<div dir="ltr">Hello!<br><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 ReadIterator.pm Segment.pm Tabix Tabix.pm Target.pm VCF.pm<br></div><br><div class="gmail_quote"><div dir="ltr">вт, 5 апр. 2016 г. в 11:01, 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>
Can I have listings for the following directories please?<br>
~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/<br>
~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB<br>
~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB/HTS<br>
<br>
Regards<br>
Rishi<br>
<br>
On 31/03/2016 16:50, Platon workaccount wrote:<br>
> After that, command 'perl biodbhts/t/00_load.t' yields the same result.<br>
><br>
> чт, 31 мар. 2016 г. в 16:30, 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>
> Hi<br>
><br>
> Could you try moving<br>
> ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS<br>
> into<br>
> ~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/DB/HTS<br>
> and give it another go please?<br>
><br>
> Regards<br>
><br>
> Rishi<br>
><br>
> On 31/03/16 11:33, Platon workaccount wrote:<br>
> > :~/ensembl-tools-release-84/scripts/variant_effect_predictor/biodbhts$ ls<br>
> > blib _build Build Build.PL Changes cpanfile DISCLAIMER INSTALL.pl lib<br>
> > LICENSE MANIFEST MANIFEST.SKIP META.json META.yml MYMETA.json MYMETA.yml<br>
> > ppport.h README scripts t typemap<br>
> ><br>
> > :~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS$ ls<br>
> > Alignment.pm AlignWrapper.pm Constants.pm Faidx.c Faidx.o Faidx.pm<br>
> > Faidx.xs FetchIterator.pm Pileup.pm PileupWrapper.pm Query.pm<br>
> > ReadIterator.pm Segment.pm Tabix Tabix.pm Target.pm VCF.pm<br>
> ><br>
> > perl biodbhts/t/00_load.t<br>
> ><br>
> ><br>
> > 1..3<br>
> ><br>
> > not ok 1 - use Bio::DB::HTS;<br>
> ><br>
> > # Failed test 'use Bio::DB::HTS;'<br>
> ><br>
> > # at biodbhts/t/00_load.t line 3.<br>
> ><br>
> > # Tried to use 'Bio::DB::HTS'.<br>
> ><br>
> > # Error: Can't locate Bio/DB/HTS.pm in @INC (you may need to install the<br>
> > Bio::DB::HTS module) (@INC contains: /home/pl/src/bioperl-live<br>
> > /home/pl/src/ensembl/modules /home/pl/src/ensembl-compara/modules<br>
> > /home/pl/src/ensembl-variation/modules<br>
> > /home/pl/src/ensembl-funcgen/modules<br>
> > /home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/<br>
> > /home/pl/src/ensembl-io/modules<br>
> > /home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor<br>
> > /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1<br>
> > /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22<br>
> > /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22<br>
> > /usr/share/perl/5.22 /usr/local/lib/site_perl<br>
> > /usr/lib/x86_64-linux-gnu/perl-base .) at biodbhts/t/00_load.t line 3.<br>
> ><br>
> > # BEGIN failed--compilation aborted at biodbhts/t/00_load.t line 3.<br>
> ><br>
> > not ok 2 - use Bio::DB::HTS::Tabix;<br>
> ><br>
> > # Failed test 'use Bio::DB::HTS::Tabix;'<br>
> ><br>
> > # at biodbhts/t/00_load.t line 4.<br>
> ><br>
> > # Tried to use 'Bio::DB::HTS::Tabix'.<br>
> ><br>
> > # Error: Can't locate Bio/DB/HTS/Tabix.pm in @INC (you may need to<br>
> > install the Bio::DB::HTS::Tabix module) (@INC contains:<br>
> > /home/pl/src/bioperl-live /home/pl/src/ensembl/modules<br>
> > /home/pl/src/ensembl-compara/modules<br>
> > /home/pl/src/ensembl-variation/modules<br>
> > /home/pl/src/ensembl-funcgen/modules<br>
> > /home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/<br>
> > /home/pl/src/ensembl-io/modules<br>
> > /home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor<br>
> > /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1<br>
> > /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22<br>
> > /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22<br>
> > /usr/share/perl/5.22 /usr/local/lib/site_perl<br>
> > /usr/lib/x86_64-linux-gnu/perl-base .) at biodbhts/t/00_load.t line 4.<br>
> ><br>
> > # BEGIN failed--compilation aborted at biodbhts/t/00_load.t line 4.<br>
> ><br>
> > not ok 3 - use Bio::DB::HTS::Tabix::Iterator;<br>
> ><br>
> > # Failed test 'use Bio::DB::HTS::Tabix::Iterator;'<br>
> ><br>
> > # at biodbhts/t/00_load.t line 5.<br>
> ><br>
> > # Tried to use 'Bio::DB::HTS::Tabix::Iterator'.<br>
> ><br>
> > # Error: Can't locate Bio/DB/HTS/Tabix/Iterator.pm in @INC (you may need<br>
> > to install the Bio::DB::HTS::Tabix::Iterator module) (@INC contains:<br>
> > /home/pl/src/bioperl-live /home/pl/src/ensembl/modules<br>
> > /home/pl/src/ensembl-compara/modules<br>
> > /home/pl/src/ensembl-variation/modules<br>
> > /home/pl/src/ensembl-funcgen/modules<br>
> > /home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/<br>
> > /home/pl/src/ensembl-io/modules<br>
> > /home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor<br>
> > /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1<br>
> > /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22<br>
> > /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22<br>
> > /usr/share/perl/5.22 /usr/local/lib/site_perl<br>
> > /usr/lib/x86_64-linux-gnu/perl-base .) at biodbhts/t/00_load.t line 5.<br>
> ><br>
> > # BEGIN failed--compilation aborted at biodbhts/t/00_load.t line 5.<br>
> ><br>
> > # Looks like you failed 3 tests of 3.<br>
> ><br>
> ><br>
> ><br>
> > чт, 31 мар. 2016 г. в 13:15, 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>
> > <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>
> > The failure occurs as the script attempts to 'use Bio::DB::HTS::Faidx'<br>
> > to perform the conversion but then can't load it.<br>
> ><br>
> > So does<br>
> > /home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor have<br>
> > a subdirectory Bio/DB/HTS and if so can you provide an ls of this<br>
> > directory please?<br>
> ><br>
> > And then from<br>
> > /home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor<br>
> > try running<br>
> > perl biodbhts/t/00_load.t<br>
> ><br>
> > This should indicate a more in-depth nature of what is causing the<br>
> > error,<br>
> ><br>
> > Regards<br>
> ><br>
> > Rishi<br>
> ><br>
> ><br>
> ><br>
> > On 31/03/16 10:18, Platon workaccount wrote:<br>
> > ><br>
> > PERL5LIB=${PERL5LIB}:${HOME}/ensembl-tools-release-84/scripts/variant_effect_predictor<br>
> > > export PERL5LIB<br>
> > > perl INSTALL.pl<br>
> > ><br>
> > > <...><br>
> > > Indexing failed - VEP will attempt to index the file the first<br>
> > time you<br>
> > > use it<br>
> > > <...><br>
> > ><br>
> > > echo $PERL5LIB<br>
> > ><br>
> > ><br>
> ><br>
> :/home/pl/src/bioperl-live:/home/pl/src/ensembl/modules:/home/pl/src/ensembl-compara/modules:/home/pl/src/ensembl-variation/modules:/home/pl/src/ensembl-funcgen/modules:/home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/:/home/pl/src/ensembl-io/modules:/home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor<br>
> > ><br>
> > > чт, 31 мар. 2016 г. в 11:24, 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>
> > <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>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>:<br>
> > ><br>
> > > Hi There<br>
> > ><br>
> > > Thanks for the information. The request should have been 'echo<br>
> > > $PERL5LIB', but it looks like (from the commands below to set the<br>
> > > PERL5LIB environment variable) that things have been set to<br>
> > install<br>
> > > the API in the ${HOME}/src directory. If you also add the<br>
> > directory<br>
> > > containing the Bio directory and the so files that were copied to<br>
> > > the PERL5LIB variable it should get picked up,<br>
> > ><br>
> > > Rishi<br>
> > ><br>
> > > On 30/03/16 19:09, Platon workaccount wrote:<br>
> > > > Hello!<br>
> > > ><br>
> > > > I tried the second set.<br>
> > > ><br>
> > > > echo PERL5LIB<br>
> > > > PERL5LIB<br>
> > > ><br>
> > > > Full command history:<br>
> > > ><br>
> > > > sudo cpan DBI<br>
> > > > sudo apt-get install libmysqlclient-dev<br>
> > > > sudo cpan DBD::mysql<br>
> > > > sudo apt-get install git<br>
> > > > cd src<br>
> > > > git clonehttps://<a href="http://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">github.com/bioperl/bioperl-live.git</a> <<a href="http://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">http://github.com/bioperl/bioperl-live.git</a>><br>
> > <<a href="http://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">http://github.com/bioperl/bioperl-live.git</a>><br>
> > > <<a href="http://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">http://github.com/bioperl/bioperl-live.git</a>><br>
> > > > cd bioperl-live<br>
> > > > git checkout release-1-6-924<br>
> > > > cd -<br>
> > > > git clonehttps://<a href="http://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">github.com/Ensembl/ensembl-git-tools.git</a> <<a href="http://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">http://github.com/Ensembl/ensembl-git-tools.git</a>><br>
> > <<a href="http://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">http://github.com/Ensembl/ensembl-git-tools.git</a>><br>
> > > <<a href="http://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">http://github.com/Ensembl/ensembl-git-tools.git</a>><br>
> > > > export PATH=$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}:${HOME}/src/ensembl-funcgen/modules<br>
> > > > export PERL5LIB<br>
> > > > git clonehttps://<a href="http://github.com/samtools/tabix.git" rel="noreferrer" target="_blank">github.com/samtools/tabix.git</a> <<a href="http://github.com/samtools/tabix.git" rel="noreferrer" target="_blank">http://github.com/samtools/tabix.git</a>><br>
> > <<a href="http://github.com/samtools/tabix.git" rel="noreferrer" target="_blank">http://github.com/samtools/tabix.git</a>><br>
> > > <<a href="http://github.com/samtools/tabix.git" rel="noreferrer" target="_blank">http://github.com/samtools/tabix.git</a>><br>
> > > > cd tabix<br>
> > > > make<br>
> > > > cd perl<br>
> > > > perl Makefile.PL PREFIX=${HOME}/src/<br>
> > > > make && make install<br>
> > > ><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<br>
> > --depth=1<a href="https://github.com/samtools/htslib.git" rel="noreferrer" target="_blank">https://github.com/samtools/htslib.git</a><br>
> > > > cd htslib<br>
> > > > make<br>
> > > > export HTSLIB_DIR="$PWD"<br>
> > > > cd ..<br>
> > > > git clonehttps://<a href="http://github.com/Ensembl/Bio-HTS.git" rel="noreferrer" target="_blank">github.com/Ensembl/Bio-HTS.git</a> <<a href="http://github.com/Ensembl/Bio-HTS.git" rel="noreferrer" target="_blank">http://github.com/Ensembl/Bio-HTS.git</a>><br>
> > <<a href="http://github.com/Ensembl/Bio-HTS.git" rel="noreferrer" target="_blank">http://github.com/Ensembl/Bio-HTS.git</a>><br>
> > > <<a href="http://github.com/Ensembl/Bio-HTS.git" rel="noreferrer" target="_blank">http://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>
> > > > cd ensembl-tools-release-84/scripts/variant_effect_predictor/<br>
> > > > sudo cpan Archive::Extract<br>
> > > > perl INSTALL.pl<br>
> > > ><br>
> > > ><br>
> > > > вт, 29 мар. 2016 г. в 13:35, 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>
> > <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>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>>:<br>
> > > ><br>
> > > ><br>
> > > > Hi<br>
> > > ><br>
> > > > Sorry to hear that and sorry for not replying earlier<br>
> > due to the<br>
> > > > Easter break.<br>
> > > ><br>
> > > > Did you try the sudo set of instructions or the second<br>
> > set?<br>
> > > And can<br>
> > > > I check what your PERL5LIB is set to please (run 'echo<br>
> > > PERL5LIB')?<br>
> > > ><br>
> > > > Regards<br>
> > > ><br>
> > > > Rishi<br>
> > > ><br>
> > > > On 23/03/2016 19:42, Platon workaccount wrote:<br>
> > > > > Unfortunately, your instructions did not help.<br>
> > > > ><br>
> > > > > Installation log:<br>
> > > > ><br>
> > > > ><br>
> > > > > $ perl INSTALL.pl<br>
> > > > ><br>
> > > > ><br>
> > > > > Hello! This installer is configured to install v84<br>
> > of the<br>
> > > Ensembl<br>
> > > > API for use by the VEP.<br>
> > > > ><br>
> > > > > It will not affect any existing installations of the<br>
> > > Ensembl API<br>
> > > > that you may have.<br>
> > > > ><br>
> > > > ><br>
> > > > > It will also download and install cache files from<br>
> > > Ensembl's FTP<br>
> > > > server.<br>
> > > > ><br>
> > > > ><br>
> > > > > Checking for installed versions of the Ensembl<br>
> > > API...Subroutine<br>
> > > > Tabix::tabix_open redefined at<br>
> > > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm<br>
> > > > > line 17.<br>
> > > > ><br>
> > > > > Subroutine Tabix::tabix_close redefined at<br>
> > > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm<br>
> > line 17.<br>
> > > > ><br>
> > > > > Subroutine Tabix::tabix_query redefined at<br>
> > > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm<br>
> > line 17.<br>
> > > > ><br>
> > > > > Subroutine Tabix::tabix_read redefined at<br>
> > > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm<br>
> > line 17.<br>
> > > > ><br>
> > > > > Subroutine Tabix::tabix_getnames redefined at<br>
> > > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm<br>
> > line 17.<br>
> > > > ><br>
> > > > > Subroutine TabixIterator::tabix_iter_free redefined at<br>
> > > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm<br>
> > line 17.<br>
> > > > ><br>
> > > > > done<br>
> > > > ><br>
> > > > > It looks like you already have v84 of the API<br>
> > installed.<br>
> > > > ><br>
> > > > > You shouldn't need to install the API<br>
> > > > ><br>
> > > > ><br>
> > > > > Skip to the next step (n) to install cache files<br>
> > > > ><br>
> > > > ><br>
> > > > > Do you want to continue installing the API (y/n)? n<br>
> > > > ><br>
> > > > > - skipping API installation<br>
> > > > ><br>
> > > > ><br>
> > > > > The VEP can either connect to remote or local<br>
> > databases,<br>
> > > or use<br>
> > > > local cache files.<br>
> > > > ><br>
> > > > > Using local cache files is the fastest and most<br>
> > efficient<br>
> > > way to<br>
> > > > run the VEP<br>
> > > > ><br>
> > > > > Cache files will be stored in /home/pl/.vep<br>
> > > > ><br>
> > > > > Do you want to install any cache files (y/n)? n<br>
> > > > ><br>
> > > > > Skipping cache installation<br>
> > > > ><br>
> > > > ><br>
> > > > > The VEP can use FASTA files to retrieve sequence<br>
> > data for HGVS<br>
> > > > notations and reference sequence checks.<br>
> > > > ><br>
> > > > > FASTA files will be stored in /home/pl/.vep<br>
> > > > ><br>
> > > > > Do you want to install any FASTA files (y/n)? y<br>
> > > > ><br>
> > > > > FASTA files for the following species are<br>
> > available; which<br>
> > > do you<br>
> > > > want (can specify multiple separated by spaces, "0" to<br>
> > > install for<br>
> > > > species specified<br>
> > > > > for cache download):<br>
> > > > ><br>
> > > > > <...><br>
> > > > ><br>
> > > > > 28 : homo_sapiens<br>
> > > > ><br>
> > > > > <...><br>
> > > > ><br>
> > > > > ? 28<br>
> > > > ><br>
> > > > > - downloading<br>
> > Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz<br>
> > > > ><br>
> > > > > - converting sequence data to bgzip format<br>
> > > > ><br>
> > > > > Going to run:<br>
> > > > ><br>
> > > > > ./biodbhts/scripts/convert_gz_2_bgz.sh<br>
> > > ><br>
> > ><br>
> > /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz<br>
> > > > ./htslib/bgzip<br>
> > > > ><br>
> > > > > This may take some time and will be removed when<br>
> > files are<br>
> > > > provided in bgzip format<br>
> > > > ><br>
> > > > > Converted FASTA gzip file to bgzip successfully<br>
> > > > ><br>
> > > > > Indexing failed - VEP will attempt to index the<br>
> > file the first<br>
> > > > time you use it<br>
> > > > ><br>
> > > > > The FASTA file should be automatically detected by<br>
> > the VEP<br>
> > > when<br>
> > > > using --cache or --offline. If it is not, use "--fasta<br>
> > > > ><br>
> > > ><br>
> > ><br>
> > /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"<br>
> > > > ><br>
> > > > ><br>
> > > > > The VEP can use plugins to add functionality and data.<br>
> > > > ><br>
> > > > > Plugins will be installed in /home/pl/.vep/Plugins<br>
> > > > ><br>
> > > > > Do you want to install any plugins (y/n)? n# #y<br>
> > > > ><br>
> > > > > ** GET<br>
> > > ><br>
> > ><br>
> > <a href="https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/84/plugin_config.txt" rel="noreferrer" target="_blank">https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/84/plugin_config.txt</a><br>
> > > > ==> 16%#### 32%#### 48%#### 64%#### 80%####<br>
> > > > > 96%####100%####200 OK<br>
> > > > ><br>
> > > > ><br>
> > > > > ср, 23 мар. 2016 г. в 19:49, Rishi Nag<br>
> > <<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>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>>>:<br>
> > > > ><br>
> > > > ><br>
> > > > > It sounds like there has been a failure to set<br>
> > up . If you<br>
> > > > could pass on the full output from your install attempt<br>
> > > relating to<br>
> > > > the API components that<br>
> > > > > would be useful.<br>
> > > > ><br>
> > > > > There are two ways forward however to complete the<br>
> > > > installation process manually.<br>
> > > > ><br>
> > > > > The first is if you have sudo permissions on your<br>
> > > machine and<br>
> > > > are happy to have libraries installed on the system level:<br>
> > > > > cd htslib<br>
> > > > > sudo make install<br>
> > > > > cd ../biodbhts<br>
> > > > > perl Build.PL<br>
> > > > > ./Build<br>
> > > > > sudo ./Build install<br>
> > > > > cd ..<br>
> > > > ><br>
> > > > ><br>
> > > > > Alternatively the following replicates what the<br>
> > INSTALL<br>
> > > > script should be doing:<br>
> > > > > cd htslib<br>
> > > > > export HTSLIB_DIR="$PWD"<br>
> > > > > cd ../biodbhts<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>
> > > > ><br>
> > > > > And finally, if these cause issues there is the<br>
> > option of<br>
> > > > re-installing with the -NO_HTSLIB flag, which will<br>
> > bypass the<br>
> > > > bgzipped sequence file<br>
> > > > > process.<br>
> > > > ><br>
> > > > > Regards<br>
> > > > ><br>
> > > > > Rishi<br>
> > > > ><br>
> > > > ><br>
> > > > > On 23/03/2016 14:52, Platon workaccount wrote:<br>
> > > > > > Thanks! "Converted FASTA gzip file to bgzip<br>
> > > successfully",<br>
> > > > but this time "Indexing failed - VEP will attempt to index<br>
> > > the file<br>
> > > > the first time<br>
> > > > > you use<br>
> > > > > > it". Is it a critical error?<br>
> > > > > ><br>
> > > > > > ср, 23 мар. 2016 г. в 12:02, Rishi Nag<br>
> > > <<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>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>>>>:<br>
> > > > > ><br>
> > > > > ><br>
> > > > > > Thanks.<br>
> > > > > ><br>
> > > > > > Change into the same directory as INSTALL.pl<br>
> > > > > ><br>
> > > > > > First check for a htslib directory being<br>
> > > present with<br>
> > > > the ls command. If not then download and compile this:<br>
> > > > > > git clone -b master --depth=1<br>
> > > > <a href="https://github.com/samtools/htslib.git" rel="noreferrer" target="_blank">https://github.com/samtools/htslib.git</a><br>
> > > > > > cd htslib<br>
> > > > > > make<br>
> > > > > > cd ..<br>
> > > > > ><br>
> > > > > > git clone<br>
> > > <a href="https://github.com/Ensembl/Bio-HTS.git" rel="noreferrer" target="_blank">https://github.com/Ensembl/Bio-HTS.git</a> biodbhts<br>
> > > > > > You should then be able to re-run the<br>
> > install<br>
> > > commands<br>
> > > > to download the sequence from this directory.<br>
> > > > > ><br>
> > > > > > Regards<br>
> > > > > ><br>
> > > > > > Rishi<br>
> > > > > ><br>
> > > > > ><br>
> > > > > > On 22/03/2016 18:17, Platon workaccount<br>
> > wrote:<br>
> > > > > > > VEP's install script was invoked by<br>
> > command perl<br>
> > > > INSTALL.pl<br>
> > > > > > ><br>
> > > > > > > вт, 22 мар. 2016 г. в 15:32, Rishi Nag<br>
> > > > <<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>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>>><br>
> > > > > <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>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>><br>
> > <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>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>><br>
> > > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>><br>
> > > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>><br>
> > <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> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>>>>>>>:<br>
> > > > > > ><br>
> > > > > > ><br>
> > > > > > > Hi<br>
> > > > > > ><br>
> > > > > > > Thanks for raising this issue.<br>
> > Can you<br>
> > > provide<br>
> > > > details on how the install script was invoked please?<br>
> > > > > > ><br>
> > > > > > > Regards<br>
> > > > > > ><br>
> > > > > > > Rishi<br>
> > > > > > ><br>
> > > > > > > On 22/03/2016 12:04, Platon<br>
> > workaccount<br>
> > > wrote:<br>
> > > > > > > ><br>
> > > > > > > ><br>
> > > > > > > > ---------- Forwarded message<br>
> > ---------<br>
> > > > > > > > From: Platon workaccount<br>
> > > > <<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>>><br>
> > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>>>><br>
> > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>>><br>
> > > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
> > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>>>>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
> > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
> > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>>>><br>
> > > > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
> > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>><br>
> > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
> > > > <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>><br>
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> > > </blockquote></div>