This document is likely somewhat out of date. We're working on that.
Prerequisites
Obtaining the software
Compiling and Installing
Testing the Installation
Example Use
Documentation
In order to install GEMS, you will need to have the following software available on your system:
openssl
git
python
python-dev
(you need the Python header files for your Linux distro, which may not be part of your existing Python package)swig
- Kernel headers (the source code for the Linux kernel, which may not be installed on your system)
qmake
qt4-dev-tools
boost
NOTE - installing some prerequisites may require root
access.
Installation instructions will vary according to the package management software your distro uses. If you use Ubuntu or any other Debian based system, you should be able to use a command like this:
sudo apt-get install openssl git python3 python3-dev swig build-essential qt4-qmake qt4-dev-tools libboost-all-dev
For other Linux distros, please follow the instructions for the package management software included with your system.
Once you have installed the prerequisites, you can install the GEMS software.
NOTE - installing GEMS does not require root
access.
Change to the directory where you will install GEMS, and clone the GEMS repo from Github:
git clone https://github.com/GLYCAM-Web/gems.git
This will create a gems
directory. Change to the gems
directory, and clone the GMML repo from Github:
cd gems/
git clone https://github.com/GLYCAM-Web/gmml.git
To compile the software, make sure you are still in the gems
directory:
pwd
/gems
Set your PYTHON_HOME
environment variable to the location of the Python.h
file for your Python version. For Ubuntu, use something like one of the following:
export PYTHON_HOME=/usr/include/python3.4
or
setenv PYTHON_HOME /usr/include/python3.4
Make sure to use the correct path to your Python version, and the correct version of Python.
For other Linux distros, please follow the instructions to set environment variables specific to your system.
To control the number of processors used during the make
process, set the GEMSMAKEPROCS environment variable.
The default value of 4 will be used if you do not set this variable. For exmaple, a command like one of the
will set the number of processors to be used during make
to 8:
export GEMSMAKEPROCS=8
or
setenv GEMSMAKEPROCS 8
After setting the PYTHON_HOME
, run the makefile in order to compile gmml
and create the gems
interface.
./make.sh
Make sure you are still in the gems
directory, and run the following command to test the installation:
./test_installation.bash
The output will tell you whether the installation was successful or not and will look similar to this:
$ ./test_installation.bash
This test should take less than 10 seconds to run on most modern computers.
This test will compare these files:
updated_pdb.txt -- this is the file the test should generate
test_pdb.txt.save -- this is the file to which it should be identical
Beginning test.
Checking for diffeences between test output and the standard output.
The test passed.
NOTE - the test suite is a Bash shell script. Bash is generally installed by default on most Linux distros. If you try to run the test suite and get any errors, make sure that Bash is installed with the which bash
command. This should return the $PATH
variable for the bash
executable, such as /bin/bash
. If you get nothing back, you will need to either install Bash (which is far outside the scope of this README) or contact your system administrator for assistance.
Make sure you are still in the gems
directory, and run the following command, which is all on one line:
python3 test_installation.py -amino_libs "gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib","gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminoct12.lib" -prep "gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep" -pdb "gmml/example/pdb/Small_to_test.pdb" > testing.log 2&> testing.error
NOTE - make sure to use your version of Python.
There are also sample commands located at the top of the *.py
files. Look in the comments for a line that says # SAMPLE COMMAND
and use the examples found below there.
You can also use the available help for most GEMS functions.
$ python3 test_installation.py --help
Available options:
-amino_libs : amino acid library file(s) (e.g. gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib)
-glycam_libs: glycam library file(s)
-other_libs : other kinds of library files
-prep : prep file(s) (e.g. gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep)
-pdb : pdb file (e.g. gmml/example/pdb/1RVZ_New.pdb)
-cnf : configuration file as an argument. sample file format:
amino_libs
gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/amino12.lib
gmml/dat/CurrentParams/leaprc.ff12SB_2014-04-24/aminont12.lib
glycam_libs
other_libs
prep
gmml/dat/CurrentParams/leaprc_GLYCAM_06j-1_2014-03-14/GLYCAM_06j-1.prep
pdb
gmml/example/pdb/1RVZ_New.pdb
The official documentation for both GEMS and GMML can be found on the main GLYCAM website:
GEMS - http://glycam.org/gems
GMML - http://glycam.org/gmml