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

Platon workaccount platon.work at gmail.com
Thu Apr 6 14:43:33 BST 2017


$ 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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