Cant Install plugins

[GianlucaMattei]

Hello, I can not install vep plugins. I am using anaconda to launch "vep_install" with the following command. Anyone know how to fix this ? Thanks

vep_install AlphaMissense

Hello! This installer will help you set up VEP v112, including:
 - Install v112 of the Ensembl API for use by the VEP. It will not affect any existing installations of the Ensembl API that you may have.
 - Download and install cache files from Ensembl's FTP server.
 - Download FASTA files from Ensembl's FTP server.
 - Download VEP plugins.

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)? Can't open AlphaMissense: No such file or directory at /data2/user1/.conda/envs/vep/bin/vep_install line 678.
Exiting

System

• VEP version: v112
• VEP Cache version: v112
• Perl version: v5.32.1
• OS: RHEL 8
• tabix installed

[nuno-agostinho]

Hi @GianlucaMattei,

Hope you are having a nice day.

Unfortunately, we do not support conda installation, as the version of VEP in that repository is not official.

As a workaround, we advise to install the official Docker image for VEP that bundles all plugins: https://hub.docker.com/r/ensemblorg/ensembl-vep

More information on using VEP Docker can be found in our documentation here.

Sorry for the inconvenience.

Cheers, Nuno

[GianlucaMattei]

Ok. I have the same issue using the "normal" vep installed with

git clone https://github.com/Ensembl/ensembl-vep.git
cd ensembl-vep
perl INSTALL.pl

I just edited the title of the issue....

Anyway, when I run the command

./INSTALL.pl AlphaMissense

I get

WARNING: DBD::mysql module not found. VEP can only run in offline (--offline) mode without DBD::mysql installed

http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements

Version check reports a newer release of 'ensembl-vep' is available (installed: 109, available: 112)

We recommend using git to update 'ensembl-vep', by exiting this installer and running:

        git pull
        git checkout release/112

Do you wish to exit so you can get updates (y) or continue (n): Can't open AlphaMissense: No such file or directory at ./INSTALL.pl line 425.
OK, bye!

NB: Remember to re-run INSTALL.pl after updating to check for API updates

System

• VEP version: v109
• VEP Cache version: v109
• Perl version: v5.32.1
• OS: RHEL 8
• tabix installed

[nuno-agostinho]

Hey @GianlucaMattei,

To install AlphaMissense, you will need to run the command ./INSTALL -a p -g AlphaMissense. Otherwise, you can also interactively follow the instructions when running the command ./INSTALL.pl.

After installing AlphaMissense and any other plugins of interest, you can look into our documentation on how to use each plugin: https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html

Hope this helps.

Best regards, Nuno

[GianlucaMattei]

It works, Thanks