我正在尝试构建一个基于Centos 7的dockerfile，它可以运行特定版本的VEP（ Variant Effect Predictor ），它是用Perl编写的，并且具有Perl依赖性，应该通过运行来处理perl INSTALL.pl。
这对我不起作用，我需要一些帮助。
我非常确信我已经安装了所有依赖项，但如果我运行安装程序，它会告诉我它无法看到它们。
已更新 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
表示所有子模块都正确安装。
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
答案 0 :(得分：0)
所以答案在于ENV声明。
如果你对此进行分组（正如我对RUN语句所做的那样）那么它们将不再有效。
我将其改为每行一个ENV，现在它可以工作。
这是工作的Dockerfile：
TIdURI.PathEncode(Edt_Sen.Text)