[ensembl-dev] An error of installation Ensembl VEP on Fedora 26

[Will McLaren]

On Fedora you should use yum to install packages, though you'll have to
find yourself the names of those required. The following may work for you:

yum install yum install gcc gcc-c++ autoconf automake

Regards

Will

On 6 April 2017 at 14:43, Platon workaccount <platon.work at gmail.com> wrote:

> $ perl INSTALL.pl
>
> Hello! This installer is configured to install v88 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
>  - fetching BioPerl
>  - unpacking ./Bio/tmp/release-1-6-924.zip
>  - moving files
> Attempting to install Bio::DB::HTS and htslib.
>
> >>> If this fails, try re-running with --NO_HTSLIB
>
> which: no cc in (/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/home/
> pl/.local/bin:/home/pl/bin)
>   'cc' command not in path. Please install it and try again.
>   (or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)
>
>   On Debian/Ubuntu systems you can do this with the command:
>
>   apt-get install build-essential
>
> ----------
> Next I tried the command "sudo dnf install build-essential". Unfortunately,
> this program is not available in the Fedora repository.
>
> чт, 6 апр. 2017 г. в 15:55, Platon workaccount <platon.work at gmail.com>:
>
>> $ perl INSTALL.pl
>>
>> Hello! This installer is configured to install v88 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
>>  - fetching BioPerl
>>  - unpacking ./Bio/tmp/release-1-6-924.zip
>> caution: filename not matched:  -qq
>> ERROR: Failed to unpack file ./Bio/tmp/release-1-6-924.zip
>>
>> ср, 5 апр. 2017 г. в 20:32, Platon workaccount <platon.work at gmail.com>:
>>
>> Thanks for the answer! I re-cloned the repository. But now a new error
>> has appeared:
>> $ perl INSTALL.pl
>> Bio/EnsEMBL/VEP/Utils.pm did not return a true value at INSTALL.pl line
>> 48.
>>
>> BEGIN failed--compilation aborted at INSTALL.pl line 48.
>>
>> ср, 5 апр. 2017 г. в 15:35, Platon workaccount <platon.work at gmail.com>:
>>
>> Hello! When installing Ensembl VEP on Fedora 26 the following error
>> occurs:
>>
>> $ cd ensembl-vep
>> $ perl INSTALL.pl
>> Global symbol "$GunzipError" requires explicit package name (did you
>> forget to declare "my $GunzipError"?) at /home/pl/ensembl-vep/modules/Bio/EnsEMBL/VEP/Utils.pm
>> line 226.
>> Compilation failed in require at INSTALL.pl line 48.
>> BEGIN failed--compilation aborted at INSTALL.pl line 48.
>>
>>
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