在dockerfile中正确设置Perl环境
我正在尝试构build一个基于Centos 7的dockerfile，它可以运行Perl编写的特定版本的VEP（ Variant Effect Predictor ），并且具有Perl依赖性，应该通过运行perl INSTALL.pl来处理。
这不适合我，我需要一些帮助。
我确信我已经安装了所有的依赖关系，但是如果我运行安装程序，它会告诉我它看不到它们。
更新 Dockerfile：
# Pull base image of centos. FROM centos:7.3.1611 # install basics RUN yum -y update && yum -y install wget \ gcc \ gcc-c++ \ kernel-devel \ make \ mlocate \ sudo \ curl \ rsync \ tar \ perl \ perl-core \ ansible \ git \ net-tools \ which \ cpan \ libcurl-devel \ python-devel \ texlive-lastpage \ texlive-misc.noarch \ texlive \ man \ epel-release \ ncurses-devel \ zlib-devel \ texinfo \ gtk+-devel \ gtk2-devel \ qt-devel \ tcl-devel \ tk-devel \ kernel-headers \ openssl-devel \ openssl \ libidn-devel \ mysql \ mysql-devel \ mysql-lib \ perl-devel \ perl-CPAN \ perl-JSON \ perl-App-cpanminus RUN yum -y groupinstall "Development Tools" # install samtools + dependancies RUN mkdir /my-software/ ; \ curl -L -o htslib-1.2.1.tar.gz https://github.com/samtools/htslib/archive/1.2.1.tar.gz ; \ curl -L -o samtools-1.2.tar.gz https://github.com/samtools/samtools/archive/1.2.tar.gz ; \ tar xzf htslib-1.2.1.tar.gz ; \ tar xzf samtools-1.2.tar.gz ; \ rm -rf htslib-1.2.1.tar.gz ; \ rm -rf samtools-1.2.tar.gz ; \ mv htslib-1.2.1 /my-software/htslib ; \ mv samtools-1.2 /my-software/samtools ; \ cd /my-software/htslib ; \ make install ; \ cd /my-software/samtools ; \ make -j HTSDIR=/my-software/htslib ; \ make prefix=/my-software/usr/local/bin/ install ; \ rm -rf /htslib* /samtools-1.2* # add samtools and htslib to path ENV PATH=/my-software/samtools/:$PATH \ PATH=/my-software/htslib/:$PATH \ PERL_PATH=~/perl5 \ PERL5LIB=$PERL_PATH/lib/perl5:$PERL_PATH/lib/perl5/x86_64-linux-thread-multi # Handle VEP's Perl dependencies using cpanminus to install them under $PERL_PATH: RUN cpanm --notest -l $PERL_PATH \ Net::SSLeay \ IO::Socket::SSL \ LWP::Simple \ LWP::Protocol::https \ Archive::Extract \ Archive::Tar \ Archive::Zip \ CGI \ DBI \ DBD::mysql \ Time::HiRes # Set temporary shell variables to store VEP and its cache ENV VEP_PATH=/isoma-software/vep/ \ VEP_DATA=/isoma-software/.vep/ # Download the v79 release of VEP: RUN sudo mkdir -p $VEP_PATH $VEP_DATA; cd $VEP_PATH \ && curl -LO "https://github.com/Ensembl/ensembl-tools/archive/release/79.tar.gz" \ && tar -zxf 79.tar.gz \ && cd ensembl-tools-release-79/scripts/variant_effect_predictor/ \ && sudo perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh38 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
当我运行上面的Dockerfile时，我得到以下更新的输出：
Step 6/8 : RUN cpanm --notest -l $PERL_PATH Net::SSLeay IO::Socket::SSL LWP::Simple LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip CGI DBI DBD::mysql Time::HiRes ---> Running in 64e74af831a9 --> Working on Net::SSLeay Fetching http://www.cpan.org/authors/id/M/MI/MIKEM/Net-SSLeay-1.81.tar.gz ... OK Configuring Net-SSLeay-1.81 ... OK Building Net-SSLeay-1.81 ... OK Successfully installed Net-SSLeay-1.81 (upgraded from 1.55) --> Working on IO::Socket::SSL Fetching http://www.cpan.org/authors/id/S/SU/SULLR/IO-Socket-SSL-2.049.tar.gz ... OK Configuring IO-Socket-SSL-2.049 ... OK Building IO-Socket-SSL-2.049 ... OK Successfully installed IO-Socket-SSL-2.049 (upgraded from 1.94) --> Working on LWP::Simple Fetching http://www.cpan.org/authors/id/O/OA/OALDERS/libwww-perl-6.26.tar.gz ... OK Configuring libwww-perl-6.26 ... OK ==> Found dependencies: Try::Tiny, Net::HTTP --> Working on Try::Tiny Fetching http://www.cpan.org/authors/id/E/ET/ETHER/Try-Tiny-0.28.tar.gz ... OK Configuring Try-Tiny-0.28 ... OK Building Try-Tiny-0.28 ... OK Successfully installed Try-Tiny-0.28 --> Working on Net::HTTP Fetching http://www.cpan.org/authors/id/O/OA/OALDERS/Net-HTTP-6.16.tar.gz ... OK Configuring Net-HTTP-6.16 ... OK Building Net-HTTP-6.16 ... OK Successfully installed Net-HTTP-6.16 (upgraded from 6.06) Building libwww-perl-6.26 ... OK Successfully installed libwww-perl-6.26 (upgraded from 6.00) --> Working on LWP::Protocol::https Fetching http://www.cpan.org/authors/id/O/OA/OALDERS/LWP-Protocol-https-6.07.tar.gz ... OK Configuring LWP-Protocol-https-6.07 ... OK ==> Found dependencies: Mozilla::CA --> Working on Mozilla::CA Fetching http://www.cpan.org/authors/id/A/AB/ABH/Mozilla-CA-20160104.tar.gz ... OK Configuring Mozilla-CA-20160104 ... OK Building Mozilla-CA-20160104 ... OK Successfully installed Mozilla-CA-20160104 Building LWP-Protocol-https-6.07 ... OK Successfully installed LWP-Protocol-https-6.07 --> Working on Archive::Extract Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/Archive-Extract-0.80.tar.gz ... OK Configuring Archive-Extract-0.80 ... OK ==> Found dependencies: Module::Load::Conditional --> Working on Module::Load::Conditional Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/Module-Load-Conditional-0.68.tar.gz ... OK Configuring Module-Load-Conditional-0.68 ... OK ==> Found dependencies: Module::Load --> Working on Module::Load Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/Module-Load-0.32.tar.gz ... OK Configuring Module-Load-0.32 ... OK Building Module-Load-0.32 ... OK Successfully installed Module-Load-0.32 (upgraded from 0.24) Building Module-Load-Conditional-0.68 ... OK Successfully installed Module-Load-Conditional-0.68 (upgraded from 0.54) Building Archive-Extract-0.80 ... OK Successfully installed Archive-Extract-0.80 (upgraded from 0.68) --> Working on Archive::Tar Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/Archive-Tar-2.26.tar.gz ... OK Configuring Archive-Tar-2.26 ... OK Building Archive-Tar-2.26 ... OK Successfully installed Archive-Tar-2.26 (upgraded from 1.92) --> Working on Archive::Zip Fetching http://www.cpan.org/authors/id/P/PH/PHRED/Archive-Zip-1.59.tar.gz ... OK Configuring Archive-Zip-1.59 ... OK Building Archive-Zip-1.59 ... OK Successfully installed Archive-Zip-1.59 (upgraded from 1.30) --> Working on CGI Fetching http://www.cpan.org/authors/id/L/LE/LEEJO/CGI-4.36.tar.gz ... OK Configuring CGI-4.36 ... OK Building CGI-4.36 ... OK Successfully installed CGI-4.36 (upgraded from 3.63) --> Working on DBI Fetching http://www.cpan.org/authors/id/T/TI/TIMB/DBI-1.636.tar.gz ... OK Configuring DBI-1.636 ... OK Building DBI-1.636 ... OK Successfully installed DBI-1.636 (upgraded from 1.627) --> Working on DBD::mysql Fetching http://www.cpan.org/authors/id/M/MI/MICHIELB/DBD-mysql-4.042.tar.gz ... OK ==> Found dependencies: Devel::CheckLib --> Working on Devel::CheckLib Fetching http://www.cpan.org/authors/id/M/MA/MATTN/Devel-CheckLib-1.11.tar.gz ... OK Configuring Devel-CheckLib-1.11 ... OK ==> Found dependencies: IO::CaptureOutput, Mock::Config --> Working on IO::CaptureOutput Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/IO-CaptureOutput-1.1104.tar.gz ... OK Configuring IO-CaptureOutput-1.1104 ... OK Building IO-CaptureOutput-1.1104 ... OK Successfully installed IO-CaptureOutput-1.1104 --> Working on Mock::Config Fetching http://www.cpan.org/authors/id/R/RU/RURBAN/Mock-Config-0.03.tar.gz ... OK Configuring Mock-Config-0.03 ... OK Building Mock-Config-0.03 ... OK Successfully installed Mock-Config-0.03 Building Devel-CheckLib-1.11 ... OK Successfully installed Devel-CheckLib-1.11 Configuring DBD-mysql-4.042 ... OK Building DBD-mysql-4.042 ... OK Successfully installed DBD-mysql-4.042 --> Working on Time::HiRes Fetching http://www.cpan.org/authors/id/J/JH/JHI/Time-HiRes-1.9742.tar.gz ... OK Configuring Time-HiRes-1.9742 ... OK Building Time-HiRes-1.9742 ... OK Successfully installed Time-HiRes-1.9742 (upgraded from 1.9725) 19 distributions installed ---> 7972d256ea2c Removing intermediate container 64e74af831a9
指示所有子模块安装正确。
但是当我运行Perl安装脚本时，它在@INC中看不到这些库。
Step 8/8 : RUN sudo mkdir -p $VEP_PATH $VEP_DATA; cd $VEP_PATH && curl -LO "https://github.com/Ensembl/ensembl-tools/archive/release/79.tar.gz" && tar -zxf 79.tar.gz && cd ensembl-tools-release-79/scripts/variant_effect_predictor/ && sudo perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh38 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA ---> Running in f0f4d991bb26 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 133 0 133 0 0 215 0 --:--:-- --:--:-- --:--:-- 214 100 161k 100 161k 0 0 105k 0 0:00:01 0:00:01 --:--:-- 569k Using non-default installation directory /isoma-software/vep/ - you will probably need to add /isoma-software/vep/ to your PERL5LIB Setting up directories Downloading required files - fetching ensembl Trying to fetch using curl ** GET https://github.com/Ensembl/ensembl/archive/release/79.zip ==> 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed) ** GET https://github.com/Ensembl/ensembl/archive/release/79.zip ==> 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed) % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 124 0 124 0 0 200 0 --:--:-- --:--:-- --:--:-- 200 100 10.8M 100 10.8M 0 0 2849k 0 0:00:03 0:00:03 --:--:-- 4539k - unpacking /isoma-software/vep//Bio/tmp/ensembl.zip - moving files - fetching ensembl-variation % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 134 0 134 0 0 180 0 --:--:-- --:--:-- --:--:-- 180 0 0 0 22.8M 0 0 3544k 0 --:--:-- 0:00:06 --:--:-- 5713k - unpacking /isoma-software/vep//Bio/tmp/ensembl-variation.zip - moving files - fetching ensembl-funcgen % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 132 0 132 0 0 204 0 --:--:-- --:--:-- --:--:-- 204 0 0 0 2034k 0 0 848k 0 --:--:-- 0:00:02 --:--:-- 2662k - unpacking /isoma-software/vep//Bio/tmp/ensembl-funcgen.zip - moving files - fetching BioPerl % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 134 0 134 0 0 210 0 --:--:-- --:--:-- --:--:-- 210 100 11.2M 100 11.2M 0 0 2259k 0 0:00:05 0:00:05 --:--:-- 2589k - unpacking /isoma-software/vep//Bio/tmp/release-1-6-924.zip - moving files Testing VEP script Can't locate Bio/EnsEMBL/Variation/Utils/VEP.pm in @INC (@INC contains: /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../ /isoma-software/vep//Bio /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 ./t/variant_effect_predictor.t line 12. BEGIN failed--compilation aborted at ./t/variant_effect_predictor.t line 12. ./t/variant_effect_predictor.t .. Dubious, test returned 2 (wstat 512, 0x200) No subtests run Can't locate Bio/EnsEMBL/Variation/Utils/VEP.pm in @INC (@INC contains: /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../ /isoma-software/vep//Bio /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 ./t/convert_cache.t line 12. BEGIN failed--compilation aborted at ./t/convert_cache.t line 12. ./t/convert_cache.t ............. Dubious, test returned 2 (wstat 512, 0x200) No subtests run Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'help message' # at ./t/filter_vep.t line 26. # Failed test 'error on no filters' # at ./t/filter_vep.t line 32. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'basic filter' # at ./t/filter_vep.t line 36. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'VCF input' # at ./t/filter_vep.t line 40. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'operator - is' # at ./t/filter_vep.t line 47. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'operator - gte' # at ./t/filter_vep.t line 71. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'operator - lte' # at ./t/filter_vep.t line 79. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'operator - match' # at ./t/filter_vep.t line 83. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'operator - in list' # at ./t/filter_vep.t line 87. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'list fields' # at ./t/filter_vep.t line 105. # Got 0, expected 57 Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. # Failed test 'count lines' # at ./t/filter_vep.t line 109. Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /isoma-software/vep//Bio /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 /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. BEGIN failed--compilation aborted at /isoma-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/t/../filter_vep.pl line 581. ./t/filter_vep.t ................ Dubious, test returned 12 (wstat 3072, 0xc00) Failed 12/21 subtests Test Summary Report ------------------- ./t/variant_effect_predictor.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: No plan found in TAP output ./t/convert_cache.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: No plan found in TAP output ./t/filter_vep.t (Wstat: 3072 Tests: 21 Failed: 12) Failed tests: 1-5, 11, 13-15, 19-21 Non-zero exit status: 12 Files=3, Tests=21, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.57 cusr 0.15 csys = 0.75 CPU) Result: FAIL # Failed test 'ontology' # at ./t/filter_vep.t line 116. # Looks like you failed 12 tests of 21. Failed 3/3 test programs. 12/21 subtests failed. The command '/bin/sh -c sudo mkdir -p $VEP_PATH $VEP_DATA; cd $VEP_PATH && curl -LO "https://github.com/Ensembl/ensembl-tools/archive/release/79.tar.gz" && tar -zxf 79.tar.gz && cd ensembl-tools-release-79/scripts/variant_effect_predictor/ && sudo perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh38 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA' returned a non-zero code: 12
所以答案就在ENV声明中。
如果你分组这个（就像我为RUN语句做的那样），那么他们不会再工作了。
我改变了这个每行有一个ENV，现在它工作。
这是工作的Dockerfile：
# Pull base image of centos. FROM centos:7.3.1611 # install basics RUN yum -y update && yum -y install wget \ gcc \ gcc-c++ \ kernel-devel \ make \ mlocate \ sudo \ curl \ rsync \ tar \ perl \ perl-core \ ansible \ git \ net-tools \ which \ cpan \ libcurl-devel \ python-devel \ texlive-lastpage \ texlive-misc.noarch \ texlive \ man \ epel-release \ ncurses-devel \ zlib-devel \ texinfo \ gtk+-devel \ gtk2-devel \ qt-devel \ tcl-devel \ tk-devel \ kernel-headers \ kernel-devel \ openssl-devel \ openssl \ libidn-devel \ mysql \ mysql-devel \ mysql-lib \ perl-devel \ perl-CPAN \ perl-JSON \ perl-App-cpanminus \ zlib RUN yum -y groupinstall "Development Tools" # create folders to install perl5 libs locally and for VEP locations RUN mkdir -p /my-software/perl ; \ mkdir -p /my-software/perl/lib/perl5 ; \ # set perl environment variables ENV PERL_PATH=/my-software/perl/ ENV PERL5LIB=$PERL_PATH:$PERL_PATH/lib/perl5:$PERL5LIB ENV PERL_MM_OPT="INSTALL_BASE=$PERL_PATH" ENV PERL_MB_OPT="--install_base $PERL_PATH" ENV PATH="$PERL_PATH/bin:$PATH" # install samtools + dependancies RUN mkdir /my-software/ ; \ curl -L -o htslib-1.2.1.tar.gz https://github.com/samtools/htslib/archive/1.2.1.tar.gz ; \ curl -L -o samtools-1.2.tar.gz https://github.com/samtools/samtools/archive/1.2.tar.gz ; \ tar xzf htslib-1.2.1.tar.gz ; \ tar xzf samtools-1.2.tar.gz ; \ rm -rf htslib-1.2.1.tar.gz ; \ rm -rf samtools-1.2.tar.gz ; \ mv htslib-1.2.1 /my-software/htslib ; \ mv samtools-1.2 /my-software/samtools ; \ cd /my-software/htslib ; \ make install ; \ cd /my-software/samtools ; \ make -j HTSDIR=/my-software/htslib ; \ make prefix=/my-software/usr/local/bin/ install ; \ rm -rf /htslib* /samtools-1.2* # Handle VEP's Perl dependencies using cpanminus to install them under $PERL_PATH: RUN cpanm --notest -l $PERL_PATH \ Net::SSLeay \ IO::Socket::SSL \ LWP::Simple \ LWP::Protocol::https \ Archive::Extract \ Archive::Tar \ Archive::Zip \ CGI \ DBI \ DBD::mysql \ Time::HiRes # Download the v79 release of VEP: RUN mkdir -p /my-software/vep ; \ cd /my-software/vep ; \ wget "https://github.com/Ensembl/ensembl-tools/archive/release/79.zip" ; \ unzip 79.zip ; \ cd /my-software/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/ ; \ perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh38