MOTHUR

Basic information

  • Installation Date: 05/09/2016
  • License: GNU LESSER GENERAL PUBLIC LICENSE Version 3
  • Installed on: Apolo II

Tested on (Requirements)

  • Dependencies to run PLUMED:
    • zlib y zlib-devel
    • bzip2 y bzip2-devel
    • boost >= 1.58.0

Installation

After solving the previously mentioned dependencies, you can proceed with the installation.

  1. Download the latest version of the software (Source code - tgz) (https://github.com/mothur/mothur/releases):

    cd ~/apps/mothur/src/
wget https://github.com/mothur/mothur/archive/v1.38.1.1.tar.gz
tar -zxvf v1.38.1.1.tar.gz

  2. Makefile configuration, make the following changes:

    cd mothur-1.38.1.1
emacs Makefile
BOOST_LIBRARY_DIR="\"/share/apps/boost-c++-lib/1.59.0/intel-15/lib\""
BOOST_INCLUDE_DIR="\"share/apps/boost-c++-lib/1.59.0/intel-15/include\""
MOTHUR_FILES="\"/home/mgomezzul/apps/mothur/src/mothur-1.38.1.1\""

Module

#%Module1.0####################################################################
##
## module load plumed/2.3.5
##
## /share/apps/modules/plumed/2.3.5
## Written by Mateo Gómez-Zuluaga
##

proc ModulesHelp {} {
    global version modroot
    puts stderr "Sets the environment for using plumed 2.3.5\
        \nin the shared directory /share/apps/plumed/2.3.5\
        \nbuilded with gcc-5.4.0, mpich2-3.2, openblas-0.2.19\
        \ngsl-2.4 and libmatheval-1.11.0."
}

module-whatis "(Name________) plumed"
module-whatis "(Version_____) 2.3.5"
module-whatis "(Compilers___) gcc-5.4.0_mpich2-3.2"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) opeblas-0.2.19, libmatheval-1.11.0, gsl-2.4"

# for Tcl script use only
set         topdir        /share/apps/plumed/2.3.5
set         version       2.3.5
set         sys           x86_64-redhat-linux

conflict plumed

module load mpich2/3.2_gcc-5.4.0
module load openblas/0.2.19_gcc-5.4.0
module load gsl/2.4_gcc-5.4.0
module load libmatheval/1.1.11


prepend-path    PATH                    $topdir/bin

prepend-path    LD_LIBRARY_PATH         $topdir/lib
prepend-path    LIBRARY_PATH            $topdir/lib
prepend-path    LD_RUN_PATH             $topdir/lib
prepend-path    DYLD_LIBRARY_PATH       $topdir/lib

prepend-path    C_INCLUDE_PATH          $topdir/include
prepend-path    CXX_INCLLUDE_PATH       $topdir/include
prepend-path    CPLUS_INCLUDE_PATH      $topdir/include

setenv          PLUMED_KERNEL           $topdir/lib/libplumedKernel.so

Mode of Use

  • The use of Plumed in this case is limited to patching the Gromacs source code for this MD to use Plumed for physical handling.

    module load wrf/3.7.1_gcc-5.4.0

Authors

  • Mateo Gómez Zuluaga