karel-brinda MiniPhy issues

karel-brinda / MiniPhy

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

https://brinda.eu/mof

Other

16 stars 0 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Cluster

#106 karel-brinda closed 6 months ago
0
Add possibility to pass cluster params

#105 karel-brinda closed 6 months ago
0
Test thoroughly on macos as well

#104 karel-brinda closed 6 months ago
0
Resume jobs

#103 shenwei356 closed 6 months ago
3
Make attotree read the list of input files from a file

#102 karel-brinda closed 6 months ago
0
Tree inference – argument list too long: '/bin/sh

#101 karel-brinda closed 6 months ago
0
Extend documentation in the readme

#100 karel-brinda opened 6 months ago
0
Fix and extend CI testing

#99 karel-brinda closed 6 months ago
0
Remove ete3 dependency

#98 karel-brinda opened 6 months ago
1
Improve GH Actions testing with various combinations of Snakemake and Python

#97 karel-brinda closed 6 months ago
0
Fix int conversion

#96 karel-brinda closed 6 months ago
0
Simplify handling .conda/ in tests

#95 karel-brinda closed 6 months ago
0
Missing int conversion by argparse in `create_batches.py`

#94 shenwei356 closed 6 months ago
2
Suggestion on create_batches.py

#93 shenwei356 opened 6 months ago
1
Iterate over species in their alphabetical order when creating dustbin

#92 karel-brinda closed 6 months ago
0
Add an -c option for adding comments to batching output

#91 karel-brinda closed 6 months ago
0
Add a param for adding comments to batching output text files

#90 karel-brinda closed 6 months ago
0
Dustbin creation – iterate over species in their alphabetical order

#89 karel-brinda closed 6 months ago
0
ProPhyle-based compression failing – but only with certain versions of Snakemake

#88 karel-brinda closed 6 months ago
8
Remove dependency on `snakemake.workflow.srcdir`

#87 karel-brinda closed 6 months ago
0
Simplify testing

#86 karel-brinda closed 6 months ago
0
Simplify test

#85 karel-brinda closed 6 months ago
0
Simplify testing

#84 karel-brinda closed 6 months ago
0
Always pass the number of threads

#83 karel-brinda closed 6 months ago
0
snakemake.workflow.srcdir discontinued in new versions of Snakemake

#82 karel-brinda closed 6 months ago
4
Add number of snakemake threads to config

#81 karel-brinda closed 6 months ago
0
Missing dependency: grpc

#80 shenwei356 closed 6 months ago
6
Move attotree to a sep env and use its latest version

#79 karel-brinda closed 7 months ago
0
Enhancement: do all the `seqtk seq` file conversion at once, parallelized eg by GNU parallel

#78 karel-brinda opened 8 months ago
0
Replace mashtree by attotree

#77 karel-brinda closed 8 months ago
0
Rename MOF-Compress to MiniPhy

#76 karel-brinda closed 9 months ago
0
Add script for batching

#75 karel-brinda closed 6 months ago
0
Cleanup

#74 karel-brinda closed 10 months ago
0
Add a small version of the logo

#73 karel-brinda closed 10 months ago
0
Fix background

#72 karel-brinda closed 10 months ago
0
Add XZ to essential dependencies

#71 karel-brinda closed 10 months ago
0
Add trees_required config option

#70 karel-brinda closed 10 months ago
0
Remove pandas & numpy as dependencies

#69 karel-brinda opened 10 months ago
1
Improve Jellyfish configurability

#68 karel-brinda closed 10 months ago
0
Make jellyfish more configurable

#67 karel-brinda closed 10 months ago
0
Update README.md

#66 karel-brinda closed 10 months ago
0
Update README.md

#65 karel-brinda closed 10 months ago
0
Add .test/ autodetection

#64 karel-brinda closed 10 months ago
0
Tests not runnable by `make` from `.test`

#63 karel-brinda closed 10 months ago
0
Update documentation and make functionality

#62 karel-brinda closed 10 months ago
0
Improve documentation, configuration, and its parsing

#61 karel-brinda closed 10 months ago
0
Config options are parsed only on the top level yaml

#60 karel-brinda closed 10 months ago
0
Add a default script for batching

#59 karel-brinda closed 6 months ago
0
Add an option for tree post-processing (to switch it off)

#58 karel-brinda opened 10 months ago
0
Add an option to fail if tree is not provided

#57 karel-brinda closed 10 months ago
0