I suggest integrating the docker code into the repository for uniformity (as in fur).
The old external repo on my account should be considered deprecated.
I also have updated the container image itself and updated the tutorial a bit.
Changes:
the code for docker is migrating into this repository
updated the contents of the docker image
enabled automated installation of up-to-date golang for the docker image
README for the docker image was rewritten
included "less" to actually enalbe reading of the README
inlcuded neighborsDoc.pdf
updated Makefile
updated repo's README with the stuff regarding docker
I've worked through the tutorial from the container, and noticed that it required an update as well.
edits in the tutorial:
-- added a pipe from dree to dot (before the dot-rendered figure)
-- as of 31.01.2024, 307 neighbor genomes are being fetched by
datasets instead of 306. I updated the references to clades
and all outputs accordingly. In the future, the number of
genomes downloaded with datasets shall differ from the
tutorial significantly, with each new genome ruining clade
picking due to shifts in node labeling. I do not see how to
make the datasets stuff more stable for the tutorial.
-- updated figure 4.2 (the reduced tree) with new node labels
-- some other little edits
haubold
commented
7 months ago
Hello Bernhard,
I suggest integrating the docker code into the repository for uniformity (as in fur). The old external repo on my account should be considered deprecated. I also have updated the container image itself and updated the tutorial a bit.
Changes:
I've worked through the tutorial from the container, and noticed that it required an update as well.
datasetsinstead of 306. I updated the references to clades and all outputs accordingly. In the future, the number of genomes downloaded with datasets shall differ from the tutorial significantly, with each new genome ruining clade picking due to shifts in node labeling. I do not see how to make the datasets stuff more stable for the tutorial. -- updated figure 4.2 (the reduced tree) with new node labels -- some other little editsCheers, Ivan