Docker file for single cell analysis.

version 0.1

The packages explicitly installed in this image are:

scanpy==1.7.0
matplotlib==3.3.4
numpy==1.20.1
scipy==1.6.0
pandas==1.2.2
networkx==2.5
seaborn==0.11.1
scikit-learn==0.24.1
fa2==0.3.5
harmonypy==0.0.5
MulticoreTSNE==0.1
scrublet==0.2.3
pygam==0.8.0
python-igraph==0.9.6
louvain==0.7.0
xlsxwriter==1.4.4
leidenalg==0.8.7
bbknn==1.5.1
scanorama==1.7.1
phate==1.0.7
pypairs==3.2.3
phenograph==1.1.14
mnnpy==0.1.9.5
pydpc==0.1.3
sam_algorithm==0.8.7
DCA==0.3.4
magic-impute==3.0.0
palantir==1.0.0
trimap==1.0.15

version 0.2

This version incorporates over version 0.2:

openpyxl==3.0.9

and the git packages for the pyslingshot algorithm.

mossjacob/pcurvepy
mossjacob/pslingshot

version 0.3

This version incorporates over version 0.2:

gprofiler-official==1.0.0
scikit-misc==0.1.4
scvi-tools==0.14.6

For being able to execute the docker with GPUs functionality see this article(Need Different base image in Dockerfile).

version 0.4

Added

mnnpy==0.1.9.5

version 0.5

Added

scikit-misc=0.1.4
cdlib=0.2.6

version 0.6

Added

pympl
pyscenic

1. Building the docker

A docker image with the required python version and packages can be created running

./build.sh

It has been very useful the information from the blog: https://www.docker.com/blog/multi-platform-docker-builds/

2. Running the docker

For running the docker and go over the analysis steps in a jupyter lab session, just run,

./run.sh

Once run, the docker will be working and executing in the channel 10000. Change the channel in the run script if you want to run it in some other channel.. In the terminal you will find a token code that is generated for security reasons:

Copy that number. For accessing the session, open your favorite folder brwoser and search localhost:10000. Directly from the terminal it will be something like,

firefox localhost::10000

it will open a jupyterlab session that will ask for a password or token.

Copy the token you obtained before and you will be set up!

Anything in the home folder can be seen by the docker and you and will be saved after the docker is finished.