<div dir="ltr">    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 time you use it<br><...><br><br>echo $PERL5LIB<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</div><br><div class="gmail_quote"><div dir="ltr">чт, 31 мар. 2016 г. в 11:24, 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">Hi There<br>
<br>
Thanks for the information. The request should have been 'echo $PERL5LIB', but it looks like (from the commands below to set the PERL5LIB environment variable) that things have been set to install the API in the ${HOME}/src directory. If you also add the directory containing the Bio directory and the so files that were copied to the PERL5LIB variable it should get picked up,<br>
<br>
Rishi<br>
<br>
On 30/03/16 19:09, Platon workaccount wrote:<br>
> Hello!<br>
><br>
> I tried the second set.<br>
><br>
> echo PERL5LIB<br>
> PERL5LIB<br>
><br>
> Full command history:<br>
><br>
> sudo cpan DBI<br>
> sudo apt-get install libmysqlclient-dev<br>
> sudo cpan DBD::mysql<br>
> sudo apt-get install git<br>
> cd src<br>
> git clonehttps://<a href="http://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">github.com/bioperl/bioperl-live.git</a><br>
> cd bioperl-live<br>
> git checkout release-1-6-924<br>
> cd -<br>
> git clonehttps://<a href="http://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">github.com/Ensembl/ensembl-git-tools.git</a><br>
> export PATH=$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}:${HOME}/src/ensembl-funcgen/modules<br>
> export PERL5LIB<br>
> git clonehttps://<a href="http://github.com/samtools/tabix.git" rel="noreferrer" target="_blank">github.com/samtools/tabix.git</a><br>
> cd tabix<br>
> make<br>
> cd perl<br>
> perl Makefile.PL PREFIX=${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" 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>  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><br>
> <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 due to the<br>
>     Easter break.<br>
><br>
>     Did you try the sudo set of instructions or the second set? And can<br>
>     I check what your PERL5LIB is set to please (run 'echo 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 of the Ensembl<br>
>     API for use by the VEP.<br>
>      ><br>
>      > It will not affect any existing installations of the Ensembl API<br>
>     that you may have.<br>
>      ><br>
>      ><br>
>      > It will also download and install cache files from Ensembl's FTP<br>
>     server.<br>
>      ><br>
>      ><br>
>      > Checking for installed versions of the Ensembl 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 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 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 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 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 line 17.<br>
>      ><br>
>      > done<br>
>      ><br>
>      > It looks like you already have v84 of the API 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 databases, or use<br>
>     local cache files.<br>
>      ><br>
>      > Using local cache files is the fastest and most efficient 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 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 available; which do you<br>
>     want (can specify multiple separated by spaces, "0" to install for<br>
>     species specified<br>
>      > for cache download):<br>
>      ><br>
>      > <...><br>
>      ><br>
>      > 28 : homo_sapiens<br>
>      ><br>
>      > <...><br>
>      ><br>
>      > ? 28<br>
>      ><br>
>      > - downloading 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>
>     /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 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 file the first<br>
>     time you use it<br>
>      ><br>
>      > The FASTA file should be automatically detected by the VEP when<br>
>     using --cache or --offline. If it is not, use "--fasta<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>
>     <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 <<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>>>>:<br>
>      ><br>
>      ><br>
>      >     It sounds like there has been a failure to set up . If you<br>
>     could pass on the full output from your install attempt 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 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 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 option of<br>
>     re-installing with the -NO_HTSLIB flag, which will 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 successfully",<br>
>     but this time "Indexing failed - VEP will attempt to index 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 <<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><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>>>>>:<br>
>      >      ><br>
>      >      ><br>
>      >      >     Thanks.<br>
>      >      ><br>
>      >      >     Change into the same directory as INSTALL.pl<br>
>      >      ><br>
>      >      >     First check for a htslib directory being 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 <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 install 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 wrote:<br>
>      >      >      > VEP's install script was invoked by 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><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><br>
>     <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>>><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>>>>>>:<br>
>      >      >      ><br>
>      >      >      ><br>
>      >      >      >     Hi<br>
>      >      >      ><br>
>      >      >      >     Thanks for raising this issue. Can you 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 workaccount wrote:<br>
>      >      >      >      ><br>
>      >      >      >      ><br>
>      >      >      >      > ---------- Forwarded message ---------<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>><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><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>>><br>
>      >      >     <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>>><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>>><br>
>      >      >     <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>>>>>>><br>
>      >      >      >      > Date: вт, 22 мар. 2016 г. в 14:58<br>
>      >      >      >      > Subject: Ensembl VEP: FASTA gzip to bgzip<br>
>     conversion failed<br>
>      >      >      >      > To: <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>>> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
>      >     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>>>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>><br>
>      >      >     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>><br>
>     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
>      >     <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>>>>>><br>
>      >      >      >      ><br>
>      >      >      >      ><br>
>      >      >      >      > Hello.<br>
>      >      >      >      ><br>
>      >      >      >      > Full API end dependencies are installed<br>
>     (bioperl-live, ensembl, ensembl-compara, ensembl-variation,<br>
>     ensembl-funcgen; tabix; DBI,<br>
>      >      >     DBD::mysql);<br>
>      >      >      >      > environment is set up<br>
>      >      >      >      > my $API_VERSION = 84<br>
>      >      >      >      > ubuntu-15.10-desktop-amd64<br>
>      >      >      >      ><br>
>      >      >      >      > Error of converting sequence data:<br>
>      >      >      >      ><br>
>      >      >      >      > ? 28<br>
>      >      >      >      > - downloading<br>
>     Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz<br>
>      >      >      >      > - converting sequence data to bgzip format<br>
>      >      >      >      > Going to run:<br>
>      >      >      >      > ./biodbhts/scripts/convert_gz_2_bgz.sh<br>
>     /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz<br>
>      >     ./htslib/bgzip<br>
>      >      >      >      > This may take some time and will be removed<br>
>     when files are provided in bgzip format<br>
>      >      >      >      > /bin/bash:<br>
>     ./biodbhts/scripts/convert_gz_2_bgz.sh: No such file or directory<br>
>      >      >      >      > FASTA gzip to bgzip conversion failed:<br>
>      >      >      >      ><br>
>      >      >      >      ><br>
>      >      >      >      > _______________________________________________<br>
>      >      >      >      > Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>>><br>
>      >     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>>>><br>
>      >      >      >      > Posting guidelines and subscribe/unsubscribe<br>
>     info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
>      >      >      >      > Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      >      >      >      ><br>
>      >      >      ><br>
>      >      >      >     _______________________________________________<br>
>      >      >      >     Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>      >     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>>>><br>
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>      >      >      >     Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      >      >      ><br>
>      >      >      ><br>
>      >      >      ><br>
>      >      >      > _______________________________________________<br>
>      >      >      > Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>>><br>
>      >      >      > Posting guidelines and subscribe/unsubscribe info:<br>
>     <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
>      >      >      > Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      >      >      ><br>
>      >      ><br>
>      >      >     _______________________________________________<br>
>      >      >     Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>>><br>
>      >      >     Posting guidelines and subscribe/unsubscribe info:<br>
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>      >      >     Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      >      ><br>
>      >      ><br>
>      >      ><br>
>      >      > _______________________________________________<br>
>      >      > Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>><br>
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>      >      > Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      >      ><br>
>      ><br>
>      >     _______________________________________________<br>
>      >     Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>     <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>><br>
>      >     Posting guidelines and subscribe/unsubscribe info:<br>
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>      >     Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      ><br>
>      ><br>
>      ><br>
>      > _______________________________________________<br>
>      > Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>      > Posting guidelines and subscribe/unsubscribe info:<br>
>     <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
>      > Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      ><br>
><br>
>     _______________________________________________<br>
>     Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
>     Posting guidelines and subscribe/unsubscribe info:<br>
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>     Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list    <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
><br>
<br>
<br>
_______________________________________________<br>
Dev mailing list    <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
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Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div>