Problem
The various Ensembl databases for genome resources (core Ensembl, Metazoa, Fungi, Protists, Plants, Bacteria) all have their own versioning. However, ZARP-cli currently provides only the option for setting a single default release version to use. This can create problems, especially if users frequently run analyses on libraries from multiple source.
For example, a version number of, say, 50 could represent the latest version of one database, but a very old version for another. It is also highly possible that the desired version in one database is not yet (or not anymore) in another.
Solution
By defining database-specific default versions, users or groups of users will be able to run all of their analyses on a common recent release version for each group of organisms/sources.
Context
For reference, the current latest versions and corresponding release dates for the individual databases are:
- Ensembl: 110 (July '23)
- Ensembl Metazoa: 57 (July '23)
- Ensembl Fungi: 57 (July '23)
- Ensembl Protists: 57 (July '23)
- Ensembl Plants: 57 (July '23)
- Ensembl Bacteria: 57 (July '23)
From this it seems that releases are coordinated and that only two different versioning schemes are used (110 and 57).
Therefore, it would -at least for the moment- be sufficient to provide just one more default version parameter (for all of Metazoa, Fungi, Protists, Plants, Bacteria).
Suggested implementation
ZARP-cli currently has no knowledge of which organism/source is fetched from which Ensembl database. Apart from adding an additional parameter, therefore this information needs to be encoded somewhere, preferably as an additional column in the ./data/genome_assemblies_map.tsv.
Problem
The various Ensembl databases for genome resources (core Ensembl, Metazoa, Fungi, Protists, Plants, Bacteria) all have their own versioning. However, ZARP-cli currently provides only the option for setting a single default release version to use. This can create problems, especially if users frequently run analyses on libraries from multiple source.
For example, a version number of, say, 50 could represent the latest version of one database, but a very old version for another. It is also highly possible that the desired version in one database is not yet (or not anymore) in another.
Solution
By defining database-specific default versions, users or groups of users will be able to run all of their analyses on a common recent release version for each group of organisms/sources.
Context
For reference, the current latest versions and corresponding release dates for the individual databases are:
From this it seems that releases are coordinated and that only two different versioning schemes are used (110 and 57).
Therefore, it would -at least for the moment- be sufficient to provide just one more default version parameter (for all of Metazoa, Fungi, Protists, Plants, Bacteria).
Suggested implementation
ZARP-cli currently has no knowledge of which organism/source is fetched from which Ensembl database. Apart from adding an additional parameter, therefore this information needs to be encoded somewhere, preferably as an additional column in the
./data/genome_assemblies_map.tsv.