iqbal-lab-org pling issues

iqbal-lab-org / pling

Plasmid analysis using rearrangement distances

MIT License

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issues

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Issue getting pling running

#65 JavierFFavieres opened 1 week ago
2
Allow to skip integerisation

#64 babayagaofficial closed 1 week ago
0
Allow skipping integerisation step

#63 babayagaofficial opened 2 weeks ago
0
Allow for both linear and circular plasmids, as well as regions

#62 babayagaofficial opened 2 weeks ago
0
Snakemake thinks there's whitespaces in filepaths?

#61 jhawkey closed 1 month ago
12
End dependency handling via --use-conda flag in snakemake

#60 babayagaofficial opened 1 month ago
0
V1.1

#59 babayagaofficial closed 3 weeks ago
0
Output SNPs in some form

#58 babayagaofficial opened 1 month ago
0
Pling! incorrectly computes containment similarity as 0 for highly similar sequences

#57 apcamargo opened 1 month ago
15
Scale cat

#56 babayagaofficial closed 2 months ago
0
Improve batching memory use with sourmash

#55 babayagaofficial closed 2 months ago
0
An attempt to fix Marjorie's whitespace bug by using python's built i…

#54 babayagaofficial closed 3 months ago
0
Update unit tests

#53 babayagaofficial closed 4 months ago
0
Nucmer block bug fix

#52 babayagaofficial closed 5 months ago
0
No easy way to unlock the current dir

#51 leoisl closed 4 months ago
3
fix: update plasnet to 0.4.1

#50 leoisl closed 6 months ago
0
Switch rule gen_minimap_input to use conda environment instead of a container

#49 leoisl closed 2 months ago
1
fix: remove poetry infrastructure and update integration tests and CI

#48 leoisl closed 6 months ago
0
Problem running pling in EBI cluster

#47 leoisl closed 6 months ago
0
Add pangraph support in time for second paper/ABC

#46 iqbal-lab opened 7 months ago
0
Add pangraph support in time for second paper/ABC

#45 iqbal-lab closed 2 months ago
0
Add option to run on regions

#44 babayagaofficial opened 7 months ago
0
Split networks for subcommunities

#43 babayagaofficial opened 7 months ago
0
Batching

#42 babayagaofficial closed 7 months ago
0
Improve overlap

#41 babayagaofficial closed 7 months ago
0
fix: fix issue with running pling outside of the repo dir

#40 leoisl closed 7 months ago
1
Implement --version command

#39 leoisl closed 6 months ago
1
Merge dev to main

#38 leoisl closed 7 months ago
0
Plasnet integration PR series (5/5): tests: add integration tests to all pling commands

#37 leoisl closed 7 months ago
0
Plasnet integration PR series (4/5): feat: integrate plasnet into pling

#36 leoisl closed 7 months ago
0
Plasnet integration PR series (3/n): refactor: refactor common rules and functions from workflows into common_rules.smk

#35 leoisl closed 7 months ago
0
Plasnet integration PR series (2/n): refactor: adding CLI to 4 python scripts

#34 leoisl closed 7 months ago
4
fix: fix GLPK to gurobi translation for long ILPs

#33 leoisl closed 7 months ago
1
For long ILPs, the GLPK solution might include some unexpected line breaks, making our downstream parsing bugged

#32 leoisl closed 7 months ago
2
Plasnet integration PR series (1/n): refactor: delete now redundant files, replaced by plasnet

#31 leoisl closed 7 months ago
0
length_threshold is not used at all in seq_jaccard.py

#30 leoisl closed 7 months ago
1
Add poetry infrastructure, making pling easily installable

#29 leoisl closed 7 months ago
0
refactor: sources into pling directory

#28 leoisl closed 7 months ago
0
Complicated overlap fix

#27 babayagaofficial closed 7 months ago
1
Add batching

#26 babayagaofficial closed 7 months ago
0
Should all roundhound plasmid comparison scripts be moved to pling?

#25 leoisl closed 7 months ago
2
Different integers assigned to genes in separate run-throughs

#24 babayagaofficial opened 8 months ago
3
Organise the different ways we have to visualise and analyse plasmid graphs in both pling and RH

#23 leoisl closed 7 months ago
2
Make command to install bakta db

#22 babayagaofficial opened 9 months ago
2
[Draft] Clean up anno

#21 babayagaofficial closed 9 months ago
0
Reduce dependencies for anno_snakemake

#20 babayagaofficial closed 9 months ago
6
Make pling pip- and conda-installable

#19 leoisl closed 7 months ago
4
Add an integration test, modularise run_pling.py and add CI pipeline

#18 leoisl closed 8 months ago
2
Add CI and an end-to-end integration test

#17 leoisl closed 8 months ago
0
Adding GLPK as default solver and other misc improvements

#16 leoisl closed 9 months ago
0