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hal_install_instructions.md

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hal & HALPER installation instructions

Instructions to install hal and HALPER.

These have been tested on Mac OS Monterey 12.6. These instructions should work on Unix systems as well.

  1. Install Homebrew (requires root access/sudo).

Not necessary on Unix systems.

Why: so that you can install wget.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

This will take ~10 minutes. It might seem to get stuck at "Receiving objects" for a few minutes; this is normal, it should finish eventually.

After this script runs, make sure to follow the Next steps to finish the install:

==> Next steps:
- Run these three commands in your terminal to add Homebrew to your PATH:
    echo '# Set PATH, MANPATH, etc., for Homebrew.' >> /Users/<username>/.zprofile
    echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> /Users/<username>/.zprofile
    eval "$(/opt/homebrew/bin/brew shellenv)"
  1. Install wget.

Not necessary on Unix systems.

Why: so that you can download the hdf5 installer.

brew install wget
  1. Download hdf5.
cd ~/Downloads/
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
  1. Clone hal and HALPER repos.

These instructions will assume that you are cloning your repos into a directory called ~/repos/. If you clone your repos into a different path, please update any paths that begin with ~/repos/ accordingly.

mkdir ~/repos
cd ~/repos
git clone https://github.com/ComparativeGenomicsToolkit/hal.git
git clone https://github.com/pfenninglab/halLiftover-postprocessing.git
  1. Install Anaconda (conda).

If conda is already installed on your system, you can skip this step.

# We will download the install file, run it, and then delete it in a temporary directory
cd /tmp

# Please choose the correct installer for your OS and architecture.
# To determine your architecture on Mac, use "About This Mac"
# all installers listed at https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links
# Linux 64-bit: Miniconda3-latest-Linux-x86_64.sh
# macOS Apple M1 64-bit: Miniconda3-latest-MacOSX-arm64.sh
# macOS Intel x86 64-bit: Miniconda3-latest-MacOSX-x86_64.sh

# Replace Miniconda3-latest-Linux-x86_64.sh with the file you chose in the previous step
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

# Run the Miniconda installer. You will need to answer a few questions. The default options should be fine.
bash Miniconda3-latest-Linux-x86_64.sh

# Delete the installer and return to the repos dir
rm Miniconda3-latest-Linux-x86_64.sh
cd ~/repos
  1. Create hal conda env.
conda create -n hal python=3 numpy matplotlib
  1. Configure hdf5.
cd ~/Downloads
tar xzf hdf5-1.10.1.tar.gz
cd hdf5-1.10.1
mkdir ~/repos/hal/hdf5
./configure --enable-cxx --prefix ~/repos/hal/hdf5

The output should look something like this:

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
  1. Build hdf5 inside the hal repo.
cd ~/Downloads/hdf5-1.10.1
make && make install
  1. Clone and build sonLib:
cd ~/repos
git clone https://github.com/ComparativeGenomicsToolkit/sonLib.git
pushd sonLib && make && popd

The output should look something like this:

~/repos/sonLib ~/repos
[...]
cc -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG   -o ../../sonLib/bin/sonLib_fastaCTest tests/fastaCTest.c ../../sonLib/lib/sonLib.a    -lz -lm 
cp sonLib_daemonize.py ./bin/sonLib_daemonize.py
chmod +x ./bin/sonLib_daemonize.py
~/repos

It is ok if you get several warnings.

  1. Set environment variables to build hal.

For these commands, please replace [repos dir] with the full path to your ~/repos directory, e.g. /Users/<username>/repos. If you use ~/repos, it is not guaranteed to work.

You do not need to add these lines to your ~/.bashrc or ~/.bash_profile. These environment settings are for building hal only.

export PATH=[repos dir]/hal/hdf5/bin:${PATH}
export h5prefix=-prefix=[repos dir]/hal/hdf5
  1. Build hal:
cd ~/repos/hal
make
  1. Setup environment variables to run hal and HALPER:

Add the following to your ~/.bash_profile. Please replace [repos dir] with the full path to your ~/repos directory, as in step 9.

# hal and HALPER
export PATH=[repos dir]/hal/bin:${PATH}
export PYTHONPATH=[repos dir]/halLiftover-postprocessing:${PYTHONPATH}
  1. Test that you can run hal:
source ~/.bash_profile
halLiftover

Expected output:

Too few (required positional) arguments

halLiftover v2.2: Map BED or PSL genome interval coordinates between two genomes.

USAGE:
halLiftover [Options] <halFile> <srcGenome> <srcBed> <tgtGenome> <tgtBed>
[...]
  1. Test that you can run HALPER:
conda activate hal
python -m orthologFind

Expected output:

usage: orthologFind.py [-h] [-max_len MAX_LEN] [-max_frac MAX_FRAC]
                       [-protect_dist PROTECT_DIST] [-min_len MIN_LEN]
                       [-min_frac MIN_FRAC] -qFile QFILE -tFile TFILE -sFile
                       SFILE -oFile OFILE [-mult_keepone] [-narrowPeak]
                       [-noHist] [-keepChrPrefix KEEPCHRPREFIX]
orthologFind.py: error: the following arguments are required: -qFile, -tFile, -sFile, -oFile