def install_snpeff(env):
    version = "1_9_5"
    genomes = ["hg37.61", "mm37.61"]
    url = "http://downloads.sourceforge.net/project/snpeff/" \
          "snpEff_v%s_core.zip" % version
    genome_url_base = "http://downloads.sourceforge.net/project/snpeff/"\
                      "databases/v%s/snpEff_v%s_%s.zip"
    install_dir = _symlinked_java_version_dir("snpeff", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                dir_name = _fetch_and_unpack(url)
                with cd(dir_name):
                    env.safe_sudo("mv *.jar %s" % install_dir)
                    run("sed -i.bak -r -e 's/data_dir = \.\/data\//data_dir = %s\/data/' %s" %
                        (install_dir.replace("/", "\/"), "snpEff.config"))
                    run("chmod a+r *.config")
                    env.safe_sudo("mv *.config %s" % install_dir)
                    data_dir = os.path.join(install_dir, "data")
                    env.safe_sudo("mkdir %s" % data_dir)
                    for org in genomes:
                        if not exists(os.path.join(data_dir, org)):
                            gurl = genome_url_base % (version, version, org)
                            _fetch_and_unpack(gurl, need_dir=False)
                            env.safe_sudo("mv data/%s %s" % (org, data_dir))

def install_snpeff(env):
    """Variant annotation and effect prediction tool.
    http://snpeff.sourceforge.net/
    """
    version = "3_3"
    genomes = ["GRCh37.71", "hg19", "GRCm38.71"]
    #genomes_notinstalled = ["NCBIM37.66","athalianaTair10"]
    url = "http://downloads.sourceforge.net/project/snpeff/" \
          "snpEff_v%s_core.zip" % version
    genome_url_base = "http://downloads.sourceforge.net/project/snpeff/"\
                      "databases/v%s/snpEff_v%s_%s.zip"
    install_dir = _symlinked_java_version_dir("snpeff", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                dir_name = _fetch_and_unpack(url)
                with cd(dir_name):
                    env.safe_sudo("mv *.jar %s" % install_dir)
                    env.safe_run("sed -i.bak -r -e 's/^data_dir.*=.*/data_dir = %s\/data/' %s" %
                                 (install_dir.replace("/", "\/"), "snpEff.config"))
                    env.safe_run("chmod a+r *.config")
                    env.safe_sudo("mv *.config %s" % install_dir)
                    data_dir = os.path.join(install_dir, "data")
                    env.safe_sudo("mkdir %s" % data_dir)
                    for org in genomes:
                        if not env.safe_exists(os.path.join(data_dir, org)):
                            gurl = genome_url_base % (version, version, org)
                            _fetch_and_unpack(gurl, need_dir=False)
                            env.safe_sudo("mv data/%s %s" % (org, data_dir))

def _unzip_install(pname, version, url, env, install_fn, dir_name="."):
    install_dir = _symlinked_java_version_dir(pname, version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                _fetch_and_unpack(url, need_dir=False)
                with cd(dir_name):
                    install_fn(env, install_dir)

def install_mutect(env):
    version = "1.1.5"
    url = "https://github.com/broadinstitute/mutect/releases/download/" \
          "%s/muTect-%s-bin.zip" % (version, version)
    install_dir = _symlinked_java_version_dir("mutect", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                env.safe_run("wget --no-check-certificate %s" % url)
                env.safe_run("unzip %s" % os.path.basename(url))
                env.safe_sudo("mv *.jar version.txt LICENSE* %s" % install_dir)

def install_mutect(env):
    version = "1.1.5"
    url = "https://github.com/broadinstitute/mutect/releases/download/" \
          "%s/muTect-%s-bin.zip" % (version, version)
    install_dir = _symlinked_java_version_dir("mutect", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                out_file = shared._remote_fetch(env, url)
                env.safe_run("unzip %s" % out_file)
                env.safe_sudo("mv *.jar version.txt LICENSE* %s" % install_dir)

def install_varscan(env):
    """Variant detection in massively parallel sequencing data
    http://varscan.sourceforge.net/
    """
    version = "2.3.6"
    url = "http://downloads.sourceforge.net/project/varscan/VarScan.v%s.jar" % version
    install_dir = _symlinked_java_version_dir("varscan", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                out_file = shared._remote_fetch(env, url)
                env.safe_sudo("mv %s %s" % (out_file, install_dir))

def install_picard(env):
    version = "1.49"
    url = "http://downloads.sourceforge.net/project/picard/" \
          "picard-tools/%s/picard-tools-%s.zip" % (version, version)
    install_dir = _symlinked_java_version_dir("picard", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                run("wget %s" % (url))
                run("unzip %s" % os.path.basename(url))
                with cd(os.path.splitext(os.path.basename(url))[0]):
                    env.safe_sudo("mv *.jar %s" % install_dir)

def install_bcbio_variation(env):
    """Toolkit to analyze genomic variation data with comparison and ensemble approaches.
    https://github.com/chapmanb/bcbio.variation
    """
    version = "0.0.6"
    url = "https://s3.amazonaws.com/bcbio.variation/" "bcbio.variation-%s-standalone.jar" % version
    install_dir = _symlinked_java_version_dir("bcbio_variation", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                run("wget %s" % url)
                env.safe_sudo("mv *.jar %s" % install_dir)

def install_varscan(env):
    """Variant detection in massively parallel sequencing data
    http://varscan.sourceforge.net/
    """
    version = "2.3.5"
    url = "http://downloads.sourceforge.net/project/varscan/VarScan.v%s.jar" % version
    install_dir = _symlinked_java_version_dir("varscan", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                run("wget --no-check-certificate %s" % url)
                env.safe_sudo("mv *.jar %s" % install_dir)

def install_gatk(env):
    version = "1.1"
    ext = ".tar.bz2"
    url = "ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/"\
          "GenomeAnalysisTK-%s%s" % (version, ext)
    install_dir = _symlinked_java_version_dir("gatk", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                run("wget %s" % (url))
                run("tar -xjvpf %s" % os.path.basename(url))
                with cd(os.path.basename(url).replace(ext, "")):
                    env.safe_sudo("mv *.jar %s" % install_dir)

def install_rnaseqc(env):
    """Quality control metrics for RNA-seq data
    https://www.broadinstitute.org/cancer/cga/rna-seqc
    """
    version = "1.1.7"
    url = ("https://github.com/chapmanb/RNA-SeQC/releases/download/"
           "v%s/RNA-SeQC_v%s.jar" % (version, version))
    install_dir = _symlinked_java_version_dir("RNA-SeQC", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                out_file = shared._remote_fetch(env, url)
                env.safe_sudo("mv %s %s" % (out_file, install_dir))

def install_bcbio_variation(env):
    """Toolkit to analyze genomic variation data with comparison and ensemble approaches.
    https://github.com/chapmanb/bcbio.variation
    """
    version = "0.1.0"
    url = "https://github.com/chapmanb/bcbio.variation/releases/download/" \
          "v%s/bcbio.variation-%s-standalone.jar" % (version, version)
    install_dir = _symlinked_java_version_dir("bcbio_variation", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                jar_file = shared._remote_fetch(env, url)
                env.safe_sudo("mv %s %s" % (jar_file, install_dir))

def install_rnaseqc(env):
    """Quality control metrics for RNA-seq data
    https://www.broadinstitute.org/cancer/cga/rna-seqc
    """
    version = "1.1.7"
    url = ("http://www.broadinstitute.org/cancer/cga/sites/default/files/"
           "data/tools/rnaseqc/RNA-SeQC_v%s.jar" % version)
    install_dir = _symlinked_java_version_dir("RNA-SeQC", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                env.safe_run("wget --no-check-certificate %s" % url)
                env.safe_sudo("mv *.jar %s" % install_dir)

def install_cram(env):
    """Highly efficient and tunable reference-based compression of sequence data.
    http://www.ebi.ac.uk/ena/about/cram_toolkit/
    """
    version = "2.0"
    url = "https://github.com/vadimzalunin/crammer/raw/master/" \
          "cramtools-%s.jar" % version
    install_dir = _symlinked_java_version_dir("cram", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                out_file = shared._remote_fetch(env, url)
                env.safe_sudo("mv %s %s" % (out_file, install_dir))

def install_rnaseqc(env):
    """Quality control metrics for RNA-seq data
    https://www.broadinstitute.org/cancer/cga/rna-seqc
    """
    version = "1.1.7"
    url = ("http://www.broadinstitute.org/cancer/cga/sites/default/files/"
           "data/tools/rnaseqc/RNA-SeQC_v%s.jar" % version)
    install_dir = _symlinked_java_version_dir("RNA-SeQC", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                out_file = shared._remote_fetch(env, url)
                env.safe_sudo("mv %s %s" % (out_file, install_dir))

def install_cram(env):
    """Highly efficient and tunable reference-based compression of sequence data.
    http://www.ebi.ac.uk/ena/about/cram_toolkit/
    """
    version = "2.0"
    url = "https://github.com/vadimzalunin/crammer/raw/master/" \
          "cramtools-%s.jar" % version
    install_dir = _symlinked_java_version_dir("cram", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                run("wget --no-check-certificate %s" % url)
                env.safe_sudo("mv *.jar %s" % install_dir)

def install_fastqc(env):
    version = "0.10.0"
    url = "http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/" "fastqc_v%s.zip" % version
    executable = "fastqc"
    install_dir = _symlinked_java_version_dir("fastqc", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                run("wget %s" % (url))
                run("unzip %s" % os.path.basename(url))
                with cd("FastQC"):
                    env.safe_sudo("chmod a+rwx %s" % executable)
                    env.safe_sudo("mv * %s" % install_dir)
                env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, executable, env.system_install, executable))

def install_shrec(env):
    version = "2.2"
    url = "http://downloads.sourceforge.net/project/shrec-ec/SHREC%%20%s/bin.zip" % version
    install_dir = _symlinked_java_version_dir("shrec", version, env)
    if install_dir:
        shrec_script = "%s/shrec" % install_dir
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                run("wget %s" % (url))
                run("unzip %s" % os.path.basename(url))
                env.safe_sudo("mv *.class %s" % install_dir)
                for line in _shrec_run.split("\n"):
                    if line.strip():
                        append(shrec_script, line, use_sudo=env.use_sudo)
                env.safe_sudo("chmod a+rwx %s" % shrec_script)
                env.safe_sudo("ln -s %s %s/bin/shrec" % (shrec_script, env.system_install))

def install_shrec(env):
    """Shrec is a bioinformatics tool for error correction of HTS read data.
    http://sourceforge.net/projects/shrec-ec/
    """
    version = "2.2"
    url = "http://downloads.sourceforge.net/project/shrec-ec/SHREC%%20%s/bin.zip" % version
    install_dir = _symlinked_java_version_dir("shrec", version, env)
    if install_dir:
        shrec_script = "%s/shrec" % install_dir
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                out_file = shared._remote_fetch(env, url)
                env.safe_run("unzip %s" % out_file)
                env.safe_sudo("mv *.class %s" % install_dir)
                for line in _shrec_run.split("\n"):
                    if line.strip():
                        env.safe_append(shrec_script, line, use_sudo=env.use_sudo)
                env.safe_sudo("chmod a+rwx %s" % shrec_script)
                env.safe_sudo("ln -s %s %s/bin/shrec" % (shrec_script, env.system_install))

def install_fastqc(env):
    """A quality control tool for high throughput sequence data.
    http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    """
    version = "0.10.1"
    url = "http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/" \
          "fastqc_v%s.zip" % version
    executable = "fastqc"
    install_dir = _symlinked_java_version_dir("fastqc", version, env)
    if install_dir:
        with _make_tmp_dir() as work_dir:
            with cd(work_dir):
                out_file = shared._remote_fetch(env, url)
                env.safe_run("unzip %s" % out_file)
                with cd("FastQC"):
                    env.safe_sudo("chmod a+rwx %s" % executable)
                    env.safe_sudo("mv * %s" % install_dir)
                env.safe_sudo("ln -s %s/%s %s/bin/%s" % (install_dir, executable,
                                                         env.system_install, executable))