如何从没有安装bioperl的anaconda中修复Perl？“为BioPerl-1.007002提供安装包”

Question

我正在使用conda安装几个软件包。我已经在conda下安装了Perl，并且在这台机器上工作(运行Ubuntu18.04)。现在我正在尝试使用一个需要bioperl的脚本。

我试图更新conda，通过conda安装bioperl，通过cpanm安装bioperl，如下所示。

我检查了当前使用的Perl是anaconda。perl脚本中的shebang是#!/home/evo-slave/anaconda_ete/bin/perl -w。

这是运行脚本时的初始错误

    Can't locate Bio/SeqIO.pm in @INC (you may need to install the 
    Bio::SeqIO module) (@INC contains: /home/evo- 
    slave/anaconda_ete/lib/site_perl/5.26.2/x86_64-linux-thread-multi 
    /home/evo-slave/anaconda_ete/lib/site_perl/5.26.2 /home/evo- 
    slave/anaconda_ete/lib/5.26.2/x86_64-linux-thread-multi /home/evo- 
    slave/anaconda_ete/lib/5.26.2 .) at ./cortador.pl line 9.
    BEGIN failed--compilation aborted at ./cortador.pl line 9.

我不知道这是bioperl没有被anaconda perl调用/安装的问题，还是在执行脚本的过程中，也许脚本中的这行应该指明其他什么。

    use File::Basename;
    use Bio::SeqIO;
    use Bio::Seq;
    use Bio::DB::SeqFeature::Store;
    use Bio::SeqFeatureI;

当我试图安装

    cpanm Bio::Perl

我犯了这个错误

    --> Working on Bio::Perl
    Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl- 
    1.007002.tar.gz ... OK
    Configuring BioPerl-1.007002 ... OK
    ==> Found dependencies: IO::String, Data::Stag, Test::Most
    --> Working on IO::String
    Fetching http://www.cpan.org/authors/id/G/GA/GAAS/IO-String-

    1.08.tar.gz ... OK
    Configuring IO-String-1.08 ... OK
    Building and testing IO-String-1.08 ... OK
    Successfully installed IO-String-1.08
    --> Working on Data::Stag
    Fetching http://www.cpan.org/authors/id/C/CM/CMUNGALL/Data-Stag- 
    0.14.tar.gz ... OK
    Configuring Data-Stag-0.14 ... OK
    ==> Found dependencies: IO::String
    ! Installing the dependencies failed: Module 'IO::String' is not 
    installed
    ! Bailing out the installation for Data-Stag-0.14.
    --> Working on Test::Most
    Fetching http://www.cpan.org/authors/id/O/OV/OVID/Test-Most- 
    0.35.tar.gz ... OK
    Configuring Test-Most-0.35 ... OK
    ==> Found dependencies: Test::Warn, Test::Deep, Test::Differences, 
    Test::Exception, Exception::Class
    --> Working on Test::Warn
    Fetching http://www.cpan.org/authors/id/B/BI/BIGJ/Test-Warn- 
    0.36.tar.gz ... OK
    Configuring Test-Warn-0.36 ... OK
    ==> Found dependencies: Sub::Uplevel
    --> Working on Sub::Uplevel
    Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel- 
    0.2800.tar.gz ... OK
    Configuring Sub-Uplevel-0.2800 ... OK
    Building and testing Sub-Uplevel-0.2800 ... OK
    Successfully installed Sub-Uplevel-0.2800
    ! Installing the dependencies failed: Module 'Sub::Uplevel' is not 
    installed
    ! Bailing out the installation for Test-Warn-0.36.
    --> Working on Test::Deep
    Fetching http://www.cpan.org/authors/id/R/RJ/RJBS/Test-Deep- 
    1.128.tar.gz ... OK
    Configuring Test-Deep-1.128 ... OK
    Building and testing Test-Deep-1.128 ... OK
    Successfully installed Test-Deep-1.128
    --> Working on Test::Differences
    Fetching http://www.cpan.org/authors/id/D/DC/DCANTRELL/Test- 
    Differences-0.67.tar.gz ... OK
    Configuring Test-Differences-0.67 ... OK
    ==> Found dependencies: Capture::Tiny, Text::Diff
    --> Working on Capture::Tiny
    Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Capture- 
    Tiny-0.48.tar.gz ... OK
    Configuring Capture-Tiny-0.48 ... OK
    Building and testing Capture-Tiny-0.48 ... OK
    Successfully installed Capture-Tiny-0.48
    --> Working on Text::Diff
    Fetching http://www.cpan.org/authors/id/N/NE/NEILB/Text-Diff- 
    1.45.tar.gz ... OK
    Configuring Text-Diff-1.45 ... OK
    ==> Found dependencies: Algorithm::Diff
    --> Working on Algorithm::Diff
    Fetching http://www.cpan.org/authors/id/T/TY/TYEMQ/Algorithm-Diff- 
    1.1903.tar.gz ... OK
    Configuring Algorithm-Diff-1.1903 ... OK
    Building and testing Algorithm-Diff-1.1903 ... OK
    Successfully installed Algorithm-Diff-1.1903
    ! Installing the dependencies failed: Module 'Algorithm::Diff' is 
     not installed
    ! Bailing out the installation for Text-Diff-1.45.
    ! Installing the dependencies failed: Module 'Text::Diff' is not 
    installed, Module 'Capture::Tiny' is not installed
    ! Bailing out the installation for Test-Differences-0.67.
    --> Working on Test::Exception
    Fetching http://www.cpan.org/authors/id/E/EX/EXODIST/Test- 
    Exception-0.43.tar.gz ... OK
    Configuring Test-Exception-0.43 ... OK
    ==> Found dependencies: Sub::Uplevel
    ! Installing the dependencies failed: Module 'Sub::Uplevel' is not 
    installed
    ! Bailing out the installation for Test-Exception-0.43.
    --> Working on Exception::Class
    Fetching http://www.cpan.org/authors/id/D/DR/DROLSKY/Exception- 
    Class-1.44.tar.gz ... OK
    Configuring Exception-Class-1.44 ... OK
    ==> Found dependencies: Class::Data::Inheritable
    --> Working on Class::Data::Inheritable
    Fetching http://www.cpan.org/authors/id/T/TM/TMTM/Class-Data- 
    Inheritable-0.08.tar.gz ... OK
    Configuring Class-Data-Inheritable-0.08 ... OK
    Building and testing Class-Data-Inheritable-0.08 ... OK
    Successfully installed Class-Data-Inheritable-0.08
    ! Installing the dependencies failed: Module 
    'Class::Data::Inheritable' is not installed
    ! Bailing out the installation for Exception-Class-1.44.
    ! Installing the dependencies failed: Module 'Test::Exception' is 
    not installed, Module 'Test::Differences' is not installed, Module 
    'Exception::Class' is not installed, Module 'Test::Warn' is not 
    installed, Module 'Test::Deep' is not installed
    ! Bailing out the installation for Test-Most-0.35.
    ! Installing the dependencies failed: Module 'Test::Most' is not 
    installed, Module 'IO::String' is not installed, Module 
    'Data::Stag' 
    is not installed
    ! Bailing out the installation for BioPerl-1.007002.
    6 distributions installed

ETA：似乎出了问题，在一个简单的cpanm示例中，没有安装所需模块的依赖项，而是尝试安装所需的所有内容。

    cpanm Sub::Uplevel

    --> Working on Sub::Uplevel
    Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz ... OK
    Configuring Sub-Uplevel-0.2800 ... OK
    Building and testing Sub-Uplevel-0.2800 ... OK
    Successfully installed Sub-Uplevel-0.2800
    1 distribution installed

然后

    cpanm Test::Warn

    --> Working on Test::Warn
    Fetching http://www.cpan.org/authors/id/B/BI/BIGJ/Test-Warn-0.36.tar.gz ... OK
    Configuring Test-Warn-0.36 ... OK
    ==> Found dependencies: Sub::Uplevel
    --> Working on Sub::Uplevel
    Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz ... OK
    Configuring Sub-Uplevel-0.2800 ... OK
    Building and testing Sub-Uplevel-0.2800 ... OK
    Successfully installed Sub-Uplevel-0.2800
    ! Installing the dependencies failed: Module 'Sub::Uplevel' is not installed
    ! Bailing out the installation for Test-Warn-0.36.
    1 distribution installed

一些帮助调试的信息：

$ set | grep ^PERL
PERL5LIB=:/media/evo-slave/Disco2/ANDRES/DOWNLOADS/GENOME/CAV-POC/GAAS/annotation
PERL_MB_OPT='--install_base "/home/evo-slave/perl5"'
PERL_MM_OPT=INSTALL_BASE=/home/evo-slave/perl5

$ which cpanm
/home/evo-slave/anaconda_ete/bin/cpanm

$ head -n 1 "$( which cpanm )"
#!/home/evo-slave/anaconda_ete/bin/perl

Answer 1

更新2

这个问题在miniconda3 bioperl安装中再次出现。

更新

对于perl包，我已经有一段时间没有遇到这个错误了，因此很可能在修复这个错误的conda/package端发生了一些更新。我建议您尝试更新您的conda并检查您的conda频道，然后再尝试这种奇怪的方法。

原始答案

我将此作为一个答案，并不是因为这是一个好主意，而是因为它提供了更多的信息。我在Amazon上工作，所以它略有不同，但也遇到了通过conda安装的bioperl依赖项的问题。在我的例子中，我试图运行VirSorter，它提到了这个问题，并提出了一个不适用于我的解决方案，但建议确认您的PERL5LIB已被正确设置。

我注意到我的perl是5.26.2：

$ perl --version

This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

但是conda是出于某种原因安装了5.22.0的perl依赖项：/home/ec2-user/anaconda3/envs/virsorter/lib/perl5/site_perl/5.22.0/

$ ls /home/ec2-user/anaconda3/envs/virsorter/lib/perl5/site_perl/5.22.0/
Algorithm  Bio  Capture  Class  Data  Devel  Exception  IO  Sub  Test  Text  URI  URI.pm  x86_64-linux-thread-multi

我发现，只要简单地将VirSorter设置为conda下的5.22.0lib，就可以运行PERL5LIB，这显然是成功的：

OLD_PER5LIB=$PERL5LIB
export PERL5LIB=/home/ec2-user/anaconda3/envs/virsorter/lib/perl5/site_perl/5.22.0/
# run virsorter
# no errors!

我确信，这会为perl人员发出一堆危险信号，而且我确信，如果它真的有效的话，它是非常脆弱的。也许问题是为什么conda将perl模块安装为错误的perl版本？