install ensembl-vep

Question

[yueli7]

Hello,

I want to install ensembl-vep in my Ubuntu 18.04.2.

I have already installed LWP::Simple. What can I do in the next step?

Thanks in advance for great help!

Best,

Yue

   Inspiron-3670:~/ensembl-vep$ perl INSTALL.pl 
    curl failed (000), trying to fetch using LWP::Simple
    LWP::Simple failed (500), trying to fetch using HTTP::Tiny
   ERROR: Failed last resort of using HTTP::Tiny to download https://raw.githubusercontent.com/Ensembl/ensembl-vep/release/104/modules/Bio/EnsEMBL/VEP/Constants.pm

[MSRS]

Try with miniconda.

conda install -c bioconda ensembl-vep

Reference

[yueli7]

Hello MSRS,

Thank you so much for your suggestion.

I am in China and because of the firewall, sorry for responding later.

I still have problem in "perl INSTALL.pl" command.

Thank you again and really appreciated!

Best Regards,

Yue

Inspiron-3670:~/miniconda3/share/ensembl-vep-88.9-1$ perl INSTALL.pl 

Version check reports a newer release of 'ensembl-vep' is available (installed: 88, available: 104)

You should exit this installer and re-download 'ensembl-vep' if you wish to update

Do you wish to exit so you can get updates (y) or continue (n): n

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
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
 - fetching BioPerl
curl failed (000), trying to fetch using LWP::Simple
 - 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 /home/jing/miniconda3/share/ensembl-vep-88.9-1/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
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
x86_64-linux-gnu-gcc -I/home/jing/miniconda3/share/ensembl-vep-88.9-1/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.26/CORE -DVERSION="2.11" -DXS_VERSION="2.11" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c
lib/Bio/DB/HTS.xs: In function ‘XS_Bio__DB__HTS__VCF__Header_fmt_text’:
lib/Bio/DB/HTS.xs:1770:5: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
     RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0);
     ^~~~~~
In file included from lib/Bio/DB/HTS.xs:59:0:
/home/jing/miniconda3/share/ensembl-vep-88.9-1/htslib/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs')
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/home/jing/miniconda3/share/ensembl-vep-88.9-1/htslib -Wl,-rpath,/home/jing/miniconda3/share/ensembl-vep-88.9-1/htslib -lhts -lpthread -lz
x86_64-linux-gnu-gcc -I/home/jing/miniconda3/share/ensembl-vep-88.9-1/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.26/CORE -DVERSION="2.11" -DXS_VERSION="2.11" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs')
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/home/jing/miniconda3/share/ensembl-vep-88.9-1/htslib -Wl,-rpath,/home/jing/miniconda3/share/ensembl-vep-88.9-1/htslib -lhts -lpthread -lz

Downloading required Ensembl API files
 - fetching ensembl
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - getting version information
 - fetching ensembl-variation
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - getting version information
 - fetching ensembl-funcgen
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - getting version information
 - fetching ensembl-io
 - unpacking ./Bio/tmp/ensembl-io.zip
 - moving files
 - getting version information

Testing VEP installation
Files=0, Tests=0,  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
Result: NOTESTS
Warning: Tests failed, VEP may not run correctly
 - OK!

The VEP can either connect to remote or local databases, or use local cache files.
Using local cache files is the fastest and most efficient way to run the VEP
Cache files will be stored in /home/jing/.vep
Do you want to install any cache files (y/n)? y
 - getting list of available cache files
ERROR: Could not change directory to indexed_vep_cache