Question

您好我正在尝试使用docker安装VelvetOptimizer。它说无法在@INC中找到Bio / SeqIO.pm。它需要安装以下内容： Velvet＆gt; = 0.7.51，Perl＆gt; = 5.8，BioPerl＆gt; = 1.4并且我安装了它们

请找到Dockerfile：

FROM amazonlinux



WORKDIR /shared
    RUN yum -y install gcc
    ADD http://www.cpan.org/src/5.0/perl-5.16.1.tar.gz /shared
    RUN tar -xzf perl-5.16.1.tar.gz
    WORKDIR /shared/perl-5.16.1
    RUN ./Configure -des -Dprefix=/shared/perl-5.16.1/localperl
    RUN make
    RUN make test
    RUN make install
    RUN echo “Perl Installation Complete”
    ENV PATH=/shared/perl-5.16.1/localperl/bin/:${PATH}

WORKDIR /shared
ADD http://www.ebi.ac.uk/~zerbino/velvet/velvet_latest.tgz .
RUN tar -xvf /shared/velvet_latest.tgz
WORKDIR /shared/velvet_1.2.10/
RUN make
ENV PATH=${PATH}:/shared/velvet_1.2.10/

WORKDIR /shared
RUN echo "BIO PERL INSTALLATION"
RUN \wget -O - https://install.perlbrew.pl | bash
ENV PATH=${PATH}:/root/perl5/perlbrew/bin/
RUN perlbrew install-cpanm
RUN cpanm Bio::Perl

WORKDIR /shared
ADD http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz .
RUN tar zxvf VelvetOptimiser-2.2.5.tar.gz
ENV PATH=${PATH}:/shared/VelvetOptimiser-2.2.4

当我运行命令/ shared / VelvetOptimiser-2.2.5 / VelvetOptimiser.pl时我收到以下错误：

错误：

Can't locate Bio/SeqIO.pm in @INC (@INC contains: /shared/VelvetOptimiser-2.2.5 /shared/vcftools/src/perl /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /shared/VelvetOptimiser-2.2.5/VelvetOpt/Assembly.pm line 238.
BEGIN failed--compilation aborted at /shared/VelvetOptimiser-2.2.5/VelvetOpt/Assembly.pm line 238.
Compilation failed in require at /shared/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 37.
BEGIN failed--compilation aborted at /shared/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 37.

但是当我使用“find”命令时：我能够找到文件。

./root/.cpanm/work/1501770319.1/BioPerl-1.007001/blib/lib/Bio/SeqIO.pm
./root/.cpanm/work/1501770319.1/BioPerl-1.007001/Bio/SeqIO.pm
./shared/perl-5.16.1/localperl/lib/site_perl/5.16.1/Bio/SeqIO.pm

我认为它不在Perl的include路径中找到，它由名为@INC的变量表示。任何人都可以让我知道如何解决这个问题。如何在perls中添加它包括路径。

Answer 1

显然，/shared/VelvetOptimiser-2.2.5/VelvetOptimiser.pl有

#!/usr/bin/env perl

作为它的shebang线。因此，它将使用它在perl中找到的第一个$PATH。

perl中可能有/usr/bin。在您的Docker文件中，您有：

ENV PATH=${PATH}:/root/perl5/perlbrew/bin/

也就是说，您可能会将/usr/bin放在perlbrew目录之前。因此，/usr/bin/env perl正在通过/usr/bin/perl（也是您安装新perl的地方）提取perlbrew而不是perl。

所以，试试

ENV PATH=/root/perl5/perlbrew/bin/:${PATH}

此外，我没有看到您实际通过perl安装了perlbrew：

你需要

perlbrew install 5.xx.x
perlbrew switch 5.xx.x

在安装cpanm并安装Bio::Perl。

之前

无法在@INC中找到Bio / SeqIO.pm

1 个答案: