def install_lumpy(env):
    """a general probabilistic framework for structural variant discovery
    https://github.com/arq5x/lumpy-sv
    """
    version = "github"
    repository = "git clone git://github.com/arq5x/lumpy-sv.git"
    _get_install(repository, env, _make_copy("ls -1 bin/*"))
    _get_install(url, env, _make_copy("ls -1 bin/* scripts/*"), post_unpack_fn=clean_libs)

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_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_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_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_tabix(env):
    """Generic indexer for TAB-delimited genome position files
    http://samtools.sourceforge.net/tabix.shtml
    """
    version = "0.2.6"
    url = "http://downloads.sourceforge.net/project/samtools/tabix/tabix-%s.tar.bz2" % version
    _get_install(url, env, _make_copy("ls -1 tabix bgzip"))

def install_lumpy(env):
    """a general probabilistic framework for structural variant discovery
    https://github.com/arq5x/lumpy-sv
    """
    version = "fca4706573"
    repository = "git clone https://github.com/arq5x/lumpy-sv.git"
    _get_install(repository, env, _make_copy("ls -1 bin/*"), revision=version)

def install_trinity(env):
    """Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
    http://trinityrnaseq.sourceforge.net/
    """
    version = "r2012-05-18"
    url = "http://downloads.sourceforge.net/project/trinityrnaseq/" "trinityrnaseq_%s.tar.gz" % version
    _get_install_local(url, env, _make_copy())

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_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_echo(env):
    """ECHO: A reference-free short-read error correction algorithm
    http://uc-echo.sourceforge.net/
    """
    version = "1_11"
    url = "http://downloads.sourceforge.net/project/uc-echo/source%20release/" "echo_v{0}.tgz".format(version)
    _get_install_local(url, env, _make_copy())

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_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_transabyss(env):
    version = "1.2.0"
    url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" "releases/%s/trans-ABySS-v%s.tar.gz" % (
        version,
        version,
    )
    _get_install_local(url, env, _make_copy(do_make=False))

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_mosaik(env):
    """MOSAIK: reference-guided aligner for next-generation sequencing technologies
    http://code.google.com/p/mosaik-aligner/
    """
    version = "2.2.3"
    url = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/mosaik-aligner/" \
          "MOSAIK-%s-Linux-x64.tar" % version
    _get_install(url, env, _make_copy("find . -perm -100 -type f", do_make=False))

def install_tophat(env):
    """TopHat is a fast splice junction mapper for RNA-Seq reads
    http://tophat.cbcb.umd.edu/
    """
    default_version = "2.0.7"
    version = env.get("tool_version", default_version)
    url = "http://tophat.cbcb.umd.edu/downloads/" "tophat-%s.Linux_x86_64.tar.gz" % version
    _get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))

def install_grabix(env):
    """a wee tool for random access into BGZF files
    https://github.com/arq5x/grabix
    """
    version = "fda4d2609"
    repository = "git clone https://github.com/arq5x/grabix.git"
    _get_install(repository, env, _make_copy("ls -1 grabix"),
                 revision=version)

def install_mosaik(env):
    repository = "git clone git://github.com/wanpinglee/MOSAIK.git"
    def _chdir_src(work_cmd):
        def do_work(env):
            with cd("src"):
                work_cmd(env)
        return do_work
    _get_install(repository, env, _chdir_src(_make_copy("ls -1 ../bin/*")))