new eggNOG

V 2.6a2 should solve the eggNOg version as we use now eggNOG mapper >2.1.2

Alos Singularity suport is comming #359

Many of you have noticed unbearable long downloading times for installing packages E.g. #390
With the update of snakemake to >6.1 mamba is used instead of conda. This makes installing packages faster and more robust.

Even though this implied big changes in the back end, the API, and dependency graph doesn't change. This means You can continue your previous project with the updated version of atlas, at least this should be possible.

I never less marked this version as alpha because I had a breaking change in the HTML reports. I don't think fixing this is now a priority as almost all the stats can be looked at as tables. Once, I have fixed this you will be able to rerun the reports without impact on the other results.

Mambo jambo

My PhD Thesis is written, I have now time to work a bit on atlas.

Many of you have noticed unbearable long downloading times for installing packages E.g. #390
With the update of snakemake to >6.1 mamba is used instead of conda. This makes installing packages faster and more robust.

Even though this implied big changes in the back end, the API, and dependency graph doesn't change. This means You can continue your previous project with the updated version of atlas, at least this should be possible.

I never less marked this version as alpha because I had a breaking change in the HTML reports. I don't think fixing this is now a priority as almost all the stats can be looked at as tables. Once, I have fixed this you will be able to rerun the reports without impact on the other results.

Update to GTDB release 6

The new GTDB data will be stored in database_folder/GTDB_V6 you can delete the folder for V5 if you have used atlas before.

Fix eggNOGmapper

2.4.5

Fix #346

Allow parameters in init qc

allows to parametrize import qc

importqc_params: 
"iupacToN=t touppercase=t qout=33 addslash=t trimreaddescription=t"

2.4.3

corrects code for normal execution of eggNOG mapper

as in 2.4.2

Makes eggNOG annotation faster if virtual memory can be used:

If you have a virtual disk e.g. /dev/shm you can enable that atlas copy the eggNOG db to this virtual drive which accelerates the eggNOg annotation considerably.

More info in the eggNOG docs

You ned to set:

eggNOG_use_virtual_disk: true

Faster annotation with eggNOG mapper

Makes eggNOG annotation faster if virtual memory can be used:

If you have a virtual disk e.g. /dev/shm you can enable that atlas copy the eggNOG db to this virtual drive which accelerates the eggNOg annotation considerably.

More info in the eggNOG docs

You ned to set:

eggNOG_use_virtual_disk: true

Fix #259

Fix #313

Smal bug in genes2genomes.tsv

full compatibility with Atlas analyze

With new GTDB v05

updae to new GTDB (#306)

* updae to new GTDB

fix #404

* new version specific download path

* update verion 2.4

* define mem 4 via --config in ciricle ci test assembly

set better default parameters

See #303