Erfan Shekarriz comments

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                                            Erfan Shekarriz

[Enhancement] Improving Multi-sample Parallelisation Strategy

Yes I think for the time being I am simply running each parallel on a cluster using Snakemake so that the memory allocation is adjusted using a formula based on...

[BUG] in writeMPS with open(filename, "w") as f: FileNotFoundError: [Errno 2] No such file or directory: 'tmp/d43ef73e150d46648f4e326813c760da-pulp.mps'

UPDATES: I've come closer to the solution here. If I restart the server and do NOT set ```export TMPDIR=tmp``` then setting the output directory ```-w``` works. Is there a way...

cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```

I've noticed that putting the function into a list returns a list of TopHits objects: ```python tophits_list = list(hmmsearch(hmm_file, seqs, cpus=cores_n, Z=Z_val, bit_cutoffs=bitcutoff)) ``` How would I then be able...

[Feature Request] Internally assigning Z for ```HMM``` class

I've found an easy workaround with: ```python with HMMFile(hmmdb) as hmm_file: hmms = list(hmm_file) Z_val = len(hmms) ``` but I'll still keep the issue open since an attribute for the...

Model selection for rank/beta penalty criterion of the SLR

Nevermind! I seem to have found it. ``` ranks

conda installation issue

for conda beginners, you can use a one-liner! `conda install -c conda-forge -c bioconda tiara numpy=1.19.4 whokaryote `. Make sure to create an environment pre-hand and activate it first .e.g...

name attribute ValueError when running on the cluster

Also wanted to add that adding a ```\``` to escape the ```:``` pythonic dictionary format works, but It makes the name printed also have a backlash which is undesirable.

More specific recommendations in Raise CreateCondaEnvironmentException: Conda must be version 24.7.1 or later,

> May I ask where you switched this off? In one of the rules? I cannot find this in the program file or in the rules of the pipeline I...