[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed
Platon workaccount
platon.work at gmail.com
Wed Apr 13 19:54:25 BST 2016
There was no previous installations. For this discussion, I installed API
and VEP in a single pass into a clean Ubuntu in VirtualBox.
As it turned out, correct installation requires 54 (!) commands:
sudo cpan DBI
sudo apt-get install libmysqlclient-dev
sudo cpan DBD::mysql
sudo apt-get install git
mkdir src
cd src/
git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
git checkout release-1-6-924
cd -
git clone https://github.com/Ensembl/ensembl-git-tools.git
export PATH=$PWD/ensembl-git-tools/bin:$PATH
git ensembl --clone api
PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-funcgen/modules
export PERL5LIB
git clone https://github.com/samtools/tabix.git
cd tabix
make
cd perl
perl Makefile.PL PREFIX=${HOME}/src/
make && make install
PERL5LIB=${PERL5LIB}:${HOME}/src//lib/x86_64-linux-gnu/perl/5.22.1/
export PERL5LIB
PATH=${PATH}:${HOME}/src/tabix/
export PATH
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-io/modules
export PERL5LIB
cd ~
cd ensembl-tools-release-84/scripts/variant_effect_predictor/
git clone -b master --depth=1 https://github.com/samtools/htslib.git
cd htslib/
make
export HTSLIB_DIR="$PWD"
cd ..
git clone https://github.com/Ensembl/Bio-HTS.git biodbhts
cd biodbhts/
sudo cpan Module::Build
perl Build.PL
./Build
cp blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so ..
cp blib/arch/auto/Bio/DB/HTS/HTS.so ..
cp -r lib/Bio/* ../Bio/
cd ..
mkdir ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB
mv ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS
~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB
mv ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS.*
~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB
PERL5LIB=${PERL5LIB}:${HOME}/ensembl-tools-release-84/scripts/variant_effect_predictor
export PERL5LIB
sudo cpan Archive::Extract
perl INSTALL.pl
#perl variant_effect_predictor.pl -i example_GRCh38.vcf --cache
Are there plans to eliminate from installation process at least cp and mv
operations?
ср, 13 апр. 2016 г. в 11:12, Rishi Nag <rishi at ebi.ac.uk>:
>
> It usually isn't so complicated. It looks like an initial install was only
> partially successful on your machine, or something got deleted. If you have
> output from your initial install it might assist diagnosis,
>
> Regards
>
> Rishi
>
>
> On 13/04/2016 00:56, Platon workaccount wrote:
> > Thanks. VEP has been installed successfully. Will the installation be
> simplified in the future?
> >
> > пн, 11 апр. 2016 г. в 16:53, Rishi Nag <rishi at ebi.ac.uk <mailto:
> rishi at ebi.ac.uk>>:
> >
> >
> > That looks good, you should be able to proceed
> >
> > Regards
> >
> > Rishi
> >
> > On 11/04/2016 13:57, Platon workaccount wrote:
> > > perl biodbhts/t/00_load.t
> > >
> > > 1..3
> > > ok 1 - use Bio::DB::HTS;
> > > ok 2 - use Bio::DB::HTS::Tabix;
> > > ok 3 - use Bio::DB::HTS::Tabix::Iterator;
> > >
> > > пн, 11 апр. 2016 г. в 15:41, Rishi Nag <rishi at ebi.ac.uk <mailto:
> rishi at ebi.ac.uk> <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>:
> > >
> > >
> > > Hi
> > >
> > > OK - there are some further files that should be moved:
> > >
> > > Can you try
> > > mv
> ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS.*
> ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB
> > >
> > > and then let me know how it goes?
> > >
> > > Regards
> > >
> > > Rishi
> > >
> > > On 10/04/2016 20:38, Platon workaccount wrote:
> > > >
> ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio$ ls
> > > > DB HTS.c HTS.o HTS.pm HTS.xs
> > > >
> > > >
> ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB$ ls
> > > > HTS
> > > >
> > > >
> ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB/HTS$ ls
> > > > Alignment.pm AlignWrapper.pm Constants.pm Faidx.c Faidx.o
> Faidx.pm Faidx.xs FetchIterator.pm Pileup.pm PileupWrapper.pm Query.pm
> > ReadIterator.pm
> > > > Segment.pm Tabix Tabix.pm Target.pm VCF.pm
> > >
> > > _______________________________________________
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