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halliftoverInstallationSpecifics.md

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Installation

For the most part, this follows the instructions at ComparativeGenomicsToolkit/hal. Some additional clarifications have been added. These instructions have been tested using hdf5 versions 5-1.10.1 and 5-1.10.4; gcc versions 4.8.5, 4.9.2, and 5.3.0; and HAL Format API version 2.1. These instructions were last updated on April 2, 2020 and are not being maintained.

Downloading HAL Format API

From the parent directory of where you want HAL installed: git clone git://github.com/glennhickey/hal.git

Installing Dependencies

  • Download hdf5: wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz --no-check-certificate

  • Follow instructions for a 'Local install from source into DIR (do not need root password)'

    mkdir [directory with hal]/hal/hdf5

    tar xzf hdf5-1.10.1.tar.gz

    cd hdf5-1.10.1

    ./configure --enable-cxx --prefix [directory with hal]/hal/hdf5

  • output will end with something like this after installation:

      		Features:
  		---------
  		                  Parallel HDF5: no
  		             High-level library: yes
  		                   Threadsafety: no
  		            Default API mapping: v110
  		 With deprecated public symbols: yes
  		         I/O filters (external): deflate(zlib)
  		                            MPE: no
  		                     Direct VFD: no
  		                        dmalloc: no
  		 Packages w/ extra debug output: none
  		                    API tracing: no
  		           Using memory checker: no
  		Memory allocation sanity checks: no
  		            Metadata trace file: no
  		         Function stack tracing: no
  		      Strict file format checks: no
  		   Optimization instrumentation: no

  • Make hdf5 by running:

      make && make install

  Output message will be something like this: 
  		make[2]: Leaving directory `[directory with hal]/hal/hdf5-1.10.1/hl/examples'
  		make[2]: Entering directory `[directory with hal]/hal/hdf5-1.10.1/hl/c++'
  		make[3]: Entering directory `[directory with hal]/hal/hdf5-1.10.1/hl/c++/examples'
  		../../../bin/mkdirs [directory with hal]/hal/hdf5/share/hdf5_examples/hl/c++
  		+ /usr/bin/install -c ./ptExampleFL.cpp [directory with hal]/hal/hdf5/share/hdf5_examples/hl/c++/.
  		+ /usr/bin/install -c run-hlc++-ex.sh [directory with hal]/hal/hdf5/share/hdf5_examples/hl/c++/.
  		make[3]: Leaving directory `[directory with hal]/hal/hdf5-1.10.1/hl/c++/examples'
  		make[2]: Leaving directory `[directory with hal]/hal/hdf5-1.10.1/hl/c++'
  		make[1]: Leaving directory `[directory with hal]/hal/hdf5-1.10.1/hl'

  		[[username]@[node-name] hdf5-1.10.1]$ cd [directory with hal]/hal/hdf5
  		[[username]@[node-name] hdf5]$ ls
  		bin  include  lib  share

Prepare GCC

Use gcc version >= 4.2. If gcc has not been installed, install it. If gcc has been installed as a module on a cluster, run: module load gcc[- gcc version]

sonLib

Add the path to your zlib library to your LD_LIBRARY_PATH.

From the same parent directory where you downloaded HAL:

  git clone https://github.com/ComparativeGenomicsToolkit/sonLib.git
  pushd sonLib && make && popd

NOTE: The version of zlib available in anaconda does not seem to be compatible with sonLib.

Building HAL

  • Update environment variables according to their instructions:

      export PATH=[directory with hal]/hal/hdf5/bin:${PATH}
  
  export h5prefix=-prefix=[directory with hal]/hal/hdf5

  • run the following (takes awhile):

      cd [directory with hal]/hal
  
  make

Running HAL

  • add as given the following to your path:

      export PATH=[directory with hal]/hal/bin:${PATH}

  export PYTHONPATH=[directory with hal]/bin:${PYTHONPATH}

~/.bashrc additions that are useful for running hal:

export PATH=[directory with hal]/hdf5/bin:${PATH}
export h5prefix=-prefix=[directory with hal]/hal/hdf5
export sonLibRootPath=[directory with hal]/sonLib
export PATH=[directory with hal]/hal/bin:${PATH}
export PYTHONPATH=[directory with hal]:${PYTHONPATH}
export PYTHONPATH=[directory with hal]/bin:${PYTHONPATH}