• 设为首页
  • 点击收藏
  • 手机版
    手机扫一扫访问
    迪恩网络手机版
  • 关注官方公众号
    微信扫一扫关注
    迪恩网络公众号
登陆 注册
描述文字

Python shared._get_install_local函数代码示例

原作者: [db:作者] 来自: [db:来源] 收藏 邀请

本文整理汇总了Python中shared._get_install_local函数的典型用法代码示例。如果您正苦于以下问题：Python _get_install_local函数的具体用法？Python _get_install_local怎么用？Python _get_install_local使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。



在下文中一共展示了_get_install_local函数的17个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。

示例1: install_echo

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())
开发者ID:hmenager，项目名称:cloudbiolinux，代码行数:7，代码来源:bio_nextgen.py


示例2: install_trinity

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())
开发者ID:hmenager，项目名称:cloudbiolinux，代码行数:7，代码来源:bio_nextgen.py


示例3: install_transabyss

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))
开发者ID:hjanime，项目名称:cloudbiolinux，代码行数:7，代码来源:bio_nextgen.py


示例4: install_cortex_var

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)
开发者ID:ccp0101，项目名称:cloudbiolinux，代码行数:32，代码来源:bio_nextgen.py


示例5: install_transabyss

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))
开发者ID:ccp0101，项目名称:cloudbiolinux，代码行数:8，代码来源:bio_nextgen.py


示例6: install_stampy

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))
开发者ID:hmenager，项目名称:cloudbiolinux，代码行数:9，代码来源:bio_nextgen.py


示例7: install_trinity

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)
开发者ID:chapmanb，项目名称:cloudbiolinux，代码行数:10，代码来源:bio_nextgen.py


示例8: install_trinity

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)
开发者ID:ccp0101，项目名称:cloudbiolinux，代码行数:11，代码来源:bio_nextgen.py


示例9: install_vep

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)
开发者ID:tistaharahap，项目名称:cloudbiolinux，代码行数:11，代码来源:bio_nextgen.py


示例10: install_vep

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)
开发者ID:ccp0101，项目名称:cloudbiolinux，代码行数:14，代码来源:bio_nextgen.py


示例11: install_vcftools

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())
开发者ID:logston，项目名称:cloudbiolinux，代码行数:14，代码来源:bio_nextgen.py


示例12: install_stampy

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)
开发者ID:nldowell，项目名称:cloudbiolinux，代码行数:17，代码来源:bio_nextgen.py


示例13: install_cortex_var

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)
开发者ID:sebhtml，项目名称:cloudbiolinux，代码行数:18，代码来源:bio_nextgen.py


示例14: install_trinity

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())
开发者ID:taoito，项目名称:cloudbiolinux，代码行数:4，代码来源:bio_nextgen.py


示例15: install_stampy

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))
开发者ID:hjanime，项目名称:cloudbiolinux，代码行数:6，代码来源:bio_nextgen.py


示例16: install_echo

def install_echo(env):
    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())
开发者ID:hjanime，项目名称:cloudbiolinux，代码行数:4，代码来源:bio_nextgen.py


示例17: install_trinity

def install_trinity(env):
    version = "03122011"
    url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
          "trinityrnaseq-%s.tgz" % version
    _get_install_local(url, env, _make_copy())
开发者ID:leebryanp，项目名称:gists，代码行数:5，代码来源:bio_nextgen.py



注：本文中的shared._get_install_local函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。

鲜花
握手
雷人
路过
鸡蛋
该文章已有0人参与评论

请发表评论

全部评论

专题导读
More+
上一篇：
Python shared._java_install函数代码示例发布时间：2022-05-27
下一篇：
Python shared._get_install函数代码示例发布时间：2022-05-27
热门推荐
More+
热门话题
More+
阅读排行榜

扫描微信二维码

查看手机版网站

随时了解更新最新资讯

139-2527-9053

在线客服（服务时间 9:00～18:00）

在线QQ客服
地址：深圳市南山区西丽大学城创智工业园
电邮：jeky_zhao#qq.com
移动电话：139-2527-9053

Powered by 互联科技 X3.4© 2001-2213 极客世界.|Sitemap