[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed
Cyriac Kandoth
kandoth at cbio.mskcc.org
Wed Apr 13 20:23:15 BST 2016
Hi PW, here are some shorter instructions that don't require sudo, except
for some core packages like "curl rsync tar make perl" that you should
already have in the VM.
https://gist.github.com/ckandoth/57d189f018b448774704d3b2191720a6
~Cyriac
On Wed, Apr 13, 2016 at 2:54 PM, Platon workaccount <platon.work at gmail.com>
wrote:
> 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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