Problem with extracting BioPerl-1.6.1.tar.gz when running VEP's INSTALL.pl script - linux

Question

I'm trying to install version 77 of Variant Effect Predictor (VEP) on a linux machine and keep encountering errors when running perl INSTALL.pl. After resolving an error with missing the perl module Archive::Extract, I ran into this error:
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.
And line 905 of the INSTALL.pl script is:
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 }
I'm not familiar enough with perl to know what's going wrong exactly, but I tried un-taring the BioPerl-1.6.1.tar.gz myself with tar -xvzf and that did not work. How can I resolve this issue?

Answer 1

this archive seems corrupted : /opt/vep/src/ensembl-vep/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/tmp/BioPerl-1.6.1.tar.gz
/bin/tar is giving you an error "/bin/tar: This does not look like a tar archive"
can you replace this file or delete it and restart the installation?