document workflow figures : add some infos on key rules, input/output/what it does
Installation:
deal with COG database: rule to download it, or specify where to get it
gtdb install....
deal with desman
learn how to create a new releases for the new panda version
create a new conda install, with right version of pandas, referring to new desman release
create a conda based install (Seb)
either a conda repos, where everything is taken care of (submodule pull, compilation of spades tk)
or just an env and add some manual installation steps
document installations
document a conda env install and additional steps needed (compilation, etc)
document an install from source of all dependencies.
Figures/Results:
colored .gfa concatenated over SCG (try to generate corresponding fig from command line) (Seb)
gtdb output (Seb)
barplot of coverage for each strain of a mag (Kim)
for each mag : a tree of strains (Seb)
number of strain(y) versus coverage of bins (x) (Seb)
summary : nb strains, coverage each strain, total mag coverage, divergence,nb mags , nb bins, quality of assembly. (Seb)
Cosmetic changes:
make it so we don't call a script named start.py (Seb) DONE
make it so that we can call start.py from anywhere, not just the STRONG repos (Seb) DONE
change folders so that users can either get all the data they need, or all the results they needs : figs, nb strains/strains freq, trees ... etc
change bayespath output, these folder are a mess, we want informative files names, gamma is not, we want a meaningfull summary. We want less file in the same folder. A bit overwhelming.
misc
change scg_data : get the mean AA length for all cogs. DONE
latest version /mnt/gpfs/chris/Projects/STRONG_Runs/Benchmarking/ResultsI/Synth_G45_S10
Before release we want :
regenerate workflow figuresrule name consistency, upper case or notinformative rule namegenerate desman workflow figdeal with COG database: rule to download it, or specify where to get itdeal with desmanlearn how to create a new releases for the new panda versioncreate a new conda install, with right version of pandas, referring to new desman releasedocument a conda env install and additional steps needed (compilation, etc)document an install from source of all dependencies.latest version /mnt/gpfs/chris/Projects/STRONG_Runs/Benchmarking/ResultsI/Synth_G45_S10