fix: github actions image name to lowercase (#27)

* fix gh actions image name to lowercase * fix readme image name to lowercase * fix def files image name to lowercase * fix docs image name to lowercase * fix repo readme image name to lowercase
NBISweden · Dec 23, 2023 · 8b48337 · 8b48337
1 parent 62fefa1
commit 8b48337
Show file tree

Hide file tree

Showing 12 changed files with 29 additions and 31 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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:<YEAR>-<TOOLKIT>-<LANGUAGE-VERSION>
+ghcr.io/nbisweden/workshop-scrnaseq:<YEAR>-<TOOLKIT>-<LANGUAGE-VERSION>
 ```
 
 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:<TAG>
-docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v /path/to/workdir:/home/rstudio/workdir ghcr.io/NBISweden/workshop-scRNAseq:<TAG>
+docker pull ghcr.io/nbisweden/workshop-scrnaseq:<TAG>
+docker run --rm -ti -p 8787:8787 -e PASSWORD=scrnaseq -v /path/to/workdir:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:<TAG>
 ```
 
 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:<TAG>
-docker run --rm -ti -p 8888:8888 -v /path/to/workdir:/home/jovyan/workshop-scRNAseq ghcr.io/NBISweden/workshop-scRNAseq:<TAG>
+docker pull ghcr.io/nbisweden/workshop-scrnaseq:<TAG>
+docker run --rm -ti -p 8888:8888 -v /path/to/workdir:/home/jovyan/workshop-scRNAseq ghcr.io/nbisweden/workshop-scrnaseq:<TAG>
 ```
 
 In the browser, go to [localhost:8888](localhost:8888).

diff --git 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
@@ -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
@@ -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
@@ -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
-