initial commit using renkulab-bioc (3.11) image

.gitattributes

+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

Dockerfile

+# 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
+#RELEASE_3_11-renku0.10.3-cb36961
+
+# 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

README.md

+# 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](https://www.sib.swiss/training/course/2020-05-adv-scrna).
+
+## 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.

install.R

+# 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
+#library(tensorflow)
+#install_tensorflow()

requirements.txt

+numpy
+scipy
+cython
+numba
+matplotlib==3.0.3
+scikit-learn
+h5py
+click
+scvelo
+tensorflow==2.0
+keras