Commit 9b1d7243 authored by Michael Stadler's avatar Michael Stadler
Browse files

initial commit using renkulab-bioc (3.11) image

data/spermatogenesis_rnavelocity/* filter=lfs diff=lfs merge=lfs -text
data/spermatogenesis_rnavelocity/* !text !filter !merge !diff
data/spermatogenesis_rnavelocity/AdultMouseRep3_alevin_GRCm38.gencode.vM21.spliced.intron.fl90.gentrome.k31_sce_nometa.rds filter=lfs diff=lfs merge=lfs -text
# FROM renku/singleuser-r-bioconductor_3_10:0.4.4-rc1-renku0.8.2
# FROM renku/renkulab:renku0.10.3-biocRELEASE_3_11-renku-cb36961
FROM renku/renkulab-bioc:RELEASE_3_11-renku0.10.3-a2b490a
# copy files from current directory into the image
COPY docs /docs
# update pip and install setuptools, wheel
RUN pip3 install --upgrade pip && \
pip3 install --upgrade setuptools wheel
# install all other python dependencies
COPY requirements.txt /tmp/
RUN pip3 install -r /tmp/requirements.txt
# install the R dependencies
COPY install.R /tmp/
RUN R -f /tmp/install.R
# install remaining python packages that require R
RUN pip3 install anndata2ri
# Advanced topics in single-cell transcriptomics
This is a Renku project - basically a git repository with some
bells and whistles, for the [Advanced topics in single-cell transcriptomics course](
## Working with the project
The simplest way to start your project is right from the Renku
platform - just click on the `Environments` tab and start a new session.
This will start an interactive environment right in your browser.
You can choose if you want to use either a JupyterLab (`/lab`) or an
RStudio (`/rstudio`) interface. Also, make sure that you tick
the box labelled "Automatically fetch LFS data".
To work with the project anywhere outside the Renku platform,
click the `Settings` tab where you will find the
git repo URLs - use `git` to clone the project on whichever machine you want.
# update existing packages
BiocManager::install(ask = FALSE)
# install additional packages and dependencies
pkgs <- c("GenomicRanges", "GenomeInfoDbData", "GenomeInfoDb", "IRanges",
"Seurat", "SingleCellExperiment", "SummarizedExperiment",
"batchelor", "ggplot2", "keras", "scater", "scran", "tensorflow")
BiocManager::install(pkgs, ask = FALSE)
# setup tensorflow
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