[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed

[Rishi Nag]

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 
would be useful.

There are two ways forward however to complete the installation process manually.

The first is if you have sudo permissions on your machine and are happy to have libraries installed on the system level:
cd htslib
sudo make install
cd ../biodbhts
perl Build.PL
./Build
sudo ./Build install
cd ..


Alternatively the following replicates what the INSTALL script should be doing:
cd htslib
export HTSLIB_DIR="$PWD"
cd ../biodbhts
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/

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.

Regards

Rishi


On 23/03/2016 14:52, Platon workaccount wrote:
> 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
> it". Is it a critical error?
>
> ср, 23 мар. 2016 г. в 12:02, Rishi Nag <rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>:
>
>
>     Thanks.
>
>     Change into the same directory as INSTALL.pl
>
>     First check for a htslib directory being present with the ls command. If not then download and compile this:
>     git clone -b master --depth=1 https://github.com/samtools/htslib.git
>     cd htslib
>     make
>     cd ..
>
>     git clone https://github.com/Ensembl/Bio-HTS.git biodbhts
>     You should then be able to re-run the install commands to download the sequence from this directory.
>
>     Regards
>
>     Rishi
>
>
>     On 22/03/2016 18:17, Platon workaccount wrote:
>      > VEP's install script was invoked by command perl INSTALL.pl
>      >
>      > вт, 22 мар. 2016 г. в 15:32, Rishi Nag <rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk> <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>:
>      >
>      >
>      >     Hi
>      >
>      >     Thanks for raising this issue. Can you provide details on how the install script was invoked please?
>      >
>      >     Regards
>      >
>      >     Rishi
>      >
>      >     On 22/03/2016 12:04, Platon workaccount wrote:
>      >      >
>      >      >
>      >      > ---------- Forwarded message ---------
>      >      > From: Platon workaccount <platon.work at gmail.com <mailto:platon.work at gmail.com> <mailto:platon.work at gmail.com
>     <mailto:platon.work at gmail.com>> <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com> <mailto:platon.work at gmail.com
>     <mailto:platon.work at gmail.com>>>>
>      >      > Date: вт, 22 мар. 2016 г. в 14:58
>      >      > Subject: Ensembl VEP: FASTA gzip to bgzip conversion failed
>      >      > To: <dev at ensembl.org <mailto:dev at ensembl.org> <mailto:dev at ensembl.org <mailto:dev at ensembl.org>> <mailto:dev at ensembl.org
>     <mailto:dev at ensembl.org> <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>>
>      >      >
>      >      >
>      >      > Hello.
>      >      >
>      >      > Full API end dependencies are installed (bioperl-live, ensembl, ensembl-compara, ensembl-variation, ensembl-funcgen; tabix; DBI,
>     DBD::mysql);
>      >      > environment is set up
>      >      > my $API_VERSION = 84
>      >      > ubuntu-15.10-desktop-amd64
>      >      >
>      >      > Error of converting sequence data:
>      >      >
>      >      > ? 28
>      >      > - downloading Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
>      >      > - converting sequence data to bgzip format
>      >      > Going to run:
>      >      > ./biodbhts/scripts/convert_gz_2_bgz.sh /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz ./htslib/bgzip
>      >      > This may take some time and will be removed when files are provided in bgzip format
>      >      > /bin/bash: ./biodbhts/scripts/convert_gz_2_bgz.sh: No such file or directory
>      >      > FASTA gzip to bgzip conversion failed:
>      >      >
>      >      >
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