<div dir="ltr"><span tabindex="-1" id="result_box" class="" lang="en"><span class="alt-edited">There was no previous installations. F</span></span><span tabindex="-1" id="result_box" class="" lang="en"><span class="alt-edited"><span tabindex="-1" id="result_box" class="short_text" lang="en"><span>or</span> <span class="">this discussion,</span></span> I installed API and VEP in a single pass into a clean Ubuntu in VirtualBox.</span></span><span tabindex="-1" id="result_box" class="" lang="en"><span class=""><br>As it turned out</span><span class="">,</span> <span class="">correct installation</span> <span class="">requires </span><span class="">54</span> <span class="">(</span><span class="">!</span><span>)</span> <span class="alt-edited">commands:<br><br>sudo cpan DBI<br>sudo apt-get install libmysqlclient-dev<br>sudo cpan DBD::mysql<br>sudo apt-get install git<br>mkdir src<br>cd src/<br>git clone <a href="https://github.com/bioperl/bioperl-live.git">https://github.com/bioperl/bioperl-live.git</a><br>cd bioperl-live<br>git checkout release-1-6-924<br>cd -<br>git clone <a href="https://github.com/Ensembl/ensembl-git-tools.git">https://github.com/Ensembl/ensembl-git-tools.git</a><br>export PATH=$PWD/ensembl-git-tools/bin:$PATH<br>git ensembl --clone api<br>PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live<br>PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules<br>PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules<br>PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules<br>PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-funcgen/modules<br>export PERL5LIB<br>git clone <a href="https://github.com/samtools/tabix.git">https://github.com/samtools/tabix.git</a><br>cd tabix<br>make<br>cd perl<br>perl Makefile.PL PREFIX=${HOME}/src/<br>make && make install<br>PERL5LIB=${PERL5LIB}:${HOME}/src//lib/x86_64-linux-gnu/perl/5.22.1/<br>export PERL5LIB<br>PATH=${PATH}:${HOME}/src/tabix/<br>export PATH<br>PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-io/modules<br>export PERL5LIB<br>cd ~<br>cd ensembl-tools-release-84/scripts/variant_effect_predictor/<br>git clone -b master --depth=1 <a href="https://github.com/samtools/htslib.git">https://github.com/samtools/htslib.git</a><br>cd htslib/<br>make<br>export HTSLIB_DIR="$PWD"<br>cd ..<br>git clone <a href="https://github.com/Ensembl/Bio-HTS.git">https://github.com/Ensembl/Bio-HTS.git</a> biodbhts<br>cd biodbhts/<br>sudo cpan Module::Build<br>perl Build.PL<br>./Build<br>cp blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so ..<br>cp blib/arch/auto/Bio/DB/HTS/HTS.so ..<br>cp -r lib/Bio/* ../Bio/<br>cd ..<br>mkdir ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB<br>mv ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB<br>mv ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS.* ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB<br>PERL5LIB=${PERL5LIB}:${HOME}/ensembl-tools-release-84/scripts/variant_effect_predictor<br>export PERL5LIB<br>sudo cpan Archive::Extract<br>perl INSTALL.pl<br>#perl <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -i example_GRCh38.vcf --cache<br><br></span></span><span tabindex="-1" id="result_box" class="short_text" lang="en"><span class="alt-edited">Are there plans to</span> <span class="">eliminate</span> </span><span tabindex="-1" id="result_box" class="short_text" lang="en"><span tabindex="-1" id="result_box" class="" lang="en"><span class="">from installation process at least </span></span>cp and mv operations<span class="alt-edited">?</span><span class=""></span></span><br></div><br><div class="gmail_quote"><div dir="ltr">ср, 13 апр. 2016 г. в 11:12, Rishi Nag <<a href="mailto:rishi@ebi.ac.uk">rishi@ebi.ac.uk</a>>:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
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<br>
output from your initial install it might assist diagnosis,<br>
<br>
Regards<br>
<br>
Rishi<br>
<br>
<br>
On 13/04/2016 00:56, Platon workaccount wrote:<br>
> Thanks. VEP has been installed successfully. Will the installation be simplified in the future?<br>
><br>
> пн, 11 апр. 2016 г. в 16:53, Rishi Nag <<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>:<br>
><br>
><br>
> That looks good, you should be able to proceed<br>
><br>
> Regards<br>
><br>
> Rishi<br>
><br>
> On 11/04/2016 13:57, Platon workaccount wrote:<br>
> > perl biodbhts/t/00_load.t<br>
> ><br>
> > 1..3<br>
> > ok 1 - use Bio::DB::HTS;<br>
> > ok 2 - use Bio::DB::HTS::Tabix;<br>
> > ok 3 - use Bio::DB::HTS::Tabix::Iterator;<br>
> ><br>
> > пн, 11 апр. 2016 г. в 15:41, Rishi Nag <<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>:<br>
> ><br>
> ><br>
> > Hi<br>
> ><br>
> > OK - there are some further files that should be moved:<br>
> ><br>
> > Can you try<br>
> > mv ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS.* ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB<br>
> ><br>
> > and then let me know how it goes?<br>
> ><br>
> > Regards<br>
> ><br>
> > Rishi<br>
> ><br>
> > On 10/04/2016 20:38, Platon workaccount wrote:<br>
> > > ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio$ ls<br>
> > > DB HTS.c HTS.o HTS.pm HTS.xs<br>
> > ><br>
> > > ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB$ ls<br>
> > > HTS<br>
> > ><br>
> > > ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB/HTS$ ls<br>
> > > Alignment.pm AlignWrapper.pm Constants.pm Faidx.c Faidx.o Faidx.pm Faidx.xs FetchIterator.pm Pileup.pm PileupWrapper.pm Query.pm<br>
> ReadIterator.pm<br>
> > > Segment.pm Tabix Tabix.pm Target.pm VCF.pm<br>
> ><br>
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</blockquote></div>