Python shared._get_install_local函数代码示例

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_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_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_cortex_var(env):
    """De novo genome assembly and variation analysis from sequence data.
    http://cortexassembler.sourceforge.net/index_cortex_var.html
    """
    version = "1.0.5.20"
    url = "http://downloads.sourceforge.net/project/cortexassembler/cortex_var/" \
          "latest/CORTEX_release_v{0}.tgz".format(version)
    def _cortex_build(env):
        env.safe_sed("Makefile", "\-L/full/path/\S*",
                     "-L{0}/lib -L/usr/lib -L/usr/local/lib".format(env.system_install))
        env.safe_sed("Makefile", "^IDIR_GSL =.*$",
                     "IDIR_GSL={0}/include -I/usr/include -I/usr/local/include".format(env.system_install))
        env.safe_sed("Makefile", "^IDIR_GSL_ALSO =.*$",
                     "IDIR_GSL_ALSO={0}/include/gsl -I/usr/include/gsl -I/usr/local/include/gsl".format(
                         env.system_install))
        with cd("libs/gsl-1.15"):
            env.safe_run("make clean")
        with cd("libs/htslib"):
            env.safe_run("make clean")
            env.safe_run("make")
        for cols in ["1", "2", "3", "4", "5"]:
            for kmer in ["31", "63", "95"]:
                env.safe_run("make MAXK={0} NUM_COLS={1} cortex_var".format(kmer, cols))
        with cd("scripts/analyse_variants/needleman_wunsch"):
            env.safe_sed("Makefile", "string_buffer.c", "string_buffer.c -lz")
            # Fix incompatibilities with gzfile struct in zlib 1.2.6+
            for fix_gz in ["libs/string_buffer/string_buffer.c", "libs/bioinf/bioinf.c",
                           "libs/string_buffer/string_buffer.h", "libs/bioinf/bioinf.h"]:
                env.safe_sed(fix_gz, "gzFile \*", "gzFile ")
                env.safe_sed(fix_gz, "gzFile\*", "gzFile")
            env.safe_run("make")
    _get_install_local(url, env, _cortex_build)

def install_transabyss(env):
    """Analyze ABySS multi-k-assembled shotgun transcriptome data.
    http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
    """
    version = "1.4.4"
    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_stampy(env):
    """Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
    http://www.well.ox.ac.uk/project-stampy
    """
    base_version = "1.0.15"
    revision = "1360"
    version = "{0}r{1}".format(base_version, revision)
    url = "http://www.well.ox.ac.uk/~gerton/software/Stampy/" "stampy-{0}.tgz".format(version)
    _get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(base_version))

def install_trinity(env):
    """Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
    http://trinityrnaseq.github.io/
    """
    version = "2.3.2"
    url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/" \
          "Trinity-v%s.tar.gz" % version
    dir_name = "trinityrnaseq-%s" % version
    _get_install_local(url, env, _make_copy(),
                       dir_name=dir_name)

def install_trinity(env):
    """Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
    http://trinityrnaseq.sourceforge.net/
    """
    version = "r2012-10-05"
    url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
          "trinityrnaseq_%s.tgz" % version
    def _remove_werror(env):
        env.safe_sed("trinity-plugins/jellyfish/Makefile.in", " -Werror", "")
    _get_install_local(url, env, _make_copy(),
                       post_unpack_fn=_remove_werror)

def install_vep(env):
    """Variant Effects Predictor (VEP) from Ensembl.
    http://ensembl.org/info/docs/variation/vep/index.html
    """
    version = "branch-ensembl-74"
    url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/" \
          "variant_effect_predictor.tar.gz?view=tar&root=ensembl" \
          "&pathrev={0}".format(version)
    def _vep_install(env):
        env.safe_run("export FTP_PASSIVE=1 && perl INSTALL.pl -a a")
    _get_install_local(url, env, _vep_install)

def install_vep(env):
    """Variant Effects Predictor (VEP) from Ensembl.
    http://ensembl.org/info/docs/variation/vep/index.html
    """
    version = "branch-ensembl-69"
    url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/" \
          "variant_effect_predictor.tar.gz?view=tar&root=ensembl" \
          "&pathrev={0}".format(version)
    cache_dbs = "24"
    def _vep_install(env):
        env.safe_sed("INSTALL.pl", 'my \$ok = <>', 'my $ok = "y"')
        env.safe_sed("INSTALL.pl", ", <>\)", ', "{0}")'.format(cache_dbs))
        env.safe_run("export FTP_PASSIVE=1 && perl INSTALL.pl")
    _get_install_local(url, env, _vep_install)

def install_vcftools(env):
    """Work with VCF files, such as those generated by the 1000 Genomes Project.
    http://vcftools.sourceforge.net/
    """
    version = "0.1.9"
    url = "http://downloads.sourceforge.net/project/vcftools/vcftools_{v}.tar.gz".format(
        v=version)
    def _vcf_make(env):
        env.safe_sudo("make install PREFIX={dir}".format(dir=env.system_install))
        for perl_module in ["FaSlice.pm", "Vcf.pm", "VcfStats.pm"]:
            env.safe_sudo("cp perl/%s %s/lib/perl5" % (perl_module, env.system_install))
        env.safe_sudo("make clean")
    _get_install(url, env, _vcf_make)
    _get_install_local(url, env, _make_copy())

def install_stampy(env):
    """Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
    http://www.well.ox.ac.uk/project-stampy
    """
    version = "1.0.21"
    # version = base_version
    # revision = "1654"
    # version = "{0}r{1}".format(base_version, revision)
    # url = "http://www.well.ox.ac.uk/bioinformatics/Software/" \
    #      "stampy-%s.tgz" % (version)
    # Ugh -- Stampy now uses a 'Stampy-latest' download target
    url = "http://www.well.ox.ac.uk/bioinformatics/Software/" "Stampy-latest.tgz"

    def _clean_makefile(env):
        sed("makefile", " -Wl", "")

    _get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(version), post_unpack_fn=_clean_makefile)

def install_cortex_var(env):
    """De novo genome assembly and variation analysis from sequence data.
    http://cortexassembler.sourceforge.net/index_cortex_var.html
    """
    version = "1.0.5.11"
    url = "http://downloads.sourceforge.net/project/cortexassembler/cortex_var/" \
          "latest/CORTEX_release_v{0}.tgz".format(version)
    def _cortex_build(env):
        sed("Makefile", "\-L/full/path/\S*", "-L{0}/lib".format(env.system_install))
        sed("Makefile", "^IDIR_GSL=.*$", "IDIR_GSL={0}/include".format(env.system_install))
        sed("Makefile", "^IDIR_GSL_ALSO=.*$", "IDIR_GSL_ALSO={0}/include/gsl".format(env.system_install))
        for cols in ["1", "2", "3", "4", "5"]:
            for kmer in ["31", "63", "95"]:
                run("make MAXK={0} NUM_COLS={1} cortex_var".format(kmer, cols))
        with cd("scripts/analyse_variants/needleman_wunsch-0.3.0"):
            sed("Makefile", "string_buffer.c", "string_buffer.c -lz")
            run("make")
    _get_install_local(url, env, _cortex_build)

def install_trinity(env):
    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_stampy(env):
    base_version = "1.0.15"
    revision = "1360"
    version = "{0}r{1}".format(base_version, revision)
    url = "http://www.well.ox.ac.uk/~gerton/software/Stampy/" "stampy-{0}.tgz".format(version)
    _get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(base_version))