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#!/usr/bin/python3
import os
import shutil
import subprocess
import tempfile
def isArm():
return subprocess.getoutput("uname -p") == "aarch64"
def runCommand(command):
if(os.system(command)):
raise Exception("Error running command: " + command)
def installPackage(package):
runCommand("sudo apt-get install --assume-yes " + package)
def installAptPackages():
packages = [
"git",
"g++",
"make",
"cmake",
"libboost-system-dev",
"libboost-program-options-dev",
"libboost-graph-dev",
"libboost-chrono-dev",
"libpng-dev",
"libblas-dev",
"liblapack-dev",
"gfortran",
"ncbi-blast+",
"graphviz",
"gnuplot",
"python3-dev",
]
runCommand("sudo apt-get install --assume-yes " + " ".join(packages))
# We don't use Ubuntu package libseqan2-dev because
# it does not include the fix for this issue:
# https://github.com/seqan/seqan/issues/2524
# Instead, we clone the GitHub seqan/seqan repository,
# then copy seqan/include/seqan to /usr/include/seqan.
def installSeqan():
# The path where the include files will go.
installPath = "/usr/include/seqan"
# First check that this path does not exist.
if os.path.exists(installPath):
raise Exception("The seqan install path %s already exists. "
"Remove it first (using apt remove if it was installed using apt)." % installPath)
with tempfile.TemporaryDirectory() as temporaryDirectory:
print("Building seqan library using temporary directory", temporaryDirectory)
# Change to the temporary directory.
oldDirectory = os.getcwd()
os.chdir(temporaryDirectory)
# Clone the Github repository.
runCommand("git clone https://github.com/seqan/seqan.git")
# Copy the include files.
shutil.copytree("seqan/include/seqan", installPath)
# Change back to the original directory.
os.chdir(oldDirectory)
def installPybind11():
try:
# This works for Ubuntu 22.04 and older
print("Attempting pybind11 installation using pip3")
installPackage("python3-pip")
runCommand("sudo pip3 install pybind11")
except:
# This works for Ubuntu 24.04 (and newer, presumably).
print("Pybind11 installation using pip3 did not work, installing using apt-get.")
installPackage("python3-pybind11")
def installSpoa():
# The spoa library is available in the stable Ubuntu repository, but
# without the static version.
# So we have to build it from source.
with tempfile.TemporaryDirectory() as temporaryDirectory:
print("Building spoa library using temporary directory", temporaryDirectory)
# Change to the temporary directory.
oldDirectory = os.getcwd()
os.chdir(temporaryDirectory)
# Get the code.
runCommand("sudo apt-get install curl")
runCommand("curl -L https://github.com/rvaser/spoa/archive/refs/tags/4.0.8.tar.gz -o 4.0.8.tar.gz")
runCommand("tar -xvf 4.0.8.tar.gz")
# Set spoa build flags.
if isArm():
spoaBuildFlags="-DCMAKE_BUILD_TYPE=Release -Dspoa_build_tests=OFF"
else:
# The spoa dispatcher feature selects code at run time based on available hardware features,
# which can improve performance.
# However, in spoa v4.0.8 it introduces two additional dependencies:
# - USCiLab/cereal
# - google/cpu_features
# To avoid these additional dependencies, we turn off the dispatcher feature for now.
# We could turn it back on if we see significant performance degradation in this area.
spoaBuildFlags = "-DCMAKE_BUILD_TYPE=Release -Dspoa_optimize_for_portability=ON -Dspoa_build_tests=OFF"
# Build the shared library.
print("\n******** Building spoa shared library")
os.mkdir("build")
os.chdir("build")
runCommand("cmake ../spoa-4.0.8 -DBUILD_SHARED_LIBS=ON " + spoaBuildFlags)
runCommand("make -j all")
runCommand("make install")
# Build the static library.
os.chdir("..")
print("\n******** Building spoa static library")
os.mkdir("build-static")
os.chdir("build-static")
runCommand("cmake ../spoa-4.0.8 -DBUILD_SHARED_LIBS=OFF " + spoaBuildFlags)
runCommand("make -j all")
runCommand("make install")
# Change back to the original directory.
os.chdir(oldDirectory)
installAptPackages()
installSeqan()
installPybind11()
installSpoa()
# Make sure the newly created libraries are immediately visible to the loader.
runCommand("ldconfig")
print("Installation of Shasta prerequisies completed successfully.")
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