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<style type="text/css">p { margin-bottom: 0.25cm; line-height: 120%; }</style>
<p style="margin-bottom:0cm;line-height:100%"><span tabindex="-1" id="result_box" class="short_text" lang="en"><span class="alt-edited">Unfortunately</span><span>,</span> <span class="alt-edited">your instructions</span> <span class="">did not help.</span><span class=""></span></span></p><p style="margin-bottom:0cm;line-height:100%"><span tabindex="-1" id="result_box" class="short_text" lang="en"><span class="">Installation log:</span></span></p><p style="margin-bottom:0cm;line-height:100%"><span tabindex="-1" id="result_box" class="short_text" lang="en"><span class=""><br></span></span></p><p style="margin-bottom:0cm;line-height:100%">$ perl INSTALL.pl</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">Hello! This
installer is configured to install v84 of the Ensembl API for use by
the VEP.</p>
<p style="margin-bottom:0cm;line-height:100%">It will not affect
any existing installations of the Ensembl API that you may have.</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">It will also
download and install cache files from Ensembl's FTP server.</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">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
line 17.</p>
<p style="margin-bottom:0cm;line-height:100%">Subroutine
Tabix::tabix_close redefined at
/home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.</p>
<p style="margin-bottom:0cm;line-height:100%">Subroutine
Tabix::tabix_query redefined at
/home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.</p>
<p style="margin-bottom:0cm;line-height:100%">Subroutine
Tabix::tabix_read redefined at
/home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.</p>
<p style="margin-bottom:0cm;line-height:100%">Subroutine
Tabix::tabix_getnames redefined at
/home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.</p>
<p style="margin-bottom:0cm;line-height:100%">Subroutine
TabixIterator::tabix_iter_free redefined at
/home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line 17.</p>
<p style="margin-bottom:0cm;line-height:100%">done</p>
<p style="margin-bottom:0cm;line-height:100%">It looks like you
already have v84 of the API installed.</p>
<p style="margin-bottom:0cm;line-height:100%">You shouldn't need
to install the API</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">Skip to the next
step (n) to install cache files</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">Do you want to
continue installing the API (y/n)? n</p>
<p style="margin-bottom:0cm;line-height:100%"> - skipping API
installation</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">The VEP can either
connect to remote or local databases, or use local cache files.</p>
<p style="margin-bottom:0cm;line-height:100%">Using local cache
files is the fastest and most efficient way to run the VEP</p>
<p style="margin-bottom:0cm;line-height:100%">Cache files will be
stored in /home/pl/.vep</p>
<p style="margin-bottom:0cm;line-height:100%">Do you want to
install any cache files (y/n)? n</p>
<p style="margin-bottom:0cm;line-height:100%">Skipping cache
installation</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">The VEP can use
FASTA files to retrieve sequence data for HGVS notations and
reference sequence checks.</p>
<p style="margin-bottom:0cm;line-height:100%">FASTA files will be
stored in /home/pl/.vep</p>
<p style="margin-bottom:0cm;line-height:100%">Do you want to
install any FASTA files (y/n)? y</p>
<p style="margin-bottom:0cm;line-height:100%">FASTA files for the
following species are available; which do you want (can specify
multiple separated by spaces, "0" to install for species
specified for cache download):
</p>
<p style="margin-bottom:0cm;line-height:100%"><...></p>
<p style="margin-bottom:0cm;line-height:100%">28 : homo_sapiens</p>
<p style="margin-bottom:0cm;line-height:100%"><...></p>
<p style="margin-bottom:0cm;line-height:100%">? 28</p>
<p style="margin-bottom:0cm;line-height:100%"> - downloading
Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</p>
<p style="margin-bottom:0cm;line-height:100%"> - converting
sequence data to bgzip format</p>
<p style="margin-bottom:0cm;line-height:100%"> Going to run:</p>
<p style="margin-bottom:0cm;line-height:100%">./biodbhts/scripts/convert_gz_2_bgz.sh
/home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
./htslib/bgzip</p>
<p style="margin-bottom:0cm;line-height:100%">This may take some
time and will be removed when files are provided in bgzip format</p>
<p style="margin-bottom:0cm;line-height:100%">Converted FASTA gzip
file to bgzip successfully</p>
<p style="margin-bottom:0cm;line-height:100%">Indexing failed -
VEP will attempt to index the file the first time you use it</p>
<p style="margin-bottom:0cm;line-height:100%">The FASTA file
should be automatically detected by the VEP when using --cache or
--offline. If it is not, use "--fasta
/home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"</p>
<p style="margin-bottom:0cm;line-height:100%"><br>
</p>
<p style="margin-bottom:0cm;line-height:100%">The VEP can use
plugins to add functionality and data.</p>
<p style="margin-bottom:0cm;line-height:100%">Plugins will be
installed in /home/pl/.vep/Plugins</p>
<p style="margin-bottom:0cm;line-height:100%">Do you want to
install any plugins (y/n)? n# #y</p>
<p style="margin-bottom:0cm;line-height:100%">** GET
<a href="https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/84/plugin_config.txt">https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/84/plugin_config.txt</a>
==> 16%#### 32%#### 48%#### 64%#### 80%#### 96%####100%####200 OK</p>
</div><br><div class="gmail_quote"><div dir="ltr">ср, 23 мар. 2016 г. в 19:49, Rishi Nag <<a href="mailto:rishi@ebi.ac.uk">rishi@ebi.ac.uk</a>>:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
It 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 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 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>>>:<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>
> ><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>> <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 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>>>>><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 ./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>
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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>> <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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> ><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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> ><br>
><br>
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</blockquote></div>