Daniel Lang

Thanks for developing, providing and maintaining orthofinder, it's a milestone tool! Your work on this is greatly appreciated! Applying it to all kinds of datasets I think these easy to...

conda installation fails - numpy>=1.14.0 does not work

3

Hi @dansondergaard , I've set up a clean env to install your tool and installing just your package works, but execution results in this error ``` Traceback (most recent call...

Changed URL for megares

1

Hi guys, the URL for megares has changed: https://megares.meglab.org/downloads/megares_v2.00.zip https://github.com/tseemann/abricate/blob/955d402a23371a61bfca48f1b9e0d30ac724e6ef/bin/abricate-get_db#L350 Best, Daniel

fix_pos in af/fixbb

2

Dear developers, I'm trying to use ColabDesign AF to design a sequence using the `fixbb` protocol fixing sites with a list of positions as follows: ```python model = mk_afdesign_model(protocol="fixbb") model.prep_inputs(pdb_filename="mystruc.pdb",...

How to improve performance for Illumina-based analysis of viral pangenome

12

Hi, I'd like to use pandora to study a viral pangenome on the basis of Illumina data. All together I'm looking at 13 input MSAs. Each comprise ~300 high-quality reference...

Question of usage of explicit import of snakemake object from snakemake.scripts

1

Hi, the doc states that one can "enable code completion, linting and type checking your python code in IDEs" by explicitely importing from snakemake.script. https://github.com/snakemake/snakemake/blob/e8735c1477a2a82110757ba86bbd1ccbcaf327ba/docs/snakefiles/rules.rst#L1138 Does this only work in...

Is there an example for how to use the --wait-for-files-file option?

1

Hi, I'm running into an "Argument list too long" issue when aggregating dynamic results in a workflow and can't quite wrap my head around how I can generate this file...