setup.py

#!/usr/bin/env python
"""Description:
Setup script for CRISPResso -- Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data
@status:  beta
@version: $Revision$
@author:  Luca Pinello
@updater:  Tony Reina
@contact: tbreina@bu.edu

python setup.py bdist_wheel

"""

import os
import sys
import re
from setuptools import setup, Extension
import os
import pickle as cp
import glob
import subprocess as sb
import sys
import platform
import shutil
from os.path import expanduser
import urllib

# TO INSTALL CRISPRESSO DEPENDENCIES IN A CUSTOM LOCATION SET THE ENV VARIABLE: CRISPRESSO_DEPENDENCIES_FOLDER
if os.environ.get("CRISPRESSO_DEPENDENCIES_FOLDER"):
    INSTALLATION_PATH = os.environ.get("CRISPRESSO_DEPENDENCIES_FOLDER")
else:
    INSTALLATION_PATH = "%s/CRISPResso_dependencies" % os.environ["HOME"]

BIN_FOLDER = os.path.join(INSTALLATION_PATH, "bin")


def main():
    # if float(sys.version[:3])<2.6 or float(sys.version[:3])>=2.8:
    # 	sys.stdout.write("CRITICAL: Python version must be 2.7!\n")
    # 	sys.exit(1)

    version = re.search(
        '^__version__\s*=\s*"(.*)"', open("CRISPResso/CRISPRessoCORE.py").read(), re.M
    ).group(1)

    # if float(sys.version[:3])<2.6 or float(sys.version[:3])>=2.8:
    # 		sys.stdout.write("ERROR: Python version must be 2.6 or 2.7!\n")
    # 		sys.exit(1)

    setup(
        version="1.1.0",
        name="CRISPResso-1.1",
        include_package_data=True,
        packages=["CRISPResso"],
        package_dir={"CRISPResso": "CRISPResso"},
        package_data={"CRISPResso": ["data/*"]},
        entry_points={
            "console_scripts": [
                "CRISPResso = CRISPResso.CRISPRessoCORE:main",
                "CRISPRessoPooled = CRISPResso.CRISPRessoPooledCORE:main",
                "CRISPRessoWGS = CRISPResso.CRISPRessoWGSCORE:main",
                "CRISPRessoCompare = CRISPResso.CRISPRessoCompareCORE:main",
                "CRISPRessoPooledWGSCompare = CRISPResso.CRISPRessoPooledWGSCompareCORE:main",
                "CRISPRessoCount = CRISPResso.CRISPRessoCountCORE:main",
            ]
        },
        description="Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data",
        author="Luca Pinello / Tony Reina",
        author_email="tbreina@bu.edu",
        url="https://github.com/tonyreina/CRISPResso",
        classifiers=[
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: AGPL License",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: POSIX",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Programming Language :: Python :: 3",
        ],
        install_requires=[
            "numpy",
            "pandas",
            "matplotlib",
            "biopython",
            "seaborn",
        ],
    )


def which(program):
    import os

    def is_exe(fpath):
        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)

    fpath, fname = os.path.split(program)
    if fpath:
        if is_exe(program):
            return program
    else:
        for path in os.environ["PATH"].split(os.pathsep):
            path = path.strip('"')
            exe_file = os.path.join(path, program)
            if is_exe(exe_file):
                return exe_file

    return None


def check_installation(filename, tool_name):
    if os.path.isfile(filename):
        sys.stdout.write("%s was succesfully installed " % tool_name)
        return True
    else:
        sys.stdout.write(
            "Sorry I cannot install %s for you, install manually and try again."
            % tool_name
        )
        return False


def check_flash():
    if which("flash"):
        sys.stdout.write("\nflash is already installed!")
        return True
    else:
        sys.stdout.write(
            "\nCRISPResso requires a recent version FLASh from: http://ccb.jhu.edu/software/FLASH/"
        )
        sys.stdout.write("\nTrying to install it, please be patient!")
        os.chdir("dependencies/")
        sb.call("tar xvzf FLASH-1.2.11.tar.gz", shell=True)
        os.chdir("FLASH-1.2.11")
        sb.call("make", shell=True)
        shutil.copy("flash", BIN_FOLDER)
        os.chdir("..")
        sb.call("rm -Rf FLASH-1.2.11", shell=True)
        os.chdir("..")
        sys.stdout.write("\nFLASh should be installed (please check the output)")

    if not check_installation(os.path.join(BIN_FOLDER, "flash"), "flash"):
        sys.exit(1)

    else:
        return False


def check_needle():
    if which("needle"):
        sys.stdout.write("\nneedle is already installed!")
        return True
    else:
        sys.stdout.write(
            "\nCRISPResso requires a recent version needle from the EMBOSS suite(>=6): http://emboss.sourceforge.net/download/#Stable/"
        )
        sys.stdout.write("\nTrying to download and install it, please be patient!")
        os.chdir("dependencies/")
        sys.stdout.write("\nDownloading EMBOSS source please be patient...")
        urllib.urlretrieve(
            "ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz",
            "EMBOSS-6.5.7.tar.gz",
        )
        sb.call("tar xvzf EMBOSS-6.5.7.tar.gz", shell=True)
        os.chdir("EMBOSS-6.5.7")
        cmd_cfg = "./configure --prefix=%s --without-x" % INSTALLATION_PATH
        sb.call(cmd_cfg, shell=True)
        sb.call("make && make install", shell=True)
        os.chdir("..")
        sb.call("rm -Rf EMBOSS-6.5.7", shell=True)
        sb.call("rm EMBOSS-6.5.7.tar.gz", shell=True)
        os.chdir("..")
        # installa needle
        sys.stdout.write("\nneedle should be installed (please check the output)")

    if not check_installation(os.path.join(BIN_FOLDER, "needle"), "needle"):
        sys.exit(1)
    else:
        return False


def install_dependencies():

    CURRENT_PLATFORM = platform.system().split("_")[0]

    if (
        CURRENT_PLATFORM not in ["Linux", "Darwin"]
        and platform.architecture() != "64bit"
    ):
        sys.stdout.write(
            "Sorry your platform is not supported\n CRISPResso is supported only on 64bit versions of Linux or OSX "
        )
        sys.exit(1)

    if not os.path.exists(INSTALLATION_PATH):
        sys.stdout.write("OK, creating the folder:%s" % INSTALLATION_PATH)
        os.makedirs(INSTALLATION_PATH)
        os.makedirs(BIN_FOLDER)
    else:
        sys.stdout.write(
            "\nI cannot create the folder!\nThe folder %s is not empty!"
            % INSTALLATION_PATH
        )

        try:
            os.makedirs(BIN_FOLDER)
        except:
            pass

    sys.stdout.write("\nCHECKING DEPENDENCIES...")

    flash_already_installed = check_flash()
    needle_already_installed = check_needle()
    dependencies_already_installed = (
        flash_already_installed and needle_already_installed
    )

    if dependencies_already_installed:

        pass

    else:

        # ADD CRISPResso  dependencies to PATH
        home = expanduser("~")
        shell = os.environ["SHELL"].split("/")[-1]

        shell_profile = [
            None,
        ]
        line_to_add = None

        if shell == "bash":
            shell_profiles = [".bash_profile", ".bashrc"]

        elif shell == "sh" or shell == "ksh":
            shell_profiles = [".profile"]

        elif shell == "tcsh":
            shell_profiles = [".tcshrc"]

        elif shell == "csh":
            shell_profiles = [".cshrc"]

        if shell in ["bash", "sh", "ksh"]:
            line_to_add = "export PATH=%s:$PATH" % BIN_FOLDER
        elif shell in ["tcsh", "csh"]:
            line_to_add = "set path = ( %s $path)" % BIN_FOLDER

        for shell_profile in shell_profiles:
            cmd_add_path = "echo '%s'  >> ~/%s" % (line_to_add, shell_profile)
            if (
                not os.path.exists(os.path.join(home, shell_profile))
                or not line_to_add in open(os.path.join(home, shell_profile)).read()
            ):

                if shell_profile is None:
                    sys.stdout.write(
                        "I cannot determine automatically the shell you are using. Please add the folder %s to your PATH manually!"
                        % BIN_FOLDER
                    )
                sys.stdout.write("\nExecuting:%s" % cmd_add_path)
                sb.call(cmd_add_path, shell=True)
                sb.call(line_to_add, shell=True)

        sys.stdout.write(
            "\n\nINSTALLATION COMPLETED, open a NEW terminal and enjoy CRISPResso!"
        )


if __name__ == "__main__":
    main()
    if sys.argv[1] == "install":
        sys.stdout.write("\nPython package installed")
        sys.stdout.write("\n\nChecking dependencies...")
        install_dependencies()
        sys.stdout.write("\nAll done!")