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karel-brinda/MiniPhy
Add possibility to pass cluster params

This is how it was done for MOF-Search: ifeq ($(SMK_CLUSTER_ARGS),) # configure local run SMK_PARAMS=--cores ${THREADS} --rerun-incomplete --printshellcmds --keep-going --use-conda --resources ...
enhancement
  • karel-brinda
  • Opened 
    on Mar 6, 2024
  • #105

karel-brinda/MiniPhy
Resume jobs

Trying to resume a finished job. There s a little bug. version: the arglist branch. $ snakemake --cores all --use-conda --conda-prefix= .conda -p Building DAG of jobs... Nothing to be done (all requested ...
  • shenwei356
  • 3
  • Opened 
    on Mar 6, 2024
  • #103

karel-brinda/MiniPhy
Tree inference – argument list too long: '/bin/sh

From @shenwei356: Morning, Karel, I manually activated the env of attotree and tried the command, it said: Traceback (most recent call last): File /hps/nobackup/iqbal/shenwei/2kk/batches.n-00.miniphy/.conda/ce9b7d8ca4029080ad672fb2aa324c3d_/bin/attotree ...
bug
  • karel-brinda
  • Opened 
    on Mar 6, 2024
  • #101

karel-brinda/MiniPhy
Extend documentation in the readme

Points to add: - Info about P3 + possibly related compilation issues - Document the batching script - Steps for building large compressed dbs
enhancement
  • karel-brinda
  • Opened 
    on Mar 5, 2024
  • #100

karel-brinda/MiniPhy
Remove ete3 dependency

It s really heavy and complicates building the conda environment. See all the unnecessary deps (from mamba search --info ete3): image
enhancement
  • karel-brinda
  • 1
  • Opened 
    on Mar 5, 2024
  • #98

karel-brinda/MiniPhy
Missing int conversion by argparse in `create_batches.py`

$ ./create_batches.py ../file2species.tsv -d input/ -s species -f file -c -m 200 Loaded 1932811 genomes across 10357 species clusters Traceback (most recent call last): File ./create_batches.py , ...
bug
  • shenwei356
  • 2
  • Opened 
    on Mar 5, 2024
  • #94

karel-brinda/MiniPhy
Suggestion on create_batches.py

Hi Karel, create_batches.py works as expected, here are just some minor suggestions. 1. In the help message, clustered_fastas.tsv is the input metafile containing file and species column, while its name ...
enhancement
  • shenwei356
  • 1
  • Opened 
    on Mar 5, 2024
  • #93

karel-brinda/MiniPhy
Add a param for adding comments to batching output text files

- possibly as a second column, starting with # - should be supported by the Snakememake input reading as well
enhancement
  • karel-brinda
  • Opened 
    on Mar 5, 2024
  • #90

karel-brinda/MiniPhy
Dustbin creation – iterate over species in their alphabetical order

This move close all eg various pseudomonas things such as 26 #pseudomonas_mandelii 1 #pseudomonas_mediterranea 11 #pseudomonas_mendocina 1 #pseudomonas_mesoacidophila 36 #pseudomonas_monteilii ...
enhancement
  • karel-brinda
  • Opened 
    on Mar 5, 2024
  • #89

karel-brinda/MiniPhy
ProPhyle-based compression failing – but only with certain versions of Snakemake

When executed make bigtest [Mon Mar 4 18:57:49 2024] localrule post_list: input: intermediate/tree/test_run_no_tree.nodes, intermediate/post/test_run_no_tree/GCGS0001-up3.simpl, intermediate/post/test_run_no_tree/GCGS0002-up1.simpl, ...
bug
  • karel-brinda
  • 8
  • Opened 
    on Mar 4, 2024
  • #88
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