Tested Linux distributions
If you successfully run SeqMule on other platforms or distributions, please email me.
- CentOS release 6.6 (Final)
- CentOS release 6.5 (Final)
- Amazon Linux AMI release 2015.03
- Ubuntu 12.04LTS
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:
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!
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
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.
Copyright 2014 USC Wang Lab