def install_hydra(env):
    version = "0.5.3"
    url = "http://hydra-sv.googlecode.com/files/Hydra.v{0}.tar.gz".format(version)
    def clean_libs(env):
        run("make clean")
    _get_install(url, env, _make_copy("ls -1 bin/* scripts/*"),
                 post_unpack_fn=clean_libs)

def install_samtools(env):
    """SAM Tools provide various utilities for manipulating alignments in the SAM format.
    http://samtools.sourceforge.net/
    """
    version = "0.1.18"
    url = "http://downloads.sourceforge.net/project/samtools/samtools/" "%s/samtools-%s.tar.bz2" % (version, version)
    _get_install(url, env, _make_copy("find -perm -100 -type f"))

def install_bedtools(env):
    """A flexible suite of utilities for comparing genomic features.
    https://code.google.com/p/bedtools/
    """
    version = "github"
    repository = "git clone git://github.com/arq5x/bedtools.git"
    _get_install(repository, env, _make_copy("ls -1 bin/*"))

def install_abyss(env):
    # XXX check for no sparehash on non-ubuntu systems
    version = "1.2.7"
    url = "http://www.bcgsc.ca/downloads/abyss/abyss-%s.tar.gz" % version
    def _remove_werror(env):
        sed("configure", " -Werror", "")
    _get_install(url, env, _configure_make, post_unpack_fn=_remove_werror)

def install_bx_python(env):
    """Tools for manipulating biological data, particularly multiple sequence alignments
    https://bitbucket.org/james_taylor/bx-python/wiki/Home
    """
    version = "bitbucket"
    url = "hg clone http://bitbucket.org/james_taylor/bx-python"
    _get_install(url, env, _python_make)

def install_stacks(env):
    """Stacks: build loci out of a set of short-read sequenced samples.
    http://creskolab.uoregon.edu/stacks/
    """
    version = "0.998"
    url = "http://creskolab.uoregon.edu/stacks/source/" "stacks-{0}.tar.gz".format(version)
    _get_install(url, env, _configure_make)

def install_gnu_parallel(env):
    """GNU parallel: build and execute command lines from standard input in parallel.
    https://savannah.gnu.org/projects/parallel/
    """
    version = "20130122"
    url = "ftp://ftp.gnu.org/gnu/parallel/parallel-%s.tar.bz2" % version
    _get_install(url, env, _configure_make)

def install_transproteomic_pipeline(env):
    """
    """
    ## version should be of form X.X.X-codename
    default_version = "4.6.2-occupy"
    version = env.get("tool_version", default_version)
    version_parts = re.match("(\d\.\d)\.(\d)-(.*)", version)
    major_version = version_parts.group(1)
    revision = version_parts.group(2)
    codename = version_parts.group(3)
    if revision == "0":
        download_rev = ""
    else:
        download_rev = ".%s" % revision
    download_version = ("%s%s" % (major_version, download_rev))
    url_pieces = (major_version, codename, revision, download_version)
    url = 'http://sourceforge.net/projects/sashimi/files/Trans-Proteomic Pipeline (TPP)/TPP v%s (%s) rev %s/TPP-%s.tgz' % url_pieces
    #install_dir = os.path.join(env["system_install"], "bin")

    def _chdir_src(work_cmd):
        def do_work(env):
            with cd("src"):
                append("Makefile.config.incl", "TPP_ROOT=%s/" % env["system_install"])
                append("Makefile.config.incl", "TPP_WEB=/tpp/")
                append("Makefile.config.incl", "XSLT_PROC=/usr/bin/xsltproc")
                append("Makefile.config.incl", "CGI_USERS_DIR=${TPP_ROOT}cgi-bin")
                work_cmd(env)
        return do_work

    def _make(env):
        run("make")
        env.safe_sudo("make install")
    _get_install(url, env, _chdir_src(_make))

def install_varianttools(env):
    version = "1.0.1"
    version_ext = "a"
    url = "http://downloads.sourceforge.net/project/varianttools/" "{ver}/variant_tools-{ver}{ext}.tar.gz".format(
        ver=version, ext=version_ext
    )
    _get_install(url, env, _python_make)

def install_bedtools(env):
    """A flexible suite of utilities for comparing genomic features.
    https://code.google.com/p/bedtools/
    """
    version = "2.17.0"
    url = "https://bedtools.googlecode.com/files/" "BEDTools.v%s.tar.gz" % version
    _get_install(url, env, _make_copy("ls -1 bin/*"))

def _install_boost(env):
    version = "1.49.0"
    url = "http://downloads.sourceforge.net/project/boost/boost" "/%s/boost_%s.tar.bz2" % (
        version,
        version.replace(".", "_"),
    )
    check_version = "_".join(version.split(".")[:2])
    boost_dir = os.path.join(env.system_install, "boost")
    boost_version_file = os.path.join(boost_dir, "include", "boost", "version.hpp")

    def _boost_build(env):
        run("./bootstrap.sh --prefix=%s --with-libraries=thread" % boost_dir)
        run("./b2")
        env.safe_sudo("./b2 install")

    thread_lib = "libboost_thread.so.%s" % version
    final_thread_lib = os.path.join(env.system_install, "lib", thread_lib)
    if (
        not exists(boost_version_file)
        or not contains(boost_version_file, check_version)
        or not exists(final_thread_lib)
    ):
        _get_install(url, env, _boost_build)
        orig_lib = os.path.join(boost_dir, "lib", thread_lib)
        if not exists(final_thread_lib):
            env.safe_sudo("ln -s %s %s" % (orig_lib, final_thread_lib))

def install_mosaik(env):
    """MOSAIK: reference-guided aligner for next-generation sequencing technologies
    http://code.google.com/p/mosaik-aligner/
    """
    version = "2.1.73"
    url = "http://mosaik-aligner.googlecode.com/files/" "MOSAIK-%s-binary.tar" % version
    _get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))

def install_snap(env):
    """Scalable Nucleotide Alignment Program
    http://snap.cs.berkeley.edu/
    """
    version = "0.15"
    url = "http://github.com/downloads/amplab/snap/" "snap-%s-linux.tar.gz" % version
    _get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))

def install_omssa(env):
    print "Installing OMSSA"
    default_version = "2.1.9"
    version = env.get("tool_version", default_version)
    url = 'ftp://ftp.ncbi.nih.gov/pub/lewisg/omssa/%s/omssa-%s.linux.tar.gz' % (version, version)
    env.safe_sudo("mkdir -p '%s'" % env["system_install"])
    _get_install(url, env, _make_copy(find_cmd="find -perm -100 -name 'omssa*'", do_make=False))

def install_macs(env):
    """Model-based Analysis for ChIP-Seq.
    http://liulab.dfci.harvard.edu/MACS/
    """
    version = "1.4.2"
    url = "https://github.com/downloads/taoliu/MACS/" "MACS-%s.tar.gz" % version
    _get_install(url, env, _python_make)

def install_freebayes(env):
    repository = "git clone --recursive git://github.com/ekg/freebayes.git"

    def _fix_library_order(env):
        sed("vcflib/tabixpp/Makefile", "-ltabix", "-ltabix -lz")

    _get_install(repository, env, _make_copy("ls -1 bin/*"), post_unpack_fn=_fix_library_order)

def install_bowtie2(env):
    """bowtie2 short read aligner, with gap support.
    http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
    """
    version = "2.0.0-beta6"
    url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/%s/" "bowtie2-%s-source.zip" % (version, version)
    _get_install(url, env, _make_copy("find -perm -100 -name 'bowtie2*'"))

def install_bowtie(env):
    """The bowtie short read aligner.
    http://bowtie-bio.sourceforge.net/index.shtml
    """
    version = "0.12.7"
    url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie/%s/" "bowtie-%s-src.zip" % (version, version)
    _get_install(url, env, _make_copy("find -perm -100 -name 'bowtie*'"))

def install_protvis(env):
    """ Installs Andrew Brock's proteomics visualize tool.
    https://bitbucket.org/Andrew_Brock/proteomics-visualise/
    """
    _setup_protvis_env(env)
    default_revision = "8cc6af1c492c"
    protvis_home = env["protvis_home"]
    revision = env.get("protvis_revision", default_revision)
    url = _get_bitbucket_download_url(revision, "https://bitbucket.org/Andrew_Brock/proteomics-visualise")
    galaxy_data_dir = env.get('galaxy_data_dir', "/mnt/galaxyData/")
    protvis_converted_files_dir = env.get('protvis_converted_files_dir')

    env.safe_sudo("sudo apt-get -y --force-yes install libxml2-dev libxslt-dev")

    def _make(env):
        env.safe_sudo("rsync -avur --delete-after . %s" % (protvis_home))
        _chown_galaxy(env, protvis_home)
        with cd(protvis_home):
            env.safe_sudo("./setup.sh", user=env.get("galaxy_user", "galaxy"))
    _get_install(url, env, _make)
    _write_to_file('''GALAXY_ROOT = "%s"
PATH_WHITELIST = ["%s/files/", "%s"]
CONVERTED_FILES = "%s"
''' % (env.galaxy_home, galaxy_data_dir, protvis_converted_files_dir, protvis_converted_files_dir), "%s/conf.py" % protvis_home, 0755)
    _setup_protvis_service(env)

def install_samtools(env):
    """SAM Tools provide various utilities for manipulating alignments in the SAM format.
    http://samtools.sourceforge.net/
    """
    default_version = "0.1.19"
    version = env.get("tool_version", default_version)
    if versioncheck.up_to_date(env, "samtools", version, stdout_flag="Version:"):
        env.logger.info("samtools version {0} is up to date; not installing"
            .format(version))
        return
    url = "http://downloads.sourceforge.net/project/samtools/samtools/" \
          "%s/samtools-%s.tar.bz2" % (version, version)
    def _safe_ncurses_make(env):
        """Combine samtools, removing ncurses refs if not present on system.
        """
        with settings(warn_only=True):
            result = env.safe_run("make")
        # no ncurses, fix Makefile and rebuild
        if result.failed:
            env.safe_sed("Makefile", "-D_CURSES_LIB=1", "-D_CURSES_LIB=0")
            env.safe_sed("Makefile", "-lcurses", "# -lcurses")
            env.safe_run("make clean")
            env.safe_run("make")
        install_dir = shared._get_bin_dir(env)
        for fname in env.safe_run_output("ls -1 samtools bcftools/bcftools bcftools/vcfutils.pl misc/wgsim").split("\n"):
            env.safe_sudo("cp -f %s %s" % (fname.rstrip("\r"), install_dir))
    _get_install(url, env, _safe_ncurses_make)