Merge branch 'cellgeni-master'

hemberg-lab · Jul 30, 2021 · c123954 · c123954
2 parents f30af7f + 98e8c9a
commit c123954
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diff --git a/.github/workflows/build-course.yml b/.github/workflows/build-course.yml
@@ -10,7 +10,7 @@ jobs:
 
     runs-on: self-hosted
     container:
-      image: quay.io/cellgeni/scrna-seq-course:v5.11
+      image: quay.io/cellgeni/scrna-seq-course:v5.14
       options: --user root
 
     env:
@@ -36,20 +36,20 @@ jobs:
         run : cp -r $GITHUB_WORKSPACE/course_files/* $BUILD_DIR
 
       - name: Retrieve course data from S3
-        run: aws s3 sync s3://test-course-bucket/data/ $BUILD_DIR/data --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }}
+        run: aws s3 sync s3://singlecellcourse/data/ $BUILD_DIR/data --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }}
 
       - name: Retrieve bookdown cache from S3
-        run: aws s3 sync s3://test-course-bucket/_bookdown_files/ $BUILD_DIR/_bookdown_files --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }}
+        run: aws s3 sync s3://singlecellcourse/_bookdown_files/ $BUILD_DIR/_bookdown_files --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }}
 
       - name: Render bookdown Rmd files for site generation
         working-directory: ${{ env.BUILD_DIR }}
-        run: Rscript -e "bookdown::render_book('index.html', 'bookdown::gitbook')"
+        run: Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"
 
       - name: Upload rendered bookdown files to S3
-        run: aws s3 sync $BUILD_DIR/website s3://test-course-bucket/website/ --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }} --acl public-read
+        run: aws s3 sync $BUILD_DIR/website s3://singlecellcourse/website/ --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }} --acl public-read
 
       - name: Upload bookdown cache to S3
-        run: aws s3 sync $BUILD_DIR/_bookdown_files s3://test-course-bucket/_bookdown_files/ --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }}
+        run: aws s3 sync $BUILD_DIR/_bookdown_files s3://singlecellcourse/_bookdown_files/ --endpoint-url ${{ secrets.AWS_S3_ENDPOINT }}
 
       - name: Clean workspace after finish
         run: rm -rf $GITHUB_WORKSPACE/*
diff --git a/Dockerfile b/Dockerfile
@@ -3,20 +3,12 @@ FROM jupyter/base-notebook
 # versions of software
 ARG r_cran_version="cran40"
 ARG rstudio_version="1.2.5019"
-ARG fastqc_version="0.11.9"            
-ARG kallisto_version="0.46.2"          
-ARG samtools_version="1.11"            
-ARG trimgalore_version="0.6.6"         
-ARG bedtools_version="2.29.2"           
-ARG featurecounts_version="2.0.1"       
-
-#old software verions
-#fastqc=0.11.5
-#kallisto=0.43.1
-#samtools=1.9
-#trimgalore=0.4.5
-#bedtools=2.27.1
-#featurecounts=1.5.1
+ARG fastqc_version="0.11.9"
+ARG kallisto_version="0.46.2"
+ARG samtools_version="1.11"
+ARG trimgalore_version="0.6.6"
+ARG bedtools_version="2.29.2"
+ARG featurecounts_version="2.0.1"
 
 USER root
 
@@ -139,31 +131,35 @@ RUN Rscript -e 'install.packages(c( \
     "snow", "bit64", "permute", "mixtools", "lars", "ica", "fpc", "ape", \
     "pbapply", "irlba", "dtw", "plotly", "metap", "lmtest", "fitdistrplus", "png", \
     "foreach", "vegan", "tidyr", "withr", "magrittr", "rmpi", "knitr", \
-    "statmod", "mvoutlier", "penalized", "mgcv", "corrplot", \
-    "lsa", "uwot", "optparse", "DrImpute", "alluvial"))'
+    "statmod", "mvoutlier", "penalized", "mgcv", "corrplot", "scales", "rliger", \
+    "lsa", "uwot", "optparse", "DrImpute", "alluvial", "dplyr", "RColorBrewer"))'
 
 # Install Bioconductor packages
 RUN Rscript -e 'BiocManager::install(c( \
     "graph", "RBGL", "gtools", "xtable", "pcaMethods", "limma", "SingleCellExperiment", \
     "Rhdf5lib", "scater", "scran", "RUVSeq", "sva", "SC3", "TSCAN", "monocle", "destiny", \
     "DESeq2", "edgeR", "MAST", "scmap", "biomaRt", "MultiAssayExperiment", "SummarizedExperiment", \
-    "beachmat", "DropletUtils", "EnsDb.Hsapiens.v86", "batchelor"))'
+    "beachmat", "DropletUtils", "EnsDb.Hsapiens.v86", "batchelor", "SingleR", "celldex", \
+    "glmGamPoi", "AnnotationDbi", "org.Hs.eg.db", "EnsDb.Hsapiens.v86"))'
 
 # Install github packages
 RUN Rscript -e 'devtools::install_github(c( \
     "immunogenomics/harmony", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs", \
     "Vivianstats/scImpute", "theislab/kBET", "kieranrcampbell/ouija", "hemberg-lab/scfind", \
-    "cole-trapnell-lab/monocle3"))'
+    "cole-trapnell-lab/monocle3", "mojaveazure/seurat-disk", "satijalab/seurat-wrappers"))'
 
 # Install python packages
 RUN pip install --upgrade --no-cache \
     cutadapt magic-impute awscli==1.16.14 \
     jupyter-server-proxy \
-    jupyter-rsession-proxy rpy2
+    jupyter-rsession-proxy rpy2 \
+    leidenalg
 
 # JupyterLab extension to launch registered applications in the python package
 RUN jupyter labextension install @jupyterlab/server-proxy
 
+RUN conda clean --all --yes
+
 # fix permissions
 RUN fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER

diff --git a/README.md b/README.md
@@ -10,6 +10,10 @@ The number of computational tools is increasing rapidly and we are doing our bes
 
 __[https://www.singlecellcourse.org](https://www.singlecellcourse.org)__
 
+#### Data
+
+__[https://singlecellcourse.cog.sanger.ac.uk/data/](https://singlecellcourse.cog.sanger.ac.uk/data/)__
+
 ## Video
 
 This video was recorded during the course (2 days) in May 2019.
@@ -28,15 +32,15 @@ Please follow this link and register for the __"Analysis of single cell RNA-seq
 
 ## Docker image
 
-[![Docker Repository on Quay](https://quay.io/repository/hemberg-group/scrna-seq-course/status "Docker Repository on Quay")](https://quay.io/repository/hemberg-group/scrna-seq-course)
+[![Docker Repository on Quay](https://quay.io/repository/cellgeni/scrna-seq-course/status "Docker Repository on Quay")](https://quay.io/repository/cellgeni/scrna-seq-course)
 
 The course can be reproduced without any package installation by running the course docker image which contains all the required packages.
 
 ### Run the image
-Make sure Docker is installed on your system. If not, please follow [these instructions](https://docs.docker.com/engine/installation/). To run the course docker image (use [the latest version](https://quay.io/repository/hemberg-group/scrna-seq-course?tab=tags) of the course instead of v3.13):
+Make sure Docker is installed on your system. If not, please follow [these instructions](https://docs.docker.com/engine/installation/). To run the course docker image (use [the latest version](https://quay.io/repository/cellgeni/scrna-seq-course?tab=tags) of the course instead of v5.14):
 
 ```
-docker run -p 8888:8888 -e PASSWORD="jupyter" quay.io/hemberg-group/scrna-seq-course:v3.13
+docker run -p 8888:8888 -e PASSWORD="jupyter" quay.io/cellgeni/scrna-seq-course:v5.14
 ```
 
 Then follow the instructions provided, e.g.:
@@ -65,7 +69,7 @@ Please click on `New -> Terminal`. In the new terminal window please run:
 
 If you want to download data files outside of Docker image you can still use the same `poststart.sh` script but you will need to install [AWS CLI](https://docs.aws.amazon.com/cli/latest/userguide/install-bundle.html) on your computer.
 
-Alternatively, you can browse and download the files in you web-browser by visiting [this link](https://scrnaseq-course.cog.sanger.ac.uk/index.html?prefix=data/).
+Alternatively, you can browse and download the files in you web-browser by visiting [this link](https://singlecellcourse.cog.sanger.ac.uk/index.html?shared=data/).
 
 ### RStudio