From ac263725582054268b80f6541b87e26b726c9d1e Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 19 Jan 2022 11:37:33 +0100 Subject: [PATCH 01/24] Add Gitpod Dockerfile --- .gitpod.Dockerfile | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .gitpod.Dockerfile diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile new file mode 100644 index 0000000000..53595fd73d --- /dev/null +++ b/.gitpod.Dockerfile @@ -0,0 +1,19 @@ +FROM gitpod/workspace-full + +USER root + +# Install Conda +RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \ + bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \ + rm Miniconda3-latest-Linux-x86_64.sh + +ENV PATH="/opt/conda/bin:$PATH" + +RUN chown -R gitpod:gitpod /opt/conda + +USER gitpod + +# Install nextflow, nf-core, Mamba, and pytest-workflow +RUN conda install nextflow nf-core pytest-workflow mamba -n base -c conda-forge -c bioconda && \ + nextflow self-update && \ + conda clean --all -f -y From 0eee68474cc2808db85942b2267763791154a519 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 19 Jan 2022 11:49:30 +0100 Subject: [PATCH 02/24] Add Gitpod yaml --- .gitpod.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 .gitpod.yml diff --git a/.gitpod.yml b/.gitpod.yml new file mode 100644 index 0000000000..1e9df7794e --- /dev/null +++ b/.gitpod.yml @@ -0,0 +1,18 @@ +image: + file: .gitpod.Dockerfile +github: + prebuilds: + # enable for the default branch (defaults to true) + master: true + # enable for all branches in this repo (defaults to false) + branches: false + # enable for pull requests coming from this repo (defaults to true) + pullRequests: true + # enable for pull requests coming from forks (defaults to false) + pullRequestsFromForks: false + # add a check to pull requests (defaults to true) + addCheck: prevent-merge-on-error + # add a "Review in Gitpod" button as a comment to pull requests (defaults to false) + addComment: false + # add a "Review in Gitpod" button to the pull request's description (defaults to false) + addBadge: false \ No newline at end of file From 585af68801e77898d6581d25aa3041d8e7173b4c Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 19 Jan 2022 15:00:47 +0100 Subject: [PATCH 03/24] Rename Dockerfile --- .gitpod.Dockerfile => nf_core/gitpod/gitpod.Dockerfile | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .gitpod.Dockerfile => nf_core/gitpod/gitpod.Dockerfile (100%) diff --git a/.gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile similarity index 100% rename from .gitpod.Dockerfile rename to nf_core/gitpod/gitpod.Dockerfile From ae1693dd263b5b6584c4b0b8c09f629d54fe48da Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 19 Jan 2022 15:02:41 +0100 Subject: [PATCH 04/24] Add gitpod to pipeline template --- nf_core/pipeline-template/.gitpod.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 nf_core/pipeline-template/.gitpod.yml diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml new file mode 100644 index 0000000000..ef0cf2c6ff --- /dev/null +++ b/nf_core/pipeline-template/.gitpod.yml @@ -0,0 +1 @@ +image: nf-core/gitpod From e487f416a0c862b6dd81f167b585d8efdab89640 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 19 Jan 2022 15:05:02 +0100 Subject: [PATCH 05/24] Add GH action to build Gitpod --- .github/workflows/build_gitpod.yml | 39 ++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 .github/workflows/build_gitpod.yml diff --git a/.github/workflows/build_gitpod.yml b/.github/workflows/build_gitpod.yml new file mode 100644 index 0000000000..c51b3643af --- /dev/null +++ b/.github/workflows/build_gitpod.yml @@ -0,0 +1,39 @@ +name: nf-core gitpod build and push +# Builds the docker image for gitpod and pushes it to DockerHub + +on: + merge: + branches: + - 'master' + paths: + - 'nf_core/gitpod/gitpod.Dockerfile' + +jobs: + push_to_registry: + name: Push Docker image to Docker Hub + runs-on: ubuntu-latest + # Only run for the nf-core repo, for releases and merged PRs + if: ${{ github.repository == 'nf-core/tools' }} + steps: + - name: Check out the repo + uses: actions/checkout@v2 + + - name: Log in to Docker Hub + uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 + with: + username: ${{ secrets.DOCKER_USERNAME }} + password: ${{ secrets.DOCKER_PASSWORD }} + + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 + with: + images: nfcore/gitpod + + - name: Build and push Docker image + uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc + with: + context: . + push: true + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} From 7407f0dfd3b50f061e6b2591dc046ecc4f3f5ef2 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 19 Jan 2022 15:05:13 +0100 Subject: [PATCH 06/24] Restore Dockerfile for testing purposes --- .gitpod.Dockerfile | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .gitpod.Dockerfile diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile new file mode 100644 index 0000000000..53595fd73d --- /dev/null +++ b/.gitpod.Dockerfile @@ -0,0 +1,19 @@ +FROM gitpod/workspace-full + +USER root + +# Install Conda +RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \ + bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \ + rm Miniconda3-latest-Linux-x86_64.sh + +ENV PATH="/opt/conda/bin:$PATH" + +RUN chown -R gitpod:gitpod /opt/conda + +USER gitpod + +# Install nextflow, nf-core, Mamba, and pytest-workflow +RUN conda install nextflow nf-core pytest-workflow mamba -n base -c conda-forge -c bioconda && \ + nextflow self-update && \ + conda clean --all -f -y From 932c1993df9b98cb1e6b0fbc44709978a87e06bd Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 19 Jan 2022 15:10:22 +0100 Subject: [PATCH 07/24] Fix GH action --- .github/workflows/build_gitpod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_gitpod.yml b/.github/workflows/build_gitpod.yml index c51b3643af..ff79193166 100644 --- a/.github/workflows/build_gitpod.yml +++ b/.github/workflows/build_gitpod.yml @@ -2,7 +2,7 @@ name: nf-core gitpod build and push # Builds the docker image for gitpod and pushes it to DockerHub on: - merge: + push: branches: - 'master' paths: From 2c6476ff3f6a95a157c19d391ea8787d56812b8d Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Thu, 20 Jan 2022 10:53:33 +0100 Subject: [PATCH 08/24] Update nf_core/pipeline-template/.gitpod.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipeline-template/.gitpod.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index ef0cf2c6ff..6cee4e130a 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -1 +1,15 @@ image: nf-core/gitpod + +vscode: + extensions: # based on nf-core.nf-core-extensionpack + - codezombiech.gitignore + # - cssho.vscode-svgviewer + - davidanson.vscode-markdownlint + - eamodio.gitlens + - EditorConfig.EditorConfig + - Gruntfuggly.todo-tree + - mechatroner.rainbow-csv + # - nextflow.nextflow + - oderwat.indent-rainbow + - redhat.vscode-yaml + - streetsidesoftware.code-spell-checker From a7d33d90b858026e7945d906e6cc82391767d4ed Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Thu, 20 Jan 2022 11:23:22 +0100 Subject: [PATCH 09/24] Update .gitpod.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .gitpod.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitpod.yml b/.gitpod.yml index 1e9df7794e..97a5d5a36b 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,5 +1,9 @@ image: file: .gitpod.Dockerfile +task: + - name: install current state of nf-core/tools + init: | + pip install --upgrade -r requirements-dev.txt -e . github: prebuilds: # enable for the default branch (defaults to true) From 1f918f9717c3e301c928cb172cf877caa7cf53bd Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Thu, 20 Jan 2022 11:20:46 +0100 Subject: [PATCH 10/24] Add extension pack explanations --- nf_core/pipeline-template/.gitpod.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index 6cee4e130a..a2fa269521 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -2,14 +2,14 @@ image: nf-core/gitpod vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore - # - cssho.vscode-svgviewer - - davidanson.vscode-markdownlint - - eamodio.gitlens - - EditorConfig.EditorConfig - - Gruntfuggly.todo-tree - - mechatroner.rainbow-csv - # - nextflow.nextflow - - oderwat.indent-rainbow - - redhat.vscode-yaml - - streetsidesoftware.code-spell-checker + - codezombiech.gitignore # Language support for .gitignore files + # - cssho.vscode-svgviewer # SVG viewer + - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + # - nextflow.nextflow # Nextflow syntax highlighting + - oderwat.indent-rainbow # Highlight indentation level + - redhat.vscode-yaml # YAML Language support + - streetsidesoftware.code-spell-checker # Spelling checker for source code From e60533af42721d04fe444d7ed1a0c2b46a8ac7d3 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Thu, 20 Jan 2022 14:22:12 +0100 Subject: [PATCH 11/24] Update base Gitpod yaml. --- .gitpod.Dockerfile | 19 ------------------- .gitpod.yml | 32 ++++++++++++++------------------ 2 files changed, 14 insertions(+), 37 deletions(-) delete mode 100644 .gitpod.Dockerfile diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile deleted file mode 100644 index 53595fd73d..0000000000 --- a/.gitpod.Dockerfile +++ /dev/null @@ -1,19 +0,0 @@ -FROM gitpod/workspace-full - -USER root - -# Install Conda -RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \ - bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \ - rm Miniconda3-latest-Linux-x86_64.sh - -ENV PATH="/opt/conda/bin:$PATH" - -RUN chown -R gitpod:gitpod /opt/conda - -USER gitpod - -# Install nextflow, nf-core, Mamba, and pytest-workflow -RUN conda install nextflow nf-core pytest-workflow mamba -n base -c conda-forge -c bioconda && \ - nextflow self-update && \ - conda clean --all -f -y diff --git a/.gitpod.yml b/.gitpod.yml index 97a5d5a36b..cd9a238867 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,22 +1,18 @@ -image: - file: .gitpod.Dockerfile +image: nf-core/gitpod task: - name: install current state of nf-core/tools init: | pip install --upgrade -r requirements-dev.txt -e . -github: - prebuilds: - # enable for the default branch (defaults to true) - master: true - # enable for all branches in this repo (defaults to false) - branches: false - # enable for pull requests coming from this repo (defaults to true) - pullRequests: true - # enable for pull requests coming from forks (defaults to false) - pullRequestsFromForks: false - # add a check to pull requests (defaults to true) - addCheck: prevent-merge-on-error - # add a "Review in Gitpod" button as a comment to pull requests (defaults to false) - addComment: false - # add a "Review in Gitpod" button to the pull request's description (defaults to false) - addBadge: false \ No newline at end of file +vscode: + extensions: # based on nf-core.nf-core-extensionpack + - codezombiech.gitignore # Language support for .gitignore files + # - cssho.vscode-svgviewer # SVG viewer + - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + # - nextflow.nextflow # Nextflow syntax highlighting + - oderwat.indent-rainbow # Highlight indentation level + - redhat.vscode-yaml # YAML Language support + - streetsidesoftware.code-spell-checker # Spelling checker for source code From 9227e86211924e391a4b8f901e597119ac96a5ff Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Thu, 20 Jan 2022 15:29:57 +0100 Subject: [PATCH 12/24] Update .github/workflows/build_gitpod.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .github/workflows/build_gitpod.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_gitpod.yml b/.github/workflows/build_gitpod.yml index ff79193166..bae98942fc 100644 --- a/.github/workflows/build_gitpod.yml +++ b/.github/workflows/build_gitpod.yml @@ -21,8 +21,8 @@ jobs: - name: Log in to Docker Hub uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_PASSWORD }} + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_PASS }} - name: Extract metadata (tags, labels) for Docker id: meta From 4de4730b5642ee2b33030e4c5ba596604b45c121 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 21 Jan 2022 13:04:22 +0100 Subject: [PATCH 13/24] Add conda update to Dockerfile --- nf_core/gitpod/gitpod.Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 53595fd73d..f0f76e3394 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -14,6 +14,7 @@ RUN chown -R gitpod:gitpod /opt/conda USER gitpod # Install nextflow, nf-core, Mamba, and pytest-workflow -RUN conda install nextflow nf-core pytest-workflow mamba -n base -c conda-forge -c bioconda && \ +RUN conda update -n base -c defaults conda && \ + conda install nextflow nf-core pytest-workflow mamba -n base -c conda-forge -c bioconda && \ nextflow self-update && \ conda clean --all -f -y From 2d601491a52476908992b1b573abf8282c0c8d31 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 21 Jan 2022 13:05:15 +0100 Subject: [PATCH 14/24] Add file to build --- .github/workflows/build_gitpod.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build_gitpod.yml b/.github/workflows/build_gitpod.yml index bae98942fc..3c6b210b0c 100644 --- a/.github/workflows/build_gitpod.yml +++ b/.github/workflows/build_gitpod.yml @@ -34,6 +34,7 @@ jobs: uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc with: context: . + file: nf_core/gitpod/gitpod.Dockerfile push: true tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} From b2230a72b66cf052fcf294d8e7d6215a6259c44a Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 21 Jan 2022 13:15:09 +0100 Subject: [PATCH 15/24] Change SHA commit to major versions --- .github/workflows/build_gitpod.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_gitpod.yml b/.github/workflows/build_gitpod.yml index 3c6b210b0c..ef73c88557 100644 --- a/.github/workflows/build_gitpod.yml +++ b/.github/workflows/build_gitpod.yml @@ -19,19 +19,19 @@ jobs: uses: actions/checkout@v2 - name: Log in to Docker Hub - uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 + uses: docker/login-action@v1 with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_PASS }} - name: Extract metadata (tags, labels) for Docker id: meta - uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 + uses: docker/metadata-action@v3 with: images: nfcore/gitpod - name: Build and push Docker image - uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc + uses: docker/build-push-action@v2 with: context: . file: nf_core/gitpod/gitpod.Dockerfile From fa9cb246fa21e2a45daa697133c1831f0df018b1 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 21 Jan 2022 13:18:45 +0100 Subject: [PATCH 16/24] Fix image name --- .gitpod.yml | 2 +- nf_core/pipeline-template/.gitpod.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index cd9a238867..f60c0c5bbc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nf-core/gitpod +image: nfcore/gitpod task: - name: install current state of nf-core/tools init: | diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index a2fa269521..179170568a 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -1,4 +1,4 @@ -image: nf-core/gitpod +image: nfcore/gitpod vscode: extensions: # based on nf-core.nf-core-extensionpack From 12665d03e1424e7ee6713258549099b3d515ffd5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Fri, 21 Jan 2022 13:28:48 +0100 Subject: [PATCH 17/24] fix typo in .gitpod.yml --- .gitpod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index f60c0c5bbc..1cb402fc3d 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,5 +1,5 @@ image: nfcore/gitpod -task: +tasks: - name: install current state of nf-core/tools init: | pip install --upgrade -r requirements-dev.txt -e . From 9d915bee0083f527fcab0199d6646bcc2d532f06 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 21 Jan 2022 16:31:09 +0100 Subject: [PATCH 18/24] Add Build path for nf-core tools dev --- .github/workflows/build_gitpod.yml | 3 +++ .gitpod.yml | 8 +++++--- nf_core/pipeline-template/.gitpod.yml | 2 +- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build_gitpod.yml b/.github/workflows/build_gitpod.yml index ef73c88557..c9858db1d4 100644 --- a/.github/workflows/build_gitpod.yml +++ b/.github/workflows/build_gitpod.yml @@ -29,6 +29,9 @@ jobs: uses: docker/metadata-action@v3 with: images: nfcore/gitpod + tags: | + type=semver,pattern={{version}} + type=raw,value=latest - name: Build and push Docker image uses: docker/build-push-action@v2 diff --git a/.gitpod.yml b/.gitpod.yml index 1cb402fc3d..79a7031ae6 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,8 +1,10 @@ -image: nfcore/gitpod +image: nfcore/gitpod:latest tasks: - name: install current state of nf-core/tools - init: | - pip install --upgrade -r requirements-dev.txt -e . + command: | + NFCORE_BUILD_PATH=$HOME/nf-core_build + pip install --upgrade -r requirements-dev.txt -e . -t $NFCORE_BUILD_PATH + PATH="$NFCORE_BUILD_PATH:$PATH" vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index 179170568a..b6c480db07 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod +image: nfcore/gitpod:latest vscode: extensions: # based on nf-core.nf-core-extensionpack From 2d01159bc38accca38be31a72c56cb70b76d055a Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 21 Jan 2022 21:23:55 +0100 Subject: [PATCH 19/24] Add GA action to workflow check --- .github/workflows/build_gitpod.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build_gitpod.yml b/.github/workflows/build_gitpod.yml index c9858db1d4..da926a310e 100644 --- a/.github/workflows/build_gitpod.yml +++ b/.github/workflows/build_gitpod.yml @@ -7,6 +7,7 @@ on: - 'master' paths: - 'nf_core/gitpod/gitpod.Dockerfile' + - '.github/workflows/build_gitpod.yml' jobs: push_to_registry: From f14c2f8f6a04e73e6b483e4806d27b946f038e4c Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Mon, 31 Jan 2022 09:56:31 +0100 Subject: [PATCH 20/24] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .gitpod.yml | 1 - nf_core/pipeline-template/.gitpod.yml | 1 - 2 files changed, 2 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index 79a7031ae6..ea900790b9 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -16,5 +16,4 @@ vscode: - mechatroner.rainbow-csv # Highlight columns in csv files in different colors # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - - redhat.vscode-yaml # YAML Language support - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index b6c480db07..b7d4cee18b 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -11,5 +11,4 @@ vscode: - mechatroner.rainbow-csv # Highlight columns in csv files in different colors # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - - redhat.vscode-yaml # YAML Language support - streetsidesoftware.code-spell-checker # Spelling checker for source code From bc04c64dd0f39bf23cf31a2f62a56f619d6ad263 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Mon, 31 Jan 2022 10:00:21 +0100 Subject: [PATCH 21/24] Add conda channel defaults --- nf_core/gitpod/gitpod.Dockerfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index f0f76e3394..598665ce4d 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -17,4 +17,7 @@ USER gitpod RUN conda update -n base -c defaults conda && \ conda install nextflow nf-core pytest-workflow mamba -n base -c conda-forge -c bioconda && \ nextflow self-update && \ + conda config --add channels defaults && \ + conda config --add channels bioconda && \ + conda config --add channels conda-forge && \ conda clean --all -f -y From 70fc9c4698ceb87924e88e2f12a92b484ce2a661 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Mon, 31 Jan 2022 11:09:13 +0100 Subject: [PATCH 22/24] Add pip to conda environment --- nf_core/gitpod/gitpod.Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 598665ce4d..d5a17cd33c 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -15,7 +15,7 @@ USER gitpod # Install nextflow, nf-core, Mamba, and pytest-workflow RUN conda update -n base -c defaults conda && \ - conda install nextflow nf-core pytest-workflow mamba -n base -c conda-forge -c bioconda && \ + conda install nextflow nf-core pytest-workflow mamba pip -n base -c conda-forge -c bioconda && \ nextflow self-update && \ conda config --add channels defaults && \ conda config --add channels bioconda && \ From 9e51064fe12b296e7473bd834ef30392d0969fe3 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Mon, 31 Jan 2022 11:10:06 +0100 Subject: [PATCH 23/24] Update pip install command --- .gitpod.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index ea900790b9..86ed680600 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -2,9 +2,7 @@ image: nfcore/gitpod:latest tasks: - name: install current state of nf-core/tools command: | - NFCORE_BUILD_PATH=$HOME/nf-core_build - pip install --upgrade -r requirements-dev.txt -e . -t $NFCORE_BUILD_PATH - PATH="$NFCORE_BUILD_PATH:$PATH" + python -m pip install --upgrade -r requirements-dev.txt -e . vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files From 1d1f5e8d3131d41425ab8ef4e0532f00a53f4c46 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 1 Feb 2022 15:13:11 +0100 Subject: [PATCH 24/24] Update changelog --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 93ec4fa4a6..841aacdeba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,11 @@ * Remove base `Dockerfile` used for DSL1 pipeline container builds * Run tests with Python 3.10 * [#1363](https://github.com/nf-core/tools/pull/1363) Fix tools CI workflow nextflow versions. +* [#1384](https://github.com/nf-core/tools/pull/1384) Adds Gitpod environment and Dockerfile. + * Adds conda, Nextflow, nf-core, pytest-workflow, mamba, and pip to base Gitpod Docker image. + * Adds GH action to build and push Gitpod Docker image. + * Adds Gitpod environment to template. + * Adds Gitpod environment to tools with auto build of nf-core tool. ### Modules