<div dir="ltr">:~/ensembl-tools-release-84/scripts/variant_effect_predictor/biodbhts$ ls<br>blib _build Build Build.PL Changes cpanfile DISCLAIMER INSTALL.pl lib LICENSE MANIFEST MANIFEST.SKIP META.json META.yml MYMETA.json MYMETA.yml 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 Faidx.xs FetchIterator.pm Pileup.pm PileupWrapper.pm Query.pm ReadIterator.pm Segment.pm Tabix Tabix.pm Target.pm VCF.pm<br><br>
<style type="text/css">p { margin-bottom: 0.25cm; line-height: 120%; }</style>
<p style="margin-bottom:0cm;line-height:100%">perl
biodbhts/t/00_load.t</p><p style="margin-bottom:0cm;line-height:100%"><br></p><p style="margin-bottom:0cm;line-height:100%">1..3</p>
<p style="margin-bottom:0cm;line-height:100%">not ok 1 - use
Bio::DB::HTS;</p>
<p style="margin-bottom:0cm;line-height:100%"># Failed test 'use
Bio::DB::HTS;'</p>
<p style="margin-bottom:0cm;line-height:100%"># at
biodbhts/t/00_load.t line 3.</p>
<p style="margin-bottom:0cm;line-height:100%"># Tried to use
'Bio::DB::HTS'.</p>
<p style="margin-bottom:0cm;line-height:100%"># Error: Can't
locate Bio/DB/HTS.pm in @INC (you may need to install the
Bio::DB::HTS module) (@INC contains: /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
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22 /usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base .) at biodbhts/t/00_load.t line
3.</p>
<p style="margin-bottom:0cm;line-height:100%"># BEGIN
failed--compilation aborted at biodbhts/t/00_load.t line 3.</p>
<p style="margin-bottom:0cm;line-height:100%">not ok 2 - use
Bio::DB::HTS::Tabix;</p>
<p style="margin-bottom:0cm;line-height:100%"># Failed test 'use
Bio::DB::HTS::Tabix;'</p>
<p style="margin-bottom:0cm;line-height:100%"># at
biodbhts/t/00_load.t line 4.</p>
<p style="margin-bottom:0cm;line-height:100%"># Tried to use
'Bio::DB::HTS::Tabix'.</p>
<p style="margin-bottom:0cm;line-height:100%"># Error: Can't
locate Bio/DB/HTS/Tabix.pm in @INC (you may need to install the
Bio::DB::HTS::Tabix module) (@INC contains: /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
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22 /usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base .) at biodbhts/t/00_load.t line
4.</p>
<p style="margin-bottom:0cm;line-height:100%"># BEGIN
failed--compilation aborted at biodbhts/t/00_load.t line 4.</p>
<p style="margin-bottom:0cm;line-height:100%">not ok 3 - use
Bio::DB::HTS::Tabix::Iterator;</p>
<p style="margin-bottom:0cm;line-height:100%"># Failed test 'use
Bio::DB::HTS::Tabix::Iterator;'</p>
<p style="margin-bottom:0cm;line-height:100%"># at
biodbhts/t/00_load.t line 5.</p>
<p style="margin-bottom:0cm;line-height:100%"># Tried to use
'Bio::DB::HTS::Tabix::Iterator'.</p>
<p style="margin-bottom:0cm;line-height:100%"># Error: Can't
locate Bio/DB/HTS/Tabix/Iterator.pm in @INC (you may need to install
the Bio::DB::HTS::Tabix::Iterator module) (@INC contains:
/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
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22 /usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base .) at biodbhts/t/00_load.t line
5.</p>
<p style="margin-bottom:0cm;line-height:100%"># BEGIN
failed--compilation aborted at biodbhts/t/00_load.t line 5.</p>
<p style="margin-bottom:0cm;line-height:100%"># Looks like you
failed 3 tests of 3.</p>
<br></div><br><div class="gmail_quote"><div dir="ltr">чт, 31 мар. 2016 г. в 13:15, 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>
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 error,<br>
<br>
Regards<br>
<br>
Rishi<br>
<br>
<br>
<br>
On 31/03/16 10:18, Platon workaccount wrote:<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 time you<br>
> 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<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><br>
> <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 install<br>
> the API in the ${HOME}/src directory. If you also add the directory<br>
> containing the Bio directory and the so files that were copied to<br>
> the PERL5LIB variable it should get picked up,<br>
><br>
> Rishi<br>
><br>
> On 30/03/16 19:09, Platon workaccount wrote:<br>
> > Hello!<br>
> ><br>
> > I tried the second set.<br>
> ><br>
> > echo PERL5LIB<br>
> > PERL5LIB<br>
> ><br>
> > Full command history:<br>
> ><br>
> > sudo cpan DBI<br>
> > sudo apt-get install libmysqlclient-dev<br>
> > sudo cpan DBD::mysql<br>
> > sudo apt-get install git<br>
> > cd src<br>
> > git clonehttps://<a href="http://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">github.com/bioperl/bioperl-live.git</a><br>
> <<a href="http://github.com/bioperl/bioperl-live.git" rel="noreferrer" target="_blank">http://github.com/bioperl/bioperl-live.git</a>><br>
> > cd bioperl-live<br>
> > git checkout release-1-6-924<br>
> > cd -<br>
> > git clonehttps://<a href="http://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">github.com/Ensembl/ensembl-git-tools.git</a><br>
> <<a href="http://github.com/Ensembl/ensembl-git-tools.git" rel="noreferrer" target="_blank">http://github.com/Ensembl/ensembl-git-tools.git</a>><br>
> > export PATH=$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}:${HOME}/src/ensembl-funcgen/modules<br>
> > export PERL5LIB<br>
> > git clonehttps://<a href="http://github.com/samtools/tabix.git" rel="noreferrer" target="_blank">github.com/samtools/tabix.git</a><br>
> <<a href="http://github.com/samtools/tabix.git" rel="noreferrer" target="_blank">http://github.com/samtools/tabix.git</a>><br>
> > cd tabix<br>
> > make<br>
> > cd perl<br>
> > perl Makefile.PL PREFIX=${HOME}/src/<br>
> > make && make install<br>
> > 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><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><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>
> ><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?<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 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 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,<br>
> or use<br>
> > local cache files.<br>
> > ><br>
> > > Using local cache files is the fastest and most 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 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<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 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>
> /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<br>
> when<br>
> > using --cache or --offline. If it is not, use "--fasta<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>
> <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>><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>
> > > It sounds like there has been a failure to set 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 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<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>><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>
> > <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>
> > > > 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 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 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>><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>
> > <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>
> <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>
> <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<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 workaccount<br>
> 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> <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><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><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>>>>>> <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>>><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> <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><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>><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>
> > <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><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>
> > > > > ><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<br>
> format<br>
> > > > > > Going to run:<br>
> > > > > > ./biodbhts/scripts/convert_gz_2_bgz.sh<br>
> ><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<br>
> 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>
> _______________________________________________<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>><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>
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> > > > > _______________________________________________<br>
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> > > > > Posting guidelines and subscribe/unsubscribe<br>
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> > > > _______________________________________________<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>
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> > > > _______________________________________________<br>
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> > > > Posting guidelines and subscribe/unsubscribe info:<br>
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> > > _______________________________________________<br>
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> > > Posting guidelines and subscribe/unsubscribe info:<br>
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> > ><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>
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> > > 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>
> > 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>
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> > 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>
> > _______________________________________________<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>
> _______________________________________________<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>
> _______________________________________________<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>