aparton
commented
5 years ago Hi Steve,
In current versions of VEP, the installer will put Bio::DB::HTS::Tabix in ensembl-vep/Bio/DB/HTS/Tabix. I’m not sure if this is the same for version 87, however we have made significant changes to the installation process since then.
While conda/bioconda installations of VEP exist, they are not maintained by us and as such not fully supported. However, you can get an up-to-date copy of VEP through BioConda here: https://anaconda.org/bioconda/ensembl-vep/files https://anaconda.org/bioconda/ensembl-vep/files. You can find official instructions for download and installation here: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html
Updating to version 96 should resolve your issue. If not (and you’re using Perl 5.26), then adding your ensembl-vep directory to your PERL5LIB variable should help VEP find Bio::DB::HTS::Tabix.
Regarding updates to our documentation, this is something that we’re actively looking at and we’ll keep making improvements over the next few months.
Kind Regards, Andrew
On 7 May 2019, at 16:21, sbberes notifications@github.com wrote:
I am trying to use VEP on bacterial genomes, largely for its ability to predict the consequences of indels. I have installed VEP Ensembl API version 96 on a workstation with Ubuntu 18.10 OS. Running the "perl INSTALL.pl" install script on vep from github completes with out giving any error messages. I have not downloaded any cache or fasta files with the install, as they primarily seem to be for eukaryotic and not bacterial organism. I have installed a few of the plugins. To use VEP with bacterial data, I have: 1) generated a file listing polymorphism in ensembl format called relative to a bacterial reference genome -- 2) Used the example commands supplied in the manual to sort, bgzip compress, and tabix index a gff v3 input feature annotation file -- 3) and have a corresponding genome fasta file. When running the command: "vep -i polys.txt --gff bac.gff.gz --fasta bac.fasta" -- I get the EXCEPTION - MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed. Googling the error takes me to issue #30 https://github.com/Ensembl/ensembl-vep/issues/30. Following the suggestions on issue #30 https://github.com/Ensembl/ensembl-vep/issues/30 I have checked to confirm the installations of htslib and Bio::DB::HTS v3. Using the command: perl -e "use Bio::DB::HTS::Tabix" perl finds the module. Despite this running vep gives the same error msg. I am now at a loss as to how to progress further. I do not know where vep/perl is looking that it cannot find Bio::DB::HTS::Tabix. I have run installations using anaconda, but the version installed v87 does not seem to have the use of gff files for polymorphism annotations implemented, this appears to be a feature added in v88. It would be nice if the vep conda package could be updated to the latest version v96. It would be nice if you could include more information in the vep manual for the setup and use of vep for prokaryotic organisms. The bacterial genome that I am working with is not present in Ensembl Bacteria and the Web version of VEP does not seem to have the option of providing the .vcf .gff.gz and .fasta files that the commandline version of VEP supposedly accepts. Looking for any guidance or additional insight I can get. Thanks in advance for any help. Steve Beres
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I am trying to use VEP on bacterial genomes, largely for its ability to predict the consequences of indels. I have installed VEP Ensembl API version 96 on a workstation with Ubuntu 18.10 OS. Running the "perl INSTALL.pl" install script on vep from github completes with out giving any error messages. I have not downloaded any cache or fasta files with the install, as they primarily seem to be for eukaryotic and not bacterial organism. I have installed a few of the plugins. To use VEP with bacterial data, I have: 1) generated a file listing polymorphism in ensembl format called relative to a bacterial reference genome -- 2) Used the example commands supplied in the manual to sort, bgzip compress, and tabix index a gff v3 input feature annotation file -- 3) and have a corresponding genome fasta file. When running the command: "vep -i polys.txt --gff bac.gff.gz --fasta bac.fasta" -- I get the EXCEPTION - MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed. Googling the error takes me to issue #30. Following the suggestions on issue #30 I have checked to confirm the installations of htslib and Bio::DB::HTS v3. Using the command: perl -e "use Bio::DB::HTS::Tabix" perl finds the module. Despite this running vep gives the same error msg. I am now at a loss as to how to progress further. I do not know where vep/perl is looking that it cannot find Bio::DB::HTS::Tabix. I have run installations using anaconda, but the version installed v87 does not seem to have the use of gff files for polymorphism annotations implemented, this appears to be a feature added in v88. It would be nice if the vep conda package could be updated to the latest version v96. It would be nice if you could include more information in the vep manual for the setup and use of vep for prokaryotic organisms. The bacterial genome that I am working with is not present in Ensembl Bacteria and the Web version of VEP does not seem to have the option of providing the .vcf .gff.gz and .fasta files that the commandline version of VEP supposedly accepts. Looking for any guidance or additional insight I can get. Thanks in advance for any help. Steve Beres