This page was last updated on Wednesday, 15-Nov-2017 13:47:04 CST

Installation notes for BLASR

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Installation using pitchfork, blasr version 5.3.f72428d

https://github.com/PacificBiosciences/pitchfork
wiki

1. $ cd /programinstallers
2. $ git clone https://github.com/PacificBiosciences/pitchfork.git
3. $ cd pitchfork
4. remove this symlink to .git/settings.mk which does not exist
   $ rm settings.mk
5. $ sudo mkdir /opt/pacbio && sudo chmod 775 /opt/pacbio
6. $ sudo mkdir /opt/pitchfork && sudo chmod 775 /opt/pitchfork
7. Omit this and just comment out the zlib location in the configuration and it will be built automatically
   Because of the way that the path to zlib is interpreted, we need simulate the expected directory structure
   $ mkdir /tmp/zlib && cd /tmp/zlib && ln -s /usr/lib/x86_64-linux-gnu lib && ln -s /usr/include include && cd -
8. Create the settings file /programinstallers/pitchfork/settings.mk as follows
   $ nano settings.mk

   PREFIX        = /opt/pacbio
   WORKDIR       = /opt/pitchfork
   #HAVE_CCACHE   = ?
   #HAVE_ZLIB     = /tmp/zlib
   HAVE_PYTHON   = /usr/bin/python
   HAVE_OPENBLAS = /usr/lib
   HAVE_BOOST    = /usr/include/boost
   HAVE_CMAKE    = /usr/local/bin/cmake
   #HAVE_HDF5     = /usr/include/hdf5

9. $ make init
10. $ make blasr
11. To run, two methods are given
    $ bash --init-file /opt/pacbio/setup-env.sh
    or
    $ source /opt/pacbio/setup-env.sh
12. $ blasr --version
    blasr   5.3.f72428d

Prerequisites for ninja installation

• cmake ≥ 3.7
  1. $ cmake --version
     cmake version 3.5.1 …
  2. $ cd /programinstallers/
  3. $ wget -N wget http://www.cmake.org/files/v3.9/cmake-3.9.4.tar.gz
  4. $ tar -zxvf cmake-3.9.4.tar.gz
  5. $ cd cmake-3.9.4
  6. $ ./configure
  7. $ make
  8. $ sudo apt-get remove cmake
  9. $ sudo apt-get install checkinstall
  10. $ sudo checkinstall
      …
      Done. The new package has been installed and saved to
      /programinstallers/cmake-3.9.4/cmake_3.9.4-1_amd64.deb
      You can remove it from your system anytime using:
      dpkg -r cmake
  11. Log out and back in, then
      $ cmake --version
      cmake version 3.9.4 …
• ninja ≥ 1.3
  1. $ cd /programinstallers/
  2. $ git clone git://github.com/ninja-build/ninja.git && cd ninja
  3. $ git checkout release
  4. $ ./configure.py --bootstrap
  5. $ sudo cp -puv ninja /usr/local/bin/
• doxygen
  1. $ sudo apt-get install doxygen
• openblas
  1. $ sudo apt-get install libopenblas-dev

Installation using ninja (failed!)

Based on installation instructions at https://github.com/PacificBiosciences/blasr/wiki/Step-by-step-blasr-installation-example

1. $ cd /programinstallers/
2. $ TOP=$(pwd)
3. $ sudo apt-get install libhdf5-dev
4. $ mkdir blasr_install && cd blasr_install
5. $ git clone https://github.com/PacificBiosciences/blasr.git --recursive
6. $ cd blasr
7. $ git submodule update --init --remote
8. $ export HTSLIB_ROOT=/usr/local/bin/samtools1/include
9. $ mkdir build
10. $ cd build
11. $ cmake -GNinja ..
12. Issue 370
    We should firstly cmake pbbam at the path "external/pbbam/build/", and then cmake blasr at the path "build/"
    $ cd external/pbbam/build
13. $ mkdir build
14. $ cd build
15. Fail - I give up and will use blasr on Ceres
16. $ ninja

Prerequisites version "20130703"

Installation version "20130703"

1. $ cd /programinstallers/
2. $ git clone https://github.com/PacificBiosciences/blasr.git
   or to update $ cd blasr ; git pull --rebase origin master && git submodule update --init
3. $ cd blasr
4. $ git submodule update --init --remote
5. $ export HDF5INCLUDEDIR=/usr/local/lib/libhdf5/include
6. $ export HDF5LIBDIR=/usr/local/lib/libhdf5/lib
7. New step 2017-10-21
   $ ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE=/usr/local/lib/libhdf5/include HDF5_LIB=/usr/local/lib/libhdf5/lib
   $ make configure-submodule
8. $ make
9. Error /usr/bin/ld: cannot find -lz (this error only occurred on Fedora 15 system)
   This was needed to allow bwtutils to compile
   $ sudo yum install zlib-static
10. Now I have this error
    ...
    

    H5PL.c:(.text+0x3be): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking

    
    ...
    

    g++ -g -O3 -Wno-div-by-zero -I ../common -I /usr/local/lib/libhdf5/include -fpermissive bin/BuildQualityValueProfile.o -static -o bin/buildQualityValueProfile -lpthread -L/usr/local/lib/libhdf5/lib -lhdf5_cpp -lhdf5 -lz
    /usr/lib/../lib64/libpthread.a(libpthread.o): In function `sem_open':
    (.text+0x68db): warning: the use of `mktemp' is dangerous, better use `mkstemp'
    /usr/local/lib/libhdf5/lib/libhdf5.a(H5PL.o): In function `H5PL_term_interface':
    H5PL.c:(.text+0xa7): undefined reference to `dlclose'
    /usr/local/lib/libhdf5/lib/libhdf5.a(H5PL.o): In function `H5PL_load':
    H5PL.c:(.text+0x2e5): undefined reference to `dlsym'
    H5PL.c:(.text+0x3be): undefined reference to `dlopen'
    H5PL.c:(.text+0x3d7): undefined reference to `dlsym'
    H5PL.c:(.text+0x504): undefined reference to `dlclose'
    H5PL.c:(.text+0x589): undefined reference to `dlerror'
    H5PL.c:(.text+0x753): undefined reference to `dlclose'
    collect2: error: ld returned 1 exit status
    make[1]: *** [bin/buildQualityValueProfile] Error 1

    
    So I modified alignment/Makefile line 142 where BuildQualityValueProfile is compiled by adding -ldl to the end of the line, i.e.
    

            $(CPP) -g $(CPPOPTS) $< $(STATIC) -o $@ -lpthread -L$(HDF5LIBDIR) -l$(HDF5LIBCPP) -l$(HDF5LIB) -lz -ldl

11. Made same additions of -ldl to line 69 for Mask, line 72 for GuidedAlign, line 75 for ExtendAlign
12. Also make same additions to sequtils/Makefile
    line 185 for filterBySubreadAgreement
13. Also make same additions to pbihdfutils/Makefile
    line 72 for CmpH5View, line 75 for DiffAlnInfoGroups, line 78 for PrintMSA, line 81 for PrintVariants, line 84 for CmpH5Information, line 87 for filterHDFPls, line 90 for writeHDFSubset, line 93 for testAdvance, line 96 for PrintHDFPlsSummary, line 99 for ToAfg, line 102 for PulseToFasta, line 108 for LoadPulses, line 114 for extractReadsByTitle, line 117 for computeRefCoverage, line 120 for SamToCmpH5
14. Also make same additions to simulator/Makefile:
    line 75 for StoreQualityByContextFromCmpH5, line 78 for StoreQualityByContext, line 81 for BasH5Simulator
    After all of these changes, blasr compiles.
15. Configure destination for install. Use the same default location as used by PacBio software
    $ sudo mkdir -m 777 /opt/smrtanalysis
16. $ sudo make install ASSEMBLY_HOME=/opt/smrtanalysis/analysis
17. Add this directory to the default path
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/opt/smrtanalysis/analysis/bin"
    ...