def install_gatk(env):
    """GATK-lite: library for writing efficient analysis tools using next-generation sequencing data
    http://www.broadinstitute.org/gatk/
    """
    # Install main gatk executable
    version = "2.3-9-gdcdccbb"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
          "GenomeAnalysisTKLite-%s%s" % (version, ext)
    _java_install("gatk", version, url, env)
    # Install R gsalib for report and pdf generation
    # XXX Currently have issues with gsalib R installation.
    # Need to make this into a proper R package and re-enable
    if False:
        with quiet():
            have_gsalib = env.safe_run("Rscript -e '\"gsalib\" %in% installed.packages()'")
        if have_gsalib and "FALSE" in have_gsalib:
            # install dependencies for gsalib
            rlib_config = get_config_file(env, "r-libs.yaml").base
            with open(rlib_config) as in_handle:
                config = yaml.load(in_handle)
            config["bioc"] = []
            config["update_packages"] = False
            config["cran"] = ["ggplot2", "gplots"]
            libraries.r_library_installer(config)
            # install gsalib
            git_repo = "git clone --depth 1 https://github.com/broadgsa/gatk.git"
            def install_gsalib(env):
                env.safe_sudo("ant gsalib")
            _get_install(git_repo, env, install_gsalib)

def install_picard(env):
    """Command-line utilities that manipulate BAM files with a Java API.
    http://picard.sourceforge.net/
    """
    version = "1.68"
    url = "http://downloads.sourceforge.net/project/picard/" "picard-tools/%s/picard-tools-%s.zip" % (version, version)
    _java_install("picard", version, url, env)

def install_gatk_protected(env):
    """Installation script for recent versions of GATK. Requires manual download from user.
    http://www.broadinstitute.org/gatk/
    """
    min_version = "2.7-2"
    version = "%s-g6bda569" % min_version
    if shared._symlinked_dir_exists("gatk", version, env, "java"):
        return
    dl_fname = "GenomeAnalysisTK-%s.tar.bz2" % min_version
    print "**** Manual intervention needed"
    print "Recent GATK versions require manual download from the GATK website"
    print "Please retrieve the latest versions from:"
    print "http://www.broadinstitute.org/gatk/download"
    print "and place %s in your home directory" % dl_fname
    userin = raw_input("**** Press <enter> when complete or type 'skip' to avoid the installation: ")
    if userin.find("skip") >= 0:
        return
    with _make_tmp_dir() as work_dir:
        work_fname = os.path.join(work_dir, dl_fname)
        def manual_gatk_download(env):
            try:
                fname = env.safe_run_output("ls $HOME/%s" % dl_fname)
            except:
                raise IOError("Could not find %s in your home directory. Please download and retry" % dl_fname)
            env.safe_put(fname, work_fname)
            return work_fname
        _java_install("gatk", version, work_fname, env, pre_fetch_fn=manual_gatk_download)

def install_gatk(env):
    """GATK: library for writing efficient analysis tools using next-generation sequencing data 
    http://www.broadinstitute.org/gsa/wiki/index.php/Home_Page
    """
    version = "1.6-11-g3b2fab9"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/" "GenomeAnalysisTK-%s%s" % (version, ext)
    _java_install("gatk", version, url, env)

def install_gatk_queue(env):
    """Command-line scripting framework for defining multi-stage genomic analysis pipelines.
    http://www.broadinstitute.org/gsa/wiki/index.php/GATK-Queue
    """
    version = "1.6-11-g3b2fab9"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/Queue/" "Queue-%s%s" % (version, ext)
    _java_install("gatk_queue", version, url, env)

def install_alientrimmer(env):
    """
    Adapter removal tool
    http://www.ncbi.nlm.nih.gov/pubmed/23912058
    """
    version = "0.3.2"
    url = ("ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/"
           "AlienTrimmer_%s.tar.gz" % version)
    _java_install("AlienTrimmer", version, url, env)

def install_gatk(env):
    """GATK-lite: library for writing efficient analysis tools using next-generation sequencing data
    http://www.broadinstitute.org/gatk/
    """
    version = "2.1-1-g426e8e7"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
          "GenomeAnalysisTKLite-%s%s" % (version, ext)
    _java_install("gatk", version, url, env)

def install_bio4j(env):
    """Bio4j graph based database: http://www.bio4j.com/
    """
    version = "0.7"
    url = "https://s3-eu-west-1.amazonaws.com/bio4j-public/releases/" \
          "{v}/bio4j-{v}.zip".format(v=version)
    def _install_fn(env, install_dir):
        targets = ["conf", "doc", "jars", "lib", "README"]
        for x in targets:
            env.safe_sudo("mv {0} {1}".format(x, install_dir))
    _java_install("bio4j", version, url, env, install_fn=_install_fn)

def install_tint_proteomics_scripts(env):
    default_version = "1.19.19"
    version = env.get("tool_version", default_version)
    url = "http://artifactory.msi.umn.edu/simple/ext-release-local/msi/umn/edu/tint-proteomics-scripts/%s/tint-proteomics-scripts-%s.zip" % (version, version)

    def install_fn(env, install_dir):
        env.safe_sudo("mv * '%s'" % install_dir)
        bin_dir = _get_bin_dir(env)
        for script in ["ITraqScanSummarizer", "LTQ-iQuant", "LTQ-iQuant-cli", "MgfFormatter"]:
            env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, script), bin_dir))
        env.safe_sudo("chmod +x '%s'/*" % bin_dir)

    _java_install("tint-proteomics-scripts", version, url, env, install_fn)

def install_mzmine(env):
    default_version = "2.9.1"
    version = env.get("tool_version", default_version)
    point_version = version.rsplit('.', 1)[0]
    url = "http://downloads.sourceforge.net/project/mzmine/mzmine2/%s/MZmine-%s.zip" % (point_version, version)

    def install_fn(env, install_dir):
        env.safe_sudo("mv * '%s'" % install_dir)
        bin_dir = os.path.join(env.get("system_install"), "bin")
        env.safe_sudo("mkdir -p '%s'" % bin_dir)
        env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "startMZmine_Linux.sh"), os.path.join(bin_dir, "MZmine")))

    _java_install("mzmine2", version, url, env, install_fn)

def install_pgdspider(env):
    """PGDSpider format conversion for population genetics programs.
    """
    version = "2.0.1.2"
    url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
        v=version)
    def _install_fn(env, install_dir):
        env.safe_sudo("mv *.jar %s" % install_dir)
        bin_dir = os.path.join(env.system_install, "bin")
        exe_file = "PGDSpider2.sh"
        jar = "PGDSpider2.jar"
        sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir, jar=jar))
        run("chmod a+x {0}".format(exe_file))
        env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
    _java_install("PGDSpider", version, url, env, install_fn=_install_fn)

def install_peptide_shaker(env):
    default_version = "0.19.0"
    version = env.get("tool_version", default_version)
    url = "http://peptide-shaker.googlecode.com/files/PeptideShaker-%s.zip" % version

    def install_fn(env, install_dir):
        _get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/ed9b48a0f01cb975f8a9e6e126965c955bbee848/PeptideShaker")
        _get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/8a17d5fb589984365284e55a98a455c2b47da54f/PeptideShakerCLI")
        env.safe_sudo("mv * '%s'" % install_dir)
        bin_dir = os.path.join(env.get("system_install"), "bin")
        env.safe_sudo("mkdir -p '%s'" % bin_dir)
        env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShaker"), os.path.join(bin_dir, "PeptideShaker")))
        env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShakerCLI"), os.path.join(bin_dir, "PeptideShakerCLI")))

    _java_install("PeptideShaker", version, url, env, install_fn)

def install_mzmine(env):
    default_version = "2.10"
    version = env.get("tool_version", default_version)
    url = "http://downloads.sourceforge.net/project/mzmine/mzmine2/%s/MZmine-%s.zip" % (version, version)

    def install_fn(env, install_dir):
        ## Enhanced MZmine startup script that works when used a symbolic link and tailored for CloudBioLinux.
        _get_gist_script(env, "https://gist.github.com/jmchilton/5474421/raw/15f3b817fa82d5f5e2143ee08bd248efee951d6a/MZmine")
        # Hack for multi-user environment.
        env.safe_sudo("chmod -R o+w conf")
        env.safe_sudo("mv * '%s'" % install_dir)
        bin_dir = os.path.join(env.get("system_install"), "bin")
        env.safe_sudo("mkdir -p '%s'" % bin_dir)
        env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "MZmine"), os.path.join(bin_dir, "MZmine")))

    _java_install("mzmine2", version, url, env, install_fn)

def install_peptide_shaker(env):
    default_version = "0.20.0"
    version = env.get("tool_version", default_version)
    url = "http://peptide-shaker.googlecode.com/files/PeptideShaker-%s.zip" % version

    def install_fn(env, install_dir):
        _get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/f1fe76d6e6eed99a768ed0b9f41c2d0a6a4b24b7/PeptideShaker")
        _get_gist_script(env, "https://gist.github.com/jmchilton/5002161/raw/8a17d5fb589984365284e55a98a455c2b47da54f/PeptideShakerCLI")
        # Hack for multi-user environment.
        env.safe_sudo("chmod -R o+w resources")
        env.safe_sudo("mv * '%s'" % install_dir)
        bin_dir = os.path.join(env.get("system_install"), "bin")
        env.safe_sudo("mkdir -p '%s'" % bin_dir)
        env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShaker"), os.path.join(bin_dir, "PeptideShaker")))
        env.safe_sudo("ln -s '%s' %s" % (os.path.join(install_dir, "PeptideShakerCLI"), os.path.join(bin_dir, "PeptideShakerCLI")))

    _java_install("PeptideShaker", version, url, env, install_fn)

def install_pgdspider(env):
    """PGDSpider format conversion for population genetics programs.
    http://www.cmpg.unibe.ch/software/PGDSpider/
    """
    if os.path.exists(os.path.join(shared._get_bin_dir(env), "PGDSpider2.sh")):
        return
    version = "2.0.2.0"
    url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_{v}.zip".format(
        v=version)
    def _install_fn(env, install_dir):
        env.safe_sudo("mv *.jar %s" % install_dir)
        bin_dir = shared._get_bin_dir(env)
        exe_file = "PGDSpider2.sh"
        jar = "PGDSpider2.jar"
        env.safe_sed(exe_file, jar, "{dir}/{jar}".format(dir=install_dir, jar=jar))
        env.safe_run("chmod a+x {0}".format(exe_file))
        env.safe_sudo("mv {exe} {bin}".format(exe=exe_file, bin=bin_dir))
    _java_install("PGDSpider", version, url, env, install_fn=_install_fn)

def install_gatk(env):
    """GATK-lite: library for writing efficient analysis tools using next-generation sequencing data
    http://www.broadinstitute.org/gatk/
    """
    # Install main gatk executable
    version = "2.3-9-gdcdccbb"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
          "GenomeAnalysisTKLite-%s%s" % (version, ext)
    _java_install("gatk", version, url, env)
    # Install R gsalib for report and pdf generation
    with quiet():
        have_gsalib = run("Rscript -e '\"gsalib\" %in% installed.packages()'")
    if have_gsalib and "FALSE" in have_gsalib:
        git_repo = "git clone --depth 1 git://github.com/broadgsa/gatk.git"
        def install_gsalib(env):
            env.safe_sudo("ant gsalib")
        _get_install(git_repo, env, install_gsalib)

def install_gatk_protected(env):
    """Installation script for recent versions of GATK. Requires manual download from user.
    http://www.broadinstitute.org/gatk/
    """
    min_version = "2.6-5"
    version = "%s-gba531bd" % min_version
    dl_fname = "GenomeAnalysisTK-%s.tar.bz2" % min_version
    with _make_tmp_dir() as work_dir:
        work_fname = os.path.join(work_dir, dl_fname)
        def manual_gatk_download(env):
            print "**** Manual intervention needed"
            print "Recent GATK versions require manual download from the GATK website"
            print "Please retrieve the latest versions from:"
            print "http://www.broadinstitute.org/gatk/download"
            print "and place %s in your home directory" % dl_fname
            raw_input("**** Press <enter> when complete ")
            try:
                fname = env.safe_run_output("ls $HOME/%s" % dl_fname)
            except:
                raise IOError("Could not find %s in your home directory. Please download and retry" % dl_fname)
            env.safe_put(fname, work_fname)
            return work_fname
        _java_install("gatk", version, work_fname, env, pre_fetch_fn=manual_gatk_download)

def install_gatk(env):
    version = "1.4-8-g63b7a70"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/" "GenomeAnalysisTK-%s%s" % (version, ext)
    _java_install("gatk", version, url, env)

def install_picard(env):
    version = "1.60"
    url = "http://downloads.sourceforge.net/project/picard/" "picard-tools/%s/picard-tools-%s.zip" % (version, version)
    _java_install("picard", version, url, env)

def install_gatk_queue(env):
    version = "1.4-8-g63b7a70"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/Queue/" "Queue-%s%s" % (version, ext)
    _java_install("gatk_queue", version, url, env)