://github.com/WGLab/SeqMule/archive/master.zip. You can either directly download the source code or use git clone (see below).

Executables of SeqMule itself are basically some scripts in Perl, you can use them right after unpacking. However, external programs do need installation. SeqMule ignores what you have outside seqmule directory for sake of compatibility.

The following commands will download and install SeqMule for you.

git clone https://github.com/WGLab/SeqMule.git
#if HTTPS is not supported, use git protocol instead
#git clone git://github.com/WGLab/SeqMule.git
cd SeqMule
./Build freshinstall

Alternatively, you can use the following command to just install MISSING programs:

./Build installexes

Due to copyright limitations, you have to download and install GATK (GATKLite does not need to install manually) yourself. Use ./Build gatk to get instructions. If everything goes smooth, you are ready to go. Enjoy!

NOTES

Install prerequisites, on RedHat, CentOS, Fedora

sudo yum install -y gcc gcc-c++ make cmake ncurses-devel ncurses R unzip automake autoconf git-core gzip tar

If you fail to install R on Centos, please run the following command.

rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
sudo yum install R     `

Please check out Amjad's procedure for installation.

Install prerequisites, on Ubuntu

sudo apt-get update
sudo apt-get install -y cmake build-essential gcc g++ ncurses-base ncurses-bin ncurses-term libncurses5 libncurses5-dev r-base unzip automake autoconf git gzip tar default-jre

SOAPsnp installation failure

If you got the following error installing SOAPsnp and msort (a dependency program), please try changing g++ to 4.4.x version.

stdhashc.cc:72:51:   required from here
stdhash.hh:496:81: error: ‘direct_insert_aux’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
^
stdhash.hh:496:81: note: declarations in dependent base ‘__lh3_hash_base_class<unsigned int>’ are not found by unqualified lookup
stdhash.hh:496:81: note: use ‘this->direct_insert_aux’ instead
make: *** [stdhashc.o] Error 1

Putting SeqMule in your path

To use seqmule without typing entire path, please modify your PATH environmental variable. Don't forget to replace absolute_path_to_seqmule by the actual path to seqmule folder If you use bash:

echo 'export PATH=$PATH:absolute_path_to_seqmule/bin' >> ~/.bashrc
source ~/.bashrc

If you use tcsh:

echo 'setenv PATH absolute_path_to_seqmule/bin:$PATH' >> ~/.tcshrc
source ~/.tcshrc

If you don't know which shell (bash/tcsh/csh etc.) you are using, type the following command to figure out

echo $0

SOAPsnp compilation

SOAPsnp can only be compiled by certain versions of g++. We have tested 4.4.7 and 4.6.3. Please use these versions if you encounter compilation issues for SOAPsnp. If you don't plan to use SOAPsnp, you can ignore this issue.