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简单命令安装Bio::Perl模块

简单命令安装Bio::Perl模块

作者: 郝永超M1racle | 来源:发表于2020-09-29 16:37 被阅读0次

    在网上搜了好几个教程下载安装Bioperl,结果一顿操作,全部失败,然后去bing上搜索英文教程,就找到一行命令,轻松解决
    链接:https://www.biostars.org/p/436784/

    cpanm Bio::Perl --> cnanm Bio::SeqIO
    

    安装信息

    --> Working on Bio::Perl
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz ... OK
    Configuring Bio-Procedural-1.7.4 ... OK
    ==> Found dependencies: Bio::Seq, Bio::DB::GenBank, Bio::DB::RefSeq, Bio::Root::Version, Bio::Root::Test, Bio::DB::EMBL, Bio::SeqIO, Bio::DB::SwissProt, Bio::DB::GenPept, Bio::Tools::Run::RemoteBlast
    --> Working on Bio::Seq
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.7.tar.gz ... OK
    Configuring BioPerl-1.7.7 ... OK
    ==> Found dependencies: XML::DOM::XPath
    --> Working on XML::DOM::XPath
    Fetching http://www.cpan.org/authors/id/M/MI/MIROD/XML-DOM-XPath-0.14.tar.gz ... OK
    Configuring XML-DOM-XPath-0.14 ... OK
    Building and testing XML-DOM-XPath-0.14 ... OK
    Successfully installed XML-DOM-XPath-0.14
    Building and testing BioPerl-1.7.7 ... OK
    Successfully installed BioPerl-1.7.7
    --> Working on Bio::DB::GenBank
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-NCBIHelper-1.7.6.tar.gz ... OK
    Configuring Bio-DB-NCBIHelper-1.7.6 ... OK
    ==> Found dependencies: Bio::SeqIO::entrezgene
    --> Working on Bio::SeqIO::entrezgene
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-ASN1-EntrezGene-1.73.tar.gz ... OK
    Configuring Bio-ASN1-EntrezGene-1.73 ... OK
    ==> Found dependencies: Bio::Cluster::SequenceFamily
    --> Working on Bio::Cluster::SequenceFamily
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Cluster-1.7.3.tar.gz ... OK
    Configuring Bio-Cluster-1.7.3 ... OK
    ==> Found dependencies: Bio::Variation::SNP
    --> Working on Bio::Variation::SNP
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Variation-1.7.5.tar.gz ... OK
    Configuring Bio-Variation-1.7.5 ... OK
    Building and testing Bio-Variation-1.7.5 ... OK
    Successfully installed Bio-Variation-1.7.5
    Building and testing Bio-Cluster-1.7.3 ... OK
    Successfully installed Bio-Cluster-1.7.3
    Building and testing Bio-ASN1-EntrezGene-1.73 ... OK
    Successfully installed Bio-ASN1-EntrezGene-1.73
    Building and testing Bio-DB-NCBIHelper-1.7.6 ... FAIL
    ! Installing Bio::DB::GenBank failed. See /usrdata/users/hwwang/.cpanm/work/1601364242.405229/build.log for details. Retry with --force to force install it.
    --> Working on Bio::DB::RefSeq
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-RefSeq-1.7.4.tar.gz ... OK
    Configuring Bio-DB-RefSeq-1.7.4 ... OK
    Building and testing Bio-DB-RefSeq-1.7.4 ... OK
    Successfully installed Bio-DB-RefSeq-1.7.4
    --> Working on Bio::DB::EMBL
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-EMBL-1.7.4.tar.gz ... OK
    Configuring Bio-DB-EMBL-1.7.4 ... OK
    Building and testing Bio-DB-EMBL-1.7.4 ... FAIL
    ! Installing Bio::DB::EMBL failed. See /usrdata/users/hwwang/.cpanm/work/1601364242.405229/build.log for details. Retry with --force to force install it.
    --> Working on Bio::DB::SwissProt
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-DB-SwissProt-1.7.4.tar.gz ... OK
    Configuring Bio-DB-SwissProt-1.7.4 ... OK
    Building and testing Bio-DB-SwissProt-1.7.4 ... OK
    Successfully installed Bio-DB-SwissProt-1.7.4
    --> Working on Bio::Tools::Run::RemoteBlast
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-Tools-Run-RemoteBlast-1.7.3.tar.gz ... OK
    Configuring Bio-Tools-Run-RemoteBlast-1.7.3 ... OK
    Building and testing Bio-Tools-Run-RemoteBlast-1.7.3 ... OK
    Successfully installed Bio-Tools-Run-RemoteBlast-1.7.3
    ! Installing the dependencies failed: Module 'Bio::DB::GenBank' is not installed, Module 'Bio::DB::EMBL' is not installed, Module 'Bio::DB::GenPept' is not installed
    ! Bailing out the installation for Bio-Procedural-1.7.4.
    8 distributions installed
    

    中间有的包没有安装上,但测试了一下,我想用的模块已经可以成功调用了,就没有纠结其他问题,对于那些没有安装好的包,可以尝试一下中间信息中推荐的,加一个 --force 参数

    之前GO::Parser也因为权限和各种包的问题安装不上,刚测试了一下,竟然也OK了!

    小结

    本身不是计算机专业,面对报错实在头疼,编程学的python,还是半瓶子醋,不过遇到问题的时候,就不断的找嘛,总有人遇到过一样的问题,百度找不到就去访问一下英文网站,那里的老哥懂得也挺多

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