linux - 运行 VEP 的 INSTALL.pl 脚本时提取 BioPerl-1.6.1.tar.gz 时出现问题

Question

我正在尝试在 Linux 机器上安装版本 77 的 Variant Effect Predictor (VEP)，但在运行 perl INSTALL.pl 时一直遇到错误。在解决缺少 perl 模块 Archive::Extract 的错误后，我遇到了这个错误:

Hello! This installer is configured to install v77 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.

It will also download and install cache files from Ensembl's FTP server.

Checking for installed versions of the Ensembl API...done

Setting up directories

Downloading required files
 - fetching ensembl
** GET https://github.com/Ensembl/ensembl/archive/release/77.zip ==> 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
** GET https://github.com/Ensembl/ensembl/archive/release/77.zip ==> 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
Trying to fetch using curl
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   124    0   124    0     0    730      0 --:--:-- --:--:-- --:--:--   729
100 10.7M    0 10.7M    0     0  3535k      0 --:--:--  0:00:03 --:--:-- 4859k
 - unpacking ./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    737      0 --:--:-- --:--:-- --:--:--   740
100 3986k    0 3986k    0     0  4378k      0 --:--:-- --:--:-- --:--:-- 7182k
 - unpacking ./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    798      0 --:--:-- --:--:-- --:--:--   800
100 2016k    0 2016k    0     0  3354k      0 --:--:-- --:--:-- --:--:-- 5156k
 - unpacking ./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   178  100   178    0     0   2695      0 --:--:-- --:--:-- --:--:--  2738
100  9340  100  9340    0     0  46698      0 --:--:-- --:--:-- --:--:-- 46698
 - unpacking ./Bio/tmp/BioPerl-1.6.1.tar.gz
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Invalid header block at offset unknown at /usr/local/share/perl/5.22.1/Archive/Extract.pm line 893.
Unable to extract '/opt/vep/src/ensembl-vep/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/tmp/BioPerl-1.6.1.tar.gz': Invalid header block at offset unknown at INSTALL.pl line 905.
Error listing contents of archive '/opt/vep/src/ensembl-vep/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/tmp/BioPerl-1.6.1.tar.gz': /bin/tar: This does not look like a tar archive
/bin/tar: Skipping to next header
/bin/tar: Exiting with failure status due to previous errors
 at INSTALL.pl line 905.
Extract failed due to errors at INSTALL.pl line 905.
Can't call method "error" on an undefined value at INSTALL.pl line 905.

INSTALL.pl 脚本的第 905 行是:

900 # unpack a tarball
901 sub unpack_arch {
902   my ($arch_file, $dir) = @_;
903 
904   my $ar = Archive::Extract->new(archive => $arch_file);
905   my $ok = $ar->extract(to => $dir) or die $ae->error;
906   unlink($arch_file);
907 }

我对 perl 不够熟悉，不知道到底出了什么问题，但我尝试用 tar -xvzf 自己对 BioPerl-1.6.1.tar.gz 进行解压，但没有成功工作。我该如何解决这个问题？

Answer 1

此存档似乎已损坏:/opt/vep/src/ensembl-vep/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/tmp/BioPerl-1.6.1.tar.gz

/bin/tar 给你一个错误“/bin/tar:这看起来不像一个 tar 存档”

你能替换这个文件或删除它并重新开始安装吗？