Fail to install Ensembl VEP
3
0
Entering edit mode
4 days ago
Winson • 0

Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34.

perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006924

However, when I install the VEP, it failed.

Hello! This installer is configured to install v105 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
It looks like you already have v105 of the API installed.
You shouldn't need to install the API

Skip to the next step (n) to install cache files

Do you want to continue installing the API (y/n)? y

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
 - 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

 - checking out HTSLib
fatal: destination path 'htslib' already exists and is not an empty directory.
 - building HTSLIB in ./htslib
In /media/robunken/8357fc75-8d32-4c98-82d6-6a8a8b14511d/ab/ensembl-vep-release-105/htslib
make: Nothing to be done for 'all'.
 - unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/
./Bio/tmp/Bio-DB-HTS-2.11 - moving files to ./biodbhts
 - making Bio::DB:HTS
Can't exec "/tmp/build/80754af9/perl_1527832170752/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc": No such file or directory at /home/robunken/miniconda3/lib/site_perl/5.26.2/ExtUtils/CBuilder/Base.pm line 343.
Warning: ExtUtils::CBuilder not installed or no compiler detected
Proceeding with configuration, but compilation may fail during Build

Checking prerequisites...
  requires:
    !  Bio::Root::Version is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

Run 'Build installdeps' to install missing prerequisites.

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '2.11'
Building Bio-DB-HTS
Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'.  Aborting
ERROR: Shared Bio::DB:HTS library not found

Any idea will be appreciated.

Thanks in advance,

Winson

software error • 225 views
ADD COMMENT
0
Entering edit mode
4 days ago
Mensur Dlakic ★ 15k

It says right there at penultimate line: Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'. Aborting. You are missing a C/C++ compiler, which can be installed, along with other essential programs and libraries:

sudo apt install build-essential

After that repeating the installation should work.

ADD COMMENT
0
Entering edit mode
4 days ago

You noted that you had tabix installed. Was this installed separately from the VEP installation?

Please could you run the following 2 commands in the same environment you are running the VEP installer:

perl -MBio::DB::HTS -e 'print "$Bio::DB::HTS::VERSION\n"'

perldoc -l Bio::DB::HTS

ADD COMMENT
0
Entering edit mode

I checked the module and it was not install properly as you said. After I re-install the Bio::DB::HTS, and use sudo to install it, it works. Thanks.

ADD REPLY
0
Entering edit mode
3 days ago
colindaven ★ 3.5k

A nice alternative is their singularity container:

https://www.ensembl.info/2021/05/24/cool-stuff-the-vep-can-do-singularity/

ADD COMMENT

Login before adding your answer.

Traffic: 2351 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6