Changes to FTP directory layout in Ensembl Genomes 43 / Ensembl 96

We will make changes to the directory layouts of both the Ensembl Genomes FTP server (ftp://ftp.ensemblgenomes.org/pub/) and the Ensembl GRCh37 FTP server (ftp://ftp.ensemblorg.ebi.ac.uk/pub/grch37/) that may affect your pipelines. These changes will come into effect in Ensembl Genomes release 43/Ensembl release 96, which are scheduled for April 2019. Here are the details, so that you can plan any required updates to existing scripts and pipelines ahead of the releases.

Ensembl Genomes

We will change the directory layout of the Ensembl Genomes FTP server to make it consistent with the Ensembl FTP server. This will affect directories with variation and comparative genomics (compara) data as detailed below.

Variation

We will move the ‘gvf’, ‘vcf’ and ‘vep’ directories into a new ‘variation’ directory.

For example, the directories that are here in Ensembl Genomes 42:
ftp://ftp.ensemblgenomes.org/pub/plants/release-42/gvf/
ftp://ftp.ensemblgenomes.org/pub/plants/release-42/vcf/
ftp://ftp.ensemblgenomes.org/pub/plants/release-42/vep/

will be found here in Ensembl Genomes 43:
ftp://ftp.ensemblgenomes.org/pub/plants/release-43/variation/gvf/
ftp://ftp.ensemblgenomes.org/pub/plants/release-43/variation/vep/
ftp://ftp.ensemblgenomes.org/pub/plants/release-43/variation/vcf/

In Ensembl Genomes 43, we will provide symlinks to the files in the previous directories:
ftp://ftp.ensemblgenomes.org/pub/plants/release-43/gvf/ -> ftp://ftp.ensemblgenomes.org/pub/plants/release-43/variation/gvf/
ftp://ftp.ensemblgenomes.org/pub/plants/release-43/vcf/ -> ftp://ftp.ensemblgenomes.org/pub/plants/release-43/variation/vcf/
ftp://ftp.ensemblgenomes.org/pub/plants/release-43/vep/ -> ftp://ftp.ensemblgenomes.org/pub/plants/release-43/variation/vep/

We will remove the symlinks in Ensembl Genomes 44, which is scheduled for June 2019.
The directory layout will change in a similar fashion for fungi, protists and metazoa.

For consistency, we will also change the case of the ‘VEP’ directory for vertebrates from uppercase to lowercase in Ensembl 96. The directory:
ftp://ftp.ensembl.org/pub/release-95/variation/VEP/
will be found here in Ensembl 96:
ftp://ftp.ensembl.org/pub/release-96/variation/vep/
We will provide a symlink to the previous directory and remove it in Ensembl 97, which is scheduled for June 2019.

Compara

The change will affect the whole genome alignment files. We have implemented the changes for plants in the current release (Ensembl Genomes 42) already, while providing symlinks for backwards compatibility.

For example, the content of:
ftp://ftp.ensemblgenomes.org/pub/release-42/plants/maf/

has been moved to this new directory:
ftp://ftp.ensemblgenomes.org/pub/release-42/plants/maf/ensembl-compara/pairwise_alignments/

Currently, the directory ftp://ftp.ensemblgenomes.org/pub/release-42/plants/maf/ contains symlinks to the files in the new directory.

In Ensembl Genomes 43, the directory layout will change in a similar fashion for fungi, protists and metazoa, and we will provide symlinks to the files in the previous directories. We will remove all symlinks in Ensembl Genomes 44.

Ensembl GRCh37

We will remove the symlink from http://ftp.ensembl.org/pub/grch37/update which currently points to Ensembl 95. In Ensembl 96, all data will be available at http://ftp.ensembl.org.ebi.ac.uk/pub/grch37/current/.