I need helping to install some dependencies in perl to run vcf2maf.pl

[Martinez-Gregorio-Hector]

Hi everyone

I want to run vcf2maf to convert vcf to maf but i have some problems to install dependencies in perl.

vcf2maf need VEP to run. To install VEP packages requires:
a) ggc, g++ and make
b) Perl (>=5.10 recommended, tested on 5.10, 5.14, 5.18, 5.22, 5.26)
c) Perl libraries Archive::Zip and DBI

I have installed perl v5.26.2 but not the libraries
I am using this repository to install VEP with these comands:

# install perl and vep
# http://asia.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer
conda install -c conda-forge perl

# configure local-lib, see <https://metacpan.org/pod/local::lib#The-bootstrapping-technique>
wget -c https://cpan.metacpan.org/authors/id/H/HA/HAARG/local-lib-2.000024.tar.gz
tar -zxf local-lib-2.000024.tar.gz 
cd local-lib-2.000024/
perl Makefile.PL --bootstrap=~/perl5 # you can change the ~/perl5 to another location for managing perl modules
make test && make install
echo 'eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib=$HOME/perl5)"' >>~/.bashrc

cpan App::cpanminus
cpanm DBI

When i run the last command cpanm DBI i have a mistake and that look like

--> Working on DBI
Fetching http://www.cpan.org/authors/id/T/TI/TIMB/DBI-1.642.tar.gz ... OK
Configuring DBI-1.642 ... OK
Building and testing DBI-1.642 ... FAIL
! Installing DBI failed. **See /root/.cpanm/work/1570292956.28393/build.log** for details. Retry with --force to force install it.

Apparently I have this package installed on this route ** /root/.cpanm/work/1570292956.28393/** but as I install it or make it executable, any suggestions.

Thanks

[Martinez-Gregorio-Hector]

! Installing DBI failed. See /root/.cpanm/work/1570292956.28393/build.log for details.
It's look like that

cpanm (App::cpanminus) 1.7044 on perl 5.026002 built for x86_64-linux-thread-multi
Work directory is /root/.cpanm/work/1570292956.28393
You have make /usr/bin/make
You have /usr/bin/wget
You have /usr/bin/tar: tar (GNU tar) 1.26
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Searching DBI () on cpanmetadb ...
--> Working on DBI
Fetching http://www.cpan.org/authors/id/T/TI/TIMB/DBI-1.642.tar.gz
-> OK
Unpacking DBI-1.642.tar.gz
Entering DBI-1.642
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.24)
Configuring DBI-1.642
Running Makefile.PL

*** Your LANG environment variable is set to 'en_US.utf-8'
*** This may cause problems for some perl installations.
*** If you get test failures, please try again with LANG unset.
*** If that then works, please email [email protected] with details

[Melcatus]

You can try with
sudo perl INSTALL.pl --NO_HTSLIB

[Martinez-Gregorio-Hector]

When I run this function appear this mistake

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '2.9'
Building Bio-DB-HTS
Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'.  Aborting
ERROR: Shared Bio::DB:HTS library not found

[Melcatus]

It seems a version issue
try with:
cpanm —uninstall Bio::Root::Version
wget https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
tar zxvf BioPerl-1.6.924.tar.gz
PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-1.6.924
cpanm Module::Build

[Melcatus]

if it doesn't work, you can use a docker image that should have updated scripts
https://hub.docker.com/r/opengenomics/vcf2maf

[Martinez-Gregorio-Hector]

I am using docker, this is the command

docker pull thehyve/vcf2maf
docker images 
midirectorio=$(pwd)
docker run --rm -v $midirectorio:/data -it thehyve/vcf2maf bash 

After installing VEP, I tested the script like so

perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf

but i have another mistake, the --ref.fasta is missing or empty

ERROR: Provided --ref-fasta is missing or empty: /root/.vep/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz

[VeroIarrachtai]

You can try download the reference and add a directory /root/.vep/homo_sapiens/86_GRCh37/H and run again in a new volume

[LauraMCE]

Hi! I found this:
mskcc/vcf2maf#200 (comment)
I hope it will be usefull