<div dir="ltr"><div>
Hello!<br><br>I tried the second set.<br><br>echo PERL5LIB<br>PERL5LIB<br><br></div>Full command history:<br>
<style type="text/css">pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.25cm; line-height: 120%; }</style>
<pre class="western">sudo cpan DBI
sudo apt-get install libmysqlclient-dev
sudo cpan DBD::mysql
sudo apt-get install git
cd src
git clone <a href="https://github.com/bioperl/bioperl-live.git">https://github.com/bioperl/bioperl-live.git</a>
cd bioperl-live
git checkout release-1-6-924
cd -
git clone <a href="https://github.com/Ensembl/ensembl-git-tools.git">https://github.com/Ensembl/ensembl-git-tools.git</a>
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 <a href="https://github.com/samtools/tabix.git">https://github.com/samtools/tabix.git</a>
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}:${HOME}/src/ensembl-io/modules
export PERL5LIB
cd ~
cd ensembl-tools-release-84/scripts/variant_effect_predictor/
git clone -b master --depth=1 <a href="https://github.com/samtools/htslib.git">https://github.com/samtools/htslib.git</a>
cd htslib
make
export HTSLIB_DIR="$PWD"
cd ..
git clone <a href="https://github.com/Ensembl/Bio-HTS.git">https://github.com/Ensembl/Bio-HTS.git</a> 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 ~
cd ensembl-tools-release-84/scripts/variant_effect_predictor/
sudo cpan Archive::Extract
perl INSTALL.pl</pre>
</div><br><div class="gmail_quote"><div dir="ltr">вт, 29 мар. 2016 г. в 13:35, 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>
Hi<br>
<br>
Sorry to hear that and sorry for not replying earlier due to the Easter break.<br>
<br>
Did you try the sudo set of instructions or the second set? And can 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 API for use by the VEP.<br>
><br>
> It will not affect any existing installations of the Ensembl API that you may have.<br>
><br>
><br>
> It will also download and install cache files from Ensembl's FTP server.<br>
><br>
><br>
> Checking for installed versions of the Ensembl API...Subroutine Tabix::tabix_open redefined at /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 /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.<br>
><br>
> Subroutine Tabix::tabix_query redefined at /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.<br>
><br>
> Subroutine Tabix::tabix_read redefined at /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.<br>
><br>
> Subroutine Tabix::tabix_getnames redefined at /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 /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 local cache files.<br>
><br>
> Using local cache files is the fastest and most efficient way to 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 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 want (can specify multiple separated by spaces, "0" to install for 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 /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz ./htslib/bgzip<br>
><br>
> This may take some time and will be removed when files are 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 time you use it<br>
><br>
> The FASTA file should be automatically detected by the VEP when using --cache or --offline. If it is not, use "--fasta<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 <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> ==> 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> <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 could pass on the full output from your install attempt relating to the API components that<br>
> would be useful.<br>
><br>
> There are two ways forward however to complete the installation process manually.<br>
><br>
> The first is if you have sudo permissions on your machine and 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 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 re-installing with the -NO_HTSLIB flag, which will bypass the 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", but this time "Indexing failed - VEP will attempt to index the file 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> <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 present with the ls command. If not then download and compile this:<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>
> > 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 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 INSTALL.pl<br>
> > ><br>
> > > вт, 22 мар. 2016 г. в 15:32, 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>
> <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. Can you provide 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 <<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>><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>
> > > > Date: вт, 22 мар. 2016 г. в 14:58<br>
> > > > Subject: Ensembl VEP: FASTA gzip to bgzip conversion failed<br>
> > > > To: <<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>> <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>>> <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> <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> <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>>> <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>> <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>
> > > ><br>
> > > ><br>
> > > > Hello.<br>
> > > ><br>
> > > > Full API end dependencies are installed (bioperl-live, ensembl, ensembl-compara, ensembl-variation, 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 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 /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 when files are provided in bgzip format<br>
> > > > /bin/bash: ./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> <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> <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>> <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: <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>> <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>>> <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> <mailto:<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> <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> <mailto:<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>
> > 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>> <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: <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> <mailto:<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>
> 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: <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>
> 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>
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>
</blockquote></div>