Issues with variant effect predictor installation

Question

[cookersjs]

I am trying to install Ensembl's variant effect predictor and have run into an installation issue right off the bat. I downloaded the VEP zip file from http://uswest.ensembl.org/info/docs/tools/vep/script/index.html, unpackaged it and then ran perl INSTALL.plinside ~/ensembl-tools-release-86/scripts/variant_effect_predictor

When I run it, this is the output message:

$ perl INSTALL.pl

Hello! This installer is configured to install v86 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 Destination directory ./Bio already exists. Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y - fetching BioPerl * GET https://github.com/bioperl/bioperl-live/archive/release-1-6-924.zip ==> 302 Found * GET https://codeload.github.com/bioperl/bioperl-live/zip/release-1-6-924 ==>200 OK (2s) - unpacking ./Bio/tmp/release-1-6-924.zip format error: can't find EOCD signature at /usr/share/perl5/Archive/Zip/Archive.pm line 718. Archive::Zip::Archive::_findEndOfCentralDirectory(Archive::Zip::Archive=HASH(0x468ccc8), IO::File=GLOB(0x468cc50)) called at /usr/share/perl5/Archive/Zip/Archive.pm line 591 Archive::Zip::Archive::readFromFileHandle(Archive::Zip::Archive=HASH(0x468ccc8), IO::File=GLOB(0x468cc50), "/home/justin/ensembl-tools-release-86/scripts/variant_effect_"...) called at /usr/share/perl5/Archive/Zip/Archive.pm line 559 Archive::Zip::Archive::read(Archive::Zip::Archive=HASH(0x468ccc8), "/home/justin/ensembl-tools-release-86/scripts/variant_effect_"...) called at /usr/share/perl5/Archive/Extract.pm line 1154 Archive::Extract::_unzip_az(Archive::Extract=HASH(0x303f9f0)) called at /usr/share/perl5/Archive/Extract.pm line 432 Archive::Extract::extract(Archive::Extract=HASH(0x303f9f0), "to", "./Bio/tmp/") called at INSTALL.pl line 1526 main::unpack_arch("./Bio/tmp/release-1-6-924.zip", "./Bio/tmp/") called at INSTALL.pl line 639 main::bioperl() called at INSTALL.pl line 246 main::api() called at INSTALL.pl line 221 Unable to read '/home/justin/ensembl-tools-release-86/scripts/variant_effect_predictor/Bio/tmp/release-1-6-924.zip' at INSTALL.pl line 1526. No '/bin/unzip' program found at INSTALL.pl line 1526. Extract failed due to errors at INSTALL.pl line 1526. Unable to read '/home/justin/ensembl-tools-release-86/scripts/variant_effect_predictor/Bio/tmp/release-1-6-924.zip' No '/bin/unzip' program found Extract failed due to errors at INSTALL.pl line 1526.

• The .zip file is in a created Bio/tmp/, but I cannot unzip it using the Archive::Zip module I have installed
• If I download the .zip file from the link separately, I can unzip it, but each time the INSTALL.pl is run, it creates a new Bio/tmp directory

Answer 1

[cookersjs]

So the solution I found to this problem was to find the option near the beginning of the install file "our $use_curl = 0;" around line 54 and change it to "our $use_curl =1;".

This allowed the Installer to download the problem files using a different method, rather then the LWP::Simple that is used as the default. I believe the issue originated from the LWP::Simple module installed on my computer but I haven't got to the bottom of that quite yet.

Cheers