diff --git a/.github/workflows/docker-publish-bioconductor-spatial.yaml b/.github/workflows/docker-publish-bioconductor-spatial.yaml index 6ea68792..9227573b 100644 --- a/.github/workflows/docker-publish-bioconductor-spatial.yaml +++ b/.github/workflows/docker-publish-bioconductor-spatial.yaml @@ -12,7 +12,7 @@ on: env: REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} + IMAGE_NAME: nbisweden/workshop-scrnaseq IMAGE_TAG: 2023-bioconductor_spatial-r4.3.0 diff --git a/.github/workflows/docker-publish-bioconductor.yaml b/.github/workflows/docker-publish-bioconductor.yaml index 5746ea79..eb244b2d 100644 --- a/.github/workflows/docker-publish-bioconductor.yaml +++ b/.github/workflows/docker-publish-bioconductor.yaml @@ -12,7 +12,7 @@ on: env: REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} + IMAGE_NAME: nbisweden/workshop-scrnaseq IMAGE_TAG: 2023-bioconductor-r4.3.0 diff --git a/.github/workflows/docker-publish-scanpy-spatial.yaml b/.github/workflows/docker-publish-scanpy-spatial.yaml index d117ec5c..b6721eb1 100644 --- a/.github/workflows/docker-publish-scanpy-spatial.yaml +++ b/.github/workflows/docker-publish-scanpy-spatial.yaml @@ -12,7 +12,7 @@ on: env: REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} + IMAGE_NAME: nbisweden/workshop-scrnaseq IMAGE_TAG: 2023-scanpy_spatial-py3.10 diff --git a/.github/workflows/docker-publish-scanpy.yaml b/.github/workflows/docker-publish-scanpy.yaml index 3a62e849..621e9179 100644 --- a/.github/workflows/docker-publish-scanpy.yaml +++ b/.github/workflows/docker-publish-scanpy.yaml @@ -12,7 +12,7 @@ on: env: REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} + IMAGE_NAME: nbisweden/workshop-scrnaseq IMAGE_TAG: 2023-scanpy-py3.10 diff --git a/.github/workflows/docker-publish-seurat-spatial.yaml b/.github/workflows/docker-publish-seurat-spatial.yaml index 439474eb..ed20b7b2 100644 --- a/.github/workflows/docker-publish-seurat-spatial.yaml +++ b/.github/workflows/docker-publish-seurat-spatial.yaml @@ -12,7 +12,7 @@ on: env: REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} + IMAGE_NAME: nbisweden/workshop-scrnaseq IMAGE_TAG: 2023-seurat_spatial-r4.3.0 diff --git a/.github/workflows/docker-publish-seurat.yaml b/.github/workflows/docker-publish-seurat.yaml index a218e7bf..545fe92c 100644 --- a/.github/workflows/docker-publish-seurat.yaml +++ b/.github/workflows/docker-publish-seurat.yaml @@ -12,7 +12,7 @@ on: env: REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} + IMAGE_NAME: nbisweden/workshop-scrnaseq IMAGE_TAG: 2023-seurat-r4.3.0 diff --git a/README.md b/README.md index ae8a3dd4..2c4b510b 100644 --- a/README.md +++ b/README.md @@ -22,13 +22,13 @@ git push origin ``` # for seurat labs -docker pull ghcr.io/NBISweden/workshop-scRNAseq:2023-seurat-r4.3.0 +docker pull ghcr.io/nbisweden/workshop-scrnaseq:2023-seurat-r4.3.0 # for bioconductor labs -docker pull ghcr.io/NBISweden/workshop-scRNAseq:2023-bioconductor-r4.3.0 +docker pull ghcr.io/nbisweden/workshop-scrnaseq:2023-bioconductor-r4.3.0 # for python labs -docker pull ghcr.io/NBISweden/workshop-scRNAseq:2023-scanpy-py3.10 +docker pull ghcr.io/nbisweden/workshop-scrnaseq:2023-scanpy-py3.10 ``` ## Run labs (locally) @@ -38,8 +38,8 @@ docker pull ghcr.io/NBISweden/workshop-scRNAseq:2023-scanpy-py3.10 - To run Seurat or Bioconductor labs in RStudio ``` -docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-seurat-r4.3.0 -docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-bioconductor-r4.3.0 +docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-seurat-r4.3.0 +docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-bioconductor-r4.3.0 ``` - Open in browser: `http://localhost:8787/`, login: rstudio, pass: scrnaseq @@ -48,7 +48,7 @@ docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v - To run Python labs in JupyterLab ``` -docker run --rm -ti --platform=linux/amd64 -p 8888:8888 -v $PWD:/home/jovyan/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-scanpy-py3.10 +docker run --rm -ti --platform=linux/amd64 -p 8888:8888 -v $PWD:/home/jovyan/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-scanpy-py3.10 ``` - Open in browser: `http://127.0.0.1:8888/lab?token=xxxx` (Use exact token from terminal on launch) @@ -61,19 +61,19 @@ Instructions to render the `.qmd` files to `.html`. - For Seurat labs ``` -docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-seurat-r4.3.0 quarto render /home/rstudio/workdir/labs/seurat/seurat_01_qc.qmd +docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-seurat-r4.3.0 quarto render /home/rstudio/workdir/labs/seurat/seurat_01_qc.qmd ``` - For Bioconductor labs ``` -docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-bioconductor-r4.3.0 quarto render /home/rstudio/workdir/labs/bioc/bioc_01_qc.qmd +docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-bioconductor-r4.3.0 quarto render /home/rstudio/workdir/labs/bioc/bioc_01_qc.qmd ``` - For Python labs ``` -docker run --rm -ti --platform=linux/amd64 -p 8888:8888 -v $PWD:/home/jovyan/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-scanpy-py3.10 quarto render /home/jovyan/workdir/labs/scanpy/scanpy_01_qc.qmd +docker run --rm -ti --platform=linux/amd64 -p 8888:8888 -v $PWD:/home/jovyan/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-scanpy-py3.10 quarto render /home/jovyan/workdir/labs/scanpy/scanpy_01_qc.qmd ``` - Successfully rendered outputs are moved to `docs` folder and chunks are cached under `_freeze`. diff --git a/containers/README.md b/containers/README.md index 10ac367a..c2098505 100644 --- a/containers/README.md +++ b/containers/README.md @@ -13,7 +13,7 @@ Here we use three different toolkits, namely `Seurat` (R/RStudio), `Bioconductor The different images are differentiated by the following `registry/username/image:tag` convention: ``` -ghcr.io/NBISweden/workshop-scRNAseq:-- +ghcr.io/nbisweden/workshop-scrnaseq:-- ``` Each image contains the required packages so that, for each toolkit, the following analysis steps can be performed: @@ -95,8 +95,8 @@ For the Python based image, you can install packages using `mamba`, `pip`, or `c ### R Based Images ```bash -docker pull ghcr.io/NBISweden/workshop-scRNAseq: -docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v /path/to/workdir:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq: +docker pull ghcr.io/nbisweden/workshop-scrnaseq: +docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v /path/to/workdir:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq: ``` In the browser, go to [localhost:8787](localhost:8787). @@ -107,8 +107,8 @@ Use the following credentials to log in to the RStudio Server: ### Python Based Image ```bash -docker pull ghcr.io/NBISweden/workshop-scRNAseq: -docker run --rm -ti -p 8888:8888 -v /path/to/workdir:/home/jovyan/workshop-scRNAseq ghcr.io/NBISweden/workshop-scRNAseq: +docker pull ghcr.io/nbisweden/workshop-scrnaseq: +docker run --rm -ti -p 8888:8888 -v /path/to/workdir:/home/jovyan/workshop-scRNAseq ghcr.io/nbisweden/workshop-scrnaseq: ``` In the browser, go to [localhost:8888](localhost:8888). diff --git a/containers/docs/run-containers.qmd b/containers/docs/run-containers.qmd index a8eaf23e..e930252b 100644 --- a/containers/docs/run-containers.qmd +++ b/containers/docs/run-containers.qmd @@ -126,8 +126,8 @@ To avoid running out of memory, restart R (_Session > Restart R_) after each lab ```bash cd /path/to/workshop-dir # replace this with the full path to the workshop folder -docker pull ghcr.io/NBISweden/workshop-scRNAseq:2023-seurat-r4.3.0 -docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-seurat-r4.3.0 +docker pull ghcr.io/nbisweden/workshop-scrnaseq:2023-seurat-r4.3.0 +docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-seurat-r4.3.0 ``` In the browser, go to [localhost:8787](localhost:8787). @@ -144,8 +144,8 @@ To avoid running out of memory, restart R (_Session > Restart R_) after each lab ```bash cd /path/to/workshop-dir # replace this with the full path to the workshop folder -docker pull ghcr.io/NBISweden/workshop-scRNAseq:2023-bioconductor-r4.3.0 -docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-bioconductor-r4.3.0 +docker pull ghcr.io/nbisweden/workshop-scrnaseq:2023-bioconductor-r4.3.0 +docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-bioconductor-r4.3.0 ``` In the browser, go to [localhost:8787](localhost:8787). Use the following credentials to log in to the RStudio Server: @@ -166,8 +166,8 @@ To avoid running out of memory, restart the kernel (_Kernel > Restart Kernel_) a ```bash cd /path/to/workshop-dir # replace this with the full path to the workshop folder -docker pull ghcr.io/NBISweden/workshop-scRNAseq:2023-scanpy-py3.10 -docker run --rm -ti -p 8888:8888 -v ${PWD}:/home/jovyan/workdir ghcr.io/NBISweden/workshop-scRNAseq:2023-scanpy-py3.10 +docker pull ghcr.io/nbisweden/workshop-scrnaseq:2023-scanpy-py3.10 +docker run --rm -ti -p 8888:8888 -v ${PWD}:/home/jovyan/workdir ghcr.io/nbisweden/workshop-scrnaseq:2023-scanpy-py3.10 ``` At the end of the prompt, you will see a URL that starts with `http://127.0.0.1`, similar to the one below: diff --git a/containers/uppmax/singularity_bioconductor.def b/containers/uppmax/singularity_bioconductor.def index d1633366..6c08dfd3 100644 --- a/containers/uppmax/singularity_bioconductor.def +++ b/containers/uppmax/singularity_bioconductor.def @@ -1,7 +1,6 @@ Bootstrap: docker -From: ghcr.io/NBISweden/workshop-scRNAseq:2023-bioconductor-r4.3.0 +From: ghcr.io/nbisweden/workshop-scrnaseq:2023-bioconductor-r4.3.0 %post chmod -R 777 /opt/conda chmod -R 777 /opt/venv - diff --git a/containers/uppmax/singularity_scanpy.def b/containers/uppmax/singularity_scanpy.def index a5068acf..f6880eaf 100644 --- a/containers/uppmax/singularity_scanpy.def +++ b/containers/uppmax/singularity_scanpy.def @@ -1,5 +1,5 @@ Bootstrap: docker -From: ghcr.io/NBISweden/workshop-scRNAseq:2023-scanpy-py3.10 +From: ghcr.io/nbisweden/workshop-scrnaseq:2023-scanpy-py3.10 %post chmod -R 777 /opt/conda diff --git a/containers/uppmax/singularity_seurat.def b/containers/uppmax/singularity_seurat.def index b313392e..b988bb58 100644 --- a/containers/uppmax/singularity_seurat.def +++ b/containers/uppmax/singularity_seurat.def @@ -1,7 +1,6 @@ Bootstrap: docker -From: ghcr.io/NBISweden/workshop-scRNAseq:2023-seurat-r4.3.0 +From: ghcr.io/nbisweden/workshop-scrnaseq:2023-seurat-r4.3.0 %post chmod -R 777 /opt/conda chmod -R 777 /opt/venv -