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Note: Some of the information on this page is for our legacy systems only. The page is scheduled for an update to make it applicable to Graham.

Software Information

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Foreword

The following installation instructions are based on work done in Ticket 20865 in Oct. 2015 by Paul Preney <preney@sharcnet.ca>.

Building From Source

These instructions assume the following:

  • Tarballs are extracted to ~/sw/build/seqan-1.4.2/ .
  • CMake build is done in ~/sw/build/build-seqan/ .
  • Install is to ~/sw/install/ .

Loading the Modules

You will need to load SHARCNET modules for GCC, Boost (which has a dependency on our OpenMPI to be loaded), and CMake. For example, you might use:

module purge
module load ldwrapper
module load gcc/4.9.2
module load openmpi/gcc-4.9.2/std/1.8.7
module load boost/gcc492-openmpi187/1.59.0
module load cmake/3.3.2

Building SeqAn v1.4.2

  1. Create the ~/sw/build directory and cd into it:
    • mkdir -p ~/sw/build
    • cd ~/sw/build
  2. Untar the previously downloaded seqan*.tar.gz tarball:
    • tar xvzf ~/seqan-src-1.4.2.tar.gz
  3. cd into the seqan directory:
    • cd seqan-1.4.2
  4. Recursively change any and all find_package(Boost) lines in CMakeLists.txt files to be find_package(Boost 1.50.0). This is necessary to ensure that CMake passes the proper linking information to the linker to build various parts of SeqAn.
    • find . -type f -name CMakeLists.txt -print | xargs -n 1 perl -p -i -e 's/find_package\s+\(\s*Boost\s*\)/find_package\(Boost 1.50.0\)/i'
  5. cd to the parent directory:
    • cd ..
  6. Create a build-seqan directory and cd into it:
    • mkdir build-seqan
    • cd build-seqan
  7. Run CMake specifying one's preferred installation directory:
    • cmake -DCMAKE_INSTALL_PREFIX=/home/$USER/sw/install/seqan-1.4.2 ../seqan-1.4.2/
  8. There is a missing README file and docs/html directory which causes issues installing so run:
    • touch ../seqan-1.4.2/extras/apps/seqan_flexbar/README
    • mkdir docs/html
  9. Run:
    • make all
    • make install

Building SeqAn v2.0.0

  1. Create the ~/sw/build directory and cd into it:
    • mkdir -p ~/sw/build
    • cd ~/sw/build
  2. Untar the previously downloaded seqan*.tar.gz tarball:
    • tar xvzf ~/seqan-src-2.0.0.tar.gz
  3. cd into the seqan directory:
    • cd seqan-seqan-v2.0.0
  4. Recursively change any and all find_package(Boost) lines in CMakeLists.txt files to be find_package(Boost 1.50.0). This is necessary to ensure that CMake passes the proper linking information to the linker to build various parts of SeqAn.
    • find . -type f -name CMakeLists.txt -print | xargs -n 1 perl -p -i -e 's/find_package\s+\(\s*Boost\s*\)/find_package\(Boost 1.50.0\)/i'
  5. cd to the parent directory:
    • cd ..
  6. Create a build-seqan directory and cd into it:
    • mkdir build-seqan
    • cd build-seqan
  7. Run CMake specifying one's preferred installation directory:
    • cmake -DCMAKE_INSTALL_PREFIX=/home/$USER/sw/install/seqan-2.0.0 ../seqan-seqan-2.0.0/
  8. Run these makes:
    • make all
    • make install