- an implementation of the Message Passing Interface (MPI) standard such as mpich, open-mpi or Intel® MPI Library
- autoconf
- automake 1.13
- make
The MPI compiler but be available in your PATH or set with the CC environment variable.
Custom options can be used with configure such as --prefix to set the destination installation path or CC for the MPI compiler, for example:
./configure CC=mpi_bin_path --prefix=${HOME}/local
This should be only what you need to know about how to use ./configure but if you are interested, more details are available in the README-configure and on the command line ./configure --help.
If automake and autoconf have been installed in custom directories, be sure their are available in your PATH:
export PATH=path_to_automake/automake-1.13/bin:path_to_autoconf/autoconf-2.69/bin:${PATH}
If needed, you can set your PATH according to your configuration directly in your ${HOME}/.bashrc file.
If you have automake 1.15 you can edit in the configure.ac file and change the line AM_INIT_AUTOMAKE([1.13 foreign -Wall]) with AM_INIT_AUTOMAKE([1.15 foreign -Wall]).
git clone https://github.com/bioinfo-pf-curie/mpiBWA.git
cd mpiBWA
# Checkout the branch of the version you want to install, for example:
# git checkout version-1.0
aclocal
autoconf
automake --add-missing
# If not yet in your PATH, you can provide the PATH to `mpicc`
# or your favourite MPI compiler at the configure stage
# using the CC environment variable, for example:
#./configure CC=/usr/lib64/mpich/bin/mpicc
./configure --prefix=${HOME}/local/mpiBWA
make
make install
Download the source code archive of the version you want to install from https://github.com/bioinfo-pf-curie/mpiBWA/releases.
tar xzf mpibwa-mpibwaidx-1.0.tar.gz
cd mpbwa-1.0
# If not yet in your PATH, you can provide the PATH to `mpicc`
# or your favourite MPI compiler at the configure stage
# using the CC environment variable, for example:
#./configure CC=/usr/lib64/mpich/bin/mpicc
./configure --prefix=${HOME}/local/mpiBWA
make
make install
git clone https://github.com/bioinfo-pf-curie/mpiBWA.git
cd mpiBWA
# Checkout the branch of the version you want to package, for example:
# git checkout version-1.0
aclocal
autoconf
automake --add-missing
# If not yet in your PATH, you can provide the PATH to `mpicc`
# or your favourite MPI compiler at the configure stage
# using the CC environment variable, for example:
#./configure CC=/usr/lib64/mpich/bin/mpicc
./configure --prefix=${HOME}/local/mpiBWA
make dist
singularity recipes are provided in the containers folder. At least singularity version 3.2 is required to build the image. We provided two recipes, the first one using CentOS, the second one using ubuntu as it gives the details on how to install the software such that you can reproduce the installation process if you want to install it locally on your computer.
singularity must be available in your PATH.
sudo singularity build mpiBWA mpiBWA-ubuntu.def.
This will output the mpiBWA executable (that is actually a singularity image) that you can launch as any executable.
# Clone the BWA repository
git clone https://github.com/lh3/bwa
# Clone the mpiBWA repository
git clone https://github.com/bioinfo-pf-curie/mpiBWA.git
# Checkout the branch of the version you want to install, for example:
# git checkout version-1.0
# Copy all the .c and .h from bwa repo into the src/ of mpiBWA
cp bwa/*.c bwa/*.h mpiBWA/src/
# Now compile mpiBWA normally
cd mpiBWA
aclocal
autoconf
automake --add-missing
# If not yet in your PATH, you can provide the PATH to `mpicc`
# or your favourite MPI compiler at the configure stage
# using the CC environment variable, for example:
#./configure CC=/usr/lib64/mpich/bin/mpicc
./configure --prefix=${HOME}/local/mpiBWA
make
make install