[ensembl-dev] Problem attempting to install VEP 77

[Will McLaren]

Hi David,

Sorry to hear you've been having problems. It's not clear to me from Google
searching the error you're seeing what could be the cause; it seems there
is some particular issue with your version of the Perl Archive module.

It is possible to do the installation steps performed by the VEP installer
manually.

1) Install API and BioPerl:
http://www.ensembl.org/info/docs/api/api_git.html (follow the instructions
for setting up a specific version of the API)

2) Install the cache:
http://e77.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre

3) (optional) set up a cache file:
e77.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta

Regards

Will McLaren
Ensembl Variation

On 29 September 2015 at 22:53, Nicolas Thierry-Mieg <
Nicolas.Thierry-Mieg at imag.fr> wrote:

> Hi,
>
> works here on centos 6, but I avoid CPAN as much as possible and use the
> distro-provided perl-Archive-Extract-0.38-141.el6.x86_64 .
>
> HTH
>
>
> On 09/29/2015 05:23 PM, Murphy, David wrote:
>
>> Hi All
>>
>> We’ve been trying to install VEP 77
>> (https://github.com/Ensembl/ensembl-tools/archive/release/77.zip) in
>> order to replicate results from a previous analysis.
>>
>>
>> We’re running perl v5.10.1 on Red Hat Enterprise Linux Server release
>> 6.6 (Santiago)
>>
>> sh-4.1# perl -version
>>
>> This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
>>
>>
>> When we run Install.pl we get the error
>>
>>
>> sh-4.1# perl INSTALL.pl
>>
>> <snip>
>
>> - unpacking ./Bio/tmp/ensembl.zip
>>
>> Key 'archive' is of invalid type for Archive::Extract::new provided by
>> main::unpack_arch at /usr/share/perl5/Archive/Extract.pm line 270.
>>
>> Can't call method "extract" on an undefined value at INSTALL.pl line 905.
>>
>>
>> The file ensembl.zip  is downloaded and appears to be a valid zip
>> archive and can be extracted manually.
>>
>> The perl core module Archive::Extract appears to be there.
>>
>> Package namespace         installed    latest  in CPAN file
>>
>> Algorithm::Diff              1.1903    1.1903
>> TYEMQ/Algorithm-Diff-1.1903.tar.gz
>>
>> App::cpanminus               1.7039    1.7039
>> MIYAGAWA/App-cpanminus-1.7039.tar.gz
>>
>> Archive::Extract               0.74      0.76
>> BINGOS/Archive-Extract-0.76.tar.gz
>>
>> Archive::Zip                   1.51      1.53
>> PHRED/Archive-Zip-1.53.tar.gz
>>
>> Attribute::Handlers            0.85      0.99
>> RJBS/Attribute-Handlers-0.99.tar.gz
>>
>>
>> We also tried with the latest version of the installer to try to
>> diagnose the problem but we got the same error.
>>
>> Any ideas for what might be wrong?
>>
>> Regards
>> David
>>
>
>
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