From 7b1d35f0c596f312308c3dae35c9acd3bd69cf53 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Patrick=20H=C3=BCther?= Date: Mon, 11 Jan 2021 19:53:34 +0100 Subject: [PATCH 1/4] push containers to quay.io (#56) remove Dockerhub and Github packages --- .github/workflows/docker_base.yml | 33 +++++++++++++----------------- .github/workflows/docker_dpp.yml | 33 +++++++++++++----------------- .github/workflows/docker_shiny.yml | 33 +++++++++++++----------------- README.md | 7 ------- conf/base.config | 12 +++++------ containers/addons/dpp/Dockerfile | 2 +- containers/shiny/environment.yml | 1 - docs/parameters.md | 2 +- 8 files changed, 50 insertions(+), 73 deletions(-) diff --git a/.github/workflows/docker_base.yml b/.github/workflows/docker_base.yml index 6aa856c..0bf10f2 100644 --- a/.github/workflows/docker_base.yml +++ b/.github/workflows/docker_base.yml @@ -1,4 +1,4 @@ -name: Docker Container (Base) +name: Container build (Base) on: push: @@ -8,25 +8,20 @@ on: jobs: push_to_registry: - name: Push Docker image to GitHub Packages + name: Push to quay.io runs-on: ubuntu-latest steps: - name: Check out the repo uses: actions/checkout@v2 - - name: Push to Docker Hub - uses: docker/build-push-action@v1 - with: - username: ${{ secrets.DOCKER_USER }} - password: ${{ secrets.DOCKER_PASSWORD }} - repository: beckerlab/aradeepopsis-base - path: containers/base - tag_with_ref: true - - name: Push to GitHub Packages - uses: docker/build-push-action@v1 - with: - username: ${{ github.actor }} - password: ${{ secrets.GITHUB_TOKEN }} - registry: docker.pkg.github.com - repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-base - path: containers/base - tag_with_ref: true \ No newline at end of file + + - name: Login to quay.io + env: + QUAY_USER: ${{ secrets.REGISTRY_USER }} + QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }} + run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io + + - name: Build container + run: podman build --tag beckerlab/aradeepopsis-base containers/base + + - name: Push container + run: podman push beckerlab/aradeepopsis-base docker://quay.io/beckerlab/aradeepopsis-base:${GITHUB_REF##*/} \ No newline at end of file diff --git a/.github/workflows/docker_dpp.yml b/.github/workflows/docker_dpp.yml index fb106fd..4f56524 100644 --- a/.github/workflows/docker_dpp.yml +++ b/.github/workflows/docker_dpp.yml @@ -1,4 +1,4 @@ -name: Docker Container (DPP) +name: Container build (DPP) on: push: @@ -8,25 +8,20 @@ on: jobs: push_to_registry: - name: Push Docker image to GitHub Packages + name: Push to quay.io runs-on: ubuntu-latest steps: - name: Check out the repo uses: actions/checkout@v2 - - name: Push to Docker Hub - uses: docker/build-push-action@v1 - with: - username: ${{ secrets.DOCKER_USER }} - password: ${{ secrets.DOCKER_PASSWORD }} - repository: beckerlab/aradeepopsis-dpp - path: containers/addons/dpp - tag_with_ref: true - - name: Push to GitHub Packages - uses: docker/build-push-action@v1 - with: - username: ${{ github.actor }} - password: ${{ secrets.GITHUB_TOKEN }} - registry: docker.pkg.github.com - repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-dpp - path: containers/addons/dpp - tag_with_ref: true \ No newline at end of file + + - name: Login to quay.io + env: + QUAY_USER: ${{ secrets.REGISTRY_USER }} + QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }} + run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io + + - name: Build container + run: podman build --tag beckerlab/aradeepopsis-dpp containers/addons/dpp + + - name: Push container + run: podman push beckerlab/aradeepopsis-dpp docker://quay.io/beckerlab/aradeepopsis-dpp:${GITHUB_REF##*/} \ No newline at end of file diff --git a/.github/workflows/docker_shiny.yml b/.github/workflows/docker_shiny.yml index 27656a3..eca5602 100644 --- a/.github/workflows/docker_shiny.yml +++ b/.github/workflows/docker_shiny.yml @@ -1,4 +1,4 @@ -name: Docker Container (Shiny) +name: Container build (Shiny) on: push: @@ -8,25 +8,20 @@ on: jobs: push_to_registry: - name: Push Docker image to GitHub Packages + name: Push to quay.io runs-on: ubuntu-latest steps: - name: Check out the repo uses: actions/checkout@v2 - - name: Push to Docker Hub - uses: docker/build-push-action@v1 - with: - username: ${{ secrets.DOCKER_USER }} - password: ${{ secrets.DOCKER_PASSWORD }} - repository: beckerlab/aradeepopsis-shiny - path: containers/shiny - tag_with_ref: true - - name: Push to GitHub Packages - uses: docker/build-push-action@v1 - with: - username: ${{ github.actor }} - password: ${{ secrets.GITHUB_TOKEN }} - registry: docker.pkg.github.com - repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-shiny - path: containers/shiny - tag_with_ref: true \ No newline at end of file + + - name: Login to quay.io + env: + QUAY_USER: ${{ secrets.REGISTRY_USER }} + QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }} + run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io + + - name: Build container + run: podman build --tag beckerlab/aradeepopsis-shiny containers/shiny + + - name: Push container + run: podman push beckerlab/aradeepopsis-shiny docker://quay.io/beckerlab/aradeepopsis-shiny:${GITHUB_REF##*/} \ No newline at end of file diff --git a/README.md b/README.md index 2411069..cd6975b 100644 --- a/README.md +++ b/README.md @@ -7,13 +7,6 @@ [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.1-important.svg)](https://www.nextflow.io/) [![conda](https://img.shields.io/badge/install%20with-conda-brightgreen.svg)](https://conda.io/) -| Container | Image size | Pulls | Latest version | -| :---: | :---: | :---: | :---: | -| ![Docker Container (Base)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(Base)/badge.svg?branch=master) | ![Docker Size (Base)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-base?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-base) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-base?sort=semver) | -| ![Docker Container (Shiny)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(Shiny)/badge.svg?branch=master) | ![Docker Size (Shiny)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-shiny?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-shiny) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-shiny?sort=semver) | -| ![Docker Docker (DPP)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(DPP)/badge.svg?branch=master) | ![Docker Size (DPP)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-dpp?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-dpp) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-base?sort=semver) | - - # Introduction `ARADEEPOPSIS` is a software tool that enables plant researchers to non-invasively score plant growth, biomass accumulation and senescence from image data in a highly parallelized, high throughput, yet easy to use manner. diff --git a/conf/base.config b/conf/base.config index 174411c..eed9bc5 100644 --- a/conf/base.config +++ b/conf/base.config @@ -28,36 +28,36 @@ env { process { withName: build_records { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'quay.io/beckerlab/aradeepopsis-base:dev' cpus = 1 memory = 2.GB time = 1.h } withName: run_predictions { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'quay.io/beckerlab/aradeepopsis-base:dev' cpus = 2 memory = params.multiscale ? 12.GB : 6.GB time = 4.h } withName: run_predictions_DPP { - container = 'beckerlab/aradeepopsis-dpp:dev' + container = 'quay.io/beckerlab/aradeepopsis-dpp:dev' cpus = 2 memory = 2.GB time = 4.h } withName: extract_traits { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'quay.io/beckerlab/aradeepopsis-base:dev' cpus = 1 memory = 2.GB time = 1.h } withName: draw_diagnostics { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'quay.io/beckerlab/aradeepopsis-base:dev' cpus = 1 memory = 2.GB time = 1.h } withName: launch_shiny { - container = 'beckerlab/aradeepopsis-shiny:dev' + container = 'quay.io/beckerlab/aradeepopsis-shiny:dev' } } diff --git a/containers/addons/dpp/Dockerfile b/containers/addons/dpp/Dockerfile index 611163a..f7881f6 100644 --- a/containers/addons/dpp/Dockerfile +++ b/containers/addons/dpp/Dockerfile @@ -5,4 +5,4 @@ LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ COPY environment.yml / RUN apt-get update && apt-get install -y procps graphviz && apt-get clean -y RUN conda env create -f /environment.yml && conda clean -afy -ENV PATH /opt/conda/envs/aradeepopsis-dpp-dev/bin:$PATH +ENV PATH /opt/conda/envs/aradeepopsis-dpp-dev/bin:$PATH \ No newline at end of file diff --git a/containers/shiny/environment.yml b/containers/shiny/environment.yml index 62c136f..3f9adb5 100644 --- a/containers/shiny/environment.yml +++ b/containers/shiny/environment.yml @@ -12,4 +12,3 @@ dependencies: - conda-forge::r-corrplot=0.84 - conda-forge::r-jpeg=0.1_8.1 - r::r-radarchart=0.3.1 - diff --git a/docs/parameters.md b/docs/parameters.md index 85ea75c..b124cc5 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -132,6 +132,6 @@ Launch a [Shiny](https://shiny.rstudio.com/) app as the last step of the pipelin > R -e "shiny::runApp('app.R', port=44333)" > > # if using the container image -> {docker|podman} run -v $(pwd):/mnt/shiny -p 44333:44333 beckerlab/aradeepopsis-shiny:dev R -e "shiny::runApp('/mnt/shiny/app.R', port=44333, host='0.0.0.0')" +> {docker|podman} run -v $(pwd):/mnt/shiny -p 44333:44333 quay.io/beckerlab/aradeepopsis-shiny:dev R -e "shiny::runApp('/mnt/shiny/app.R', port=44333, host='0.0.0.0')" > ``` > The shiny app can then be opened in a browser by typing localhost:44333 in the address bar. It will terminate when the browser window is closed. From bb41e5919e9139a09479664e2f0512c319cc3d35 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 11 Jan 2021 20:01:03 +0100 Subject: [PATCH 2/4] update CHANGELOG.md --- CHANGELOG.md | 1 + containers/base/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 76df3da..5adfb0d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ## [v1.3](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.3) - 2021-01-11 +* changed container registry from docker.io to quay.io * improved image visualization and plot rendering in Shiny app (see [#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) thanks @dschneiderch for input * updated `scikit-image` `0.17.2` > `0.18.1` * updated `imagemagick` dependency `7.0.10_23` > `7.0.10_28` diff --git a/containers/base/Dockerfile b/containers/base/Dockerfile index 70b9741..d8bf7f7 100644 --- a/containers/base/Dockerfile +++ b/containers/base/Dockerfile @@ -5,4 +5,4 @@ LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ COPY environment.yml / RUN apt-get update && apt-get install -y procps graphviz && apt-get clean -y RUN conda env create -f /environment.yml && conda clean -afy -ENV PATH /opt/conda/envs/aradeepopsis-base-dev/bin:$PATH \ No newline at end of file +ENV PATH /opt/conda/envs/aradeepopsis-base-dev/bin:$PATH From 8ad2a86f9367c7ec336b20b022db06af00062537 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 11 Jan 2021 20:11:35 +0100 Subject: [PATCH 3/4] CI: bump minimal nextflow version to 20.07.1 --- .github/workflows/minimal_test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/minimal_test.yml b/.github/workflows/minimal_test.yml index 2cf72df..fc1c5fe 100644 --- a/.github/workflows/minimal_test.yml +++ b/.github/workflows/minimal_test.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - nxf_ver: ["20.01.0", ""] + nxf_ver: ["20.07.1", ""] steps: - uses: actions/checkout@v2 From 8c44ec4337416432e91a460597cc4fcbd7215773 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 11 Jan 2021 20:13:20 +0100 Subject: [PATCH 4/4] v1.3 --- assets/shiny/app.R | 8 ++++---- bin/data_record.py | 8 ++++---- bin/frozen_graph.py | 8 ++++---- bin/traits.py | 8 ++++---- conf/base.config | 10 +++++----- conf/cbe.config | 8 ++++---- conf/charliecloud.config | 10 +++++----- conf/conda.config | 10 +++++----- conf/lrz.config | 8 ++++---- conf/test.config | 8 ++++---- containers/addons/dpp/Dockerfile | 2 +- containers/base/Dockerfile | 2 +- containers/shiny/Dockerfile | 2 +- lib/ParameterChecks.groovy | 8 ++++---- main.nf | 8 ++++---- nextflow.config | 10 +++++----- 16 files changed, 59 insertions(+), 59 deletions(-) diff --git a/assets/shiny/app.R b/assets/shiny/app.R index 3690913..828f171 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -1,18 +1,18 @@ # Copyright (C) 2019-2021 Patrick Hüther # -# This file is part of araDeepopsis. -# araDeepopsis free software: you can redistribute it and/or modify +# This file is part of ARADEEPOPSIS. +# ARADEEPOPSIS is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # -# araDeepopsis is distributed in the hope that it will be useful, +# ARADEEPOPSIS is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with araDeepopsis. If not, see . +# along with ARADEEPOPSIS. If not, see . library(shiny) library(slickR) diff --git a/bin/data_record.py b/bin/data_record.py index e50d0b2..a151b01 100644 --- a/bin/data_record.py +++ b/bin/data_record.py @@ -2,19 +2,19 @@ # Copyright (C) 2019-2020 Patrick Hüther # -# This file is part of araDeepopsis. -# araDeepopsis free software: you can redistribute it and/or modify +# This file is part of ARADEEPOPSIS. +# ARADEEPOPSIS is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # -# araDeepopsis is distributed in the hope that it will be useful, +# ARADEEPOPSIS is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with araDeepopsis. If not, see . +# along with ARADEEPOPSIS. If not, see . import tensorflow as tf diff --git a/bin/frozen_graph.py b/bin/frozen_graph.py index a8a266d..ed36e31 100644 --- a/bin/frozen_graph.py +++ b/bin/frozen_graph.py @@ -2,19 +2,19 @@ # Copyright (C) 2019-2020 Patrick Hüther # -# This file is part of araDeepopsis. -# araDeepopsis free software: you can redistribute it and/or modify +# This file is part of ARADEEPOPSIS. +# ARADEEPOPSIS is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # -# araDeepopsis is distributed in the hope that it will be useful, +# ARADEEPOPSIS is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with araDeepopsis. If not, see . +# along with ARADEEPOPSIS. If not, see . # ====================================================================== # Portions of this code are modifications based on work created and # shared by Google and used according to terms described in the diff --git a/bin/traits.py b/bin/traits.py index 356b485..6bd4ec6 100644 --- a/bin/traits.py +++ b/bin/traits.py @@ -2,19 +2,19 @@ # Copyright (C) 2019-2020 Patrick Hüther # -# This file is part of araDeepopsis. -# araDeepopsis free software: you can redistribute it and/or modify +# This file is part of ARADEEPOPSIS. +# ARADEEPOPSIS is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # -# araDeepopsis is distributed in the hope that it will be useful, +# ARADEEPOPSIS is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with araDeepopsis. If not, see . +# along with ARADEEPOPSIS. If not, see . import csv import os diff --git a/conf/base.config b/conf/base.config index eed9bc5..1d6997b 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,23 +1,23 @@ /* Copyright (C) 2019-2020 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* ------------------------------------------------- - * Nextflow config file for araDeepopsis + * Nextflow config file for ARADEEPOPSIS * ------------------------------------------------- */ diff --git a/conf/cbe.config b/conf/cbe.config index 0eb739e..1a75520 100644 --- a/conf/cbe.config +++ b/conf/cbe.config @@ -1,19 +1,19 @@ /* Copyright (C) 2019-2020 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* ------------------------------------------------- diff --git a/conf/charliecloud.config b/conf/charliecloud.config index e807b6e..a609011 100644 --- a/conf/charliecloud.config +++ b/conf/charliecloud.config @@ -1,23 +1,23 @@ /* Copyright (C) 2019-2021 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* ------------------------------------------------- - * Nextflow config file for araDeepopsis + * Nextflow config file for ARADEEPOPSIS * ------------------------------------------------- */ diff --git a/conf/conda.config b/conf/conda.config index 3335b5d..6b828b8 100644 --- a/conf/conda.config +++ b/conf/conda.config @@ -1,23 +1,23 @@ /* Copyright (C) 2019-2020 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* ------------------------------------------------- - * Nextflow config file for araDeepopsis + * Nextflow config file for ARADEEPOPSIS * ------------------------------------------------- */ diff --git a/conf/lrz.config b/conf/lrz.config index a35beec..56dfd4c 100644 --- a/conf/lrz.config +++ b/conf/lrz.config @@ -1,19 +1,19 @@ /* Copyright (C) 2019-2020 Patrick Hüther, Niklas Schandry -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* ------------------------------------------------- diff --git a/conf/test.config b/conf/test.config index 5933a7e..785c4a6 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,19 +1,19 @@ /* Copyright (C) 2019-2020 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* ------------------------------------------------- diff --git a/containers/addons/dpp/Dockerfile b/containers/addons/dpp/Dockerfile index f7881f6..2684651 100644 --- a/containers/addons/dpp/Dockerfile +++ b/containers/addons/dpp/Dockerfile @@ -1,6 +1,6 @@ FROM continuumio/miniconda3 LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ - description="Container image containing DPP dependencies for araDeepopsis" + description="Container image containing DPP dependencies for ARADEEPOPSIS" COPY environment.yml / RUN apt-get update && apt-get install -y procps graphviz && apt-get clean -y diff --git a/containers/base/Dockerfile b/containers/base/Dockerfile index d8bf7f7..a5f23e8 100644 --- a/containers/base/Dockerfile +++ b/containers/base/Dockerfile @@ -1,6 +1,6 @@ FROM continuumio/miniconda3 LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ - description="Container image containing base dependencies for araDeepopsis" + description="Container image containing base dependencies for ARADEEPOPSIS" COPY environment.yml / RUN apt-get update && apt-get install -y procps graphviz && apt-get clean -y diff --git a/containers/shiny/Dockerfile b/containers/shiny/Dockerfile index 1951a6a..13dd3ac 100644 --- a/containers/shiny/Dockerfile +++ b/containers/shiny/Dockerfile @@ -1,6 +1,6 @@ FROM continuumio/miniconda3 LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ - description="Container image containing shiny dependencies for araDeepopsis" + description="Container image containing shiny dependencies for ARADEEPOPSIS" COPY environment.yml / RUN apt-get update && apt-get install -y procps graphviz && apt-get clean -y diff --git a/lib/ParameterChecks.groovy b/lib/ParameterChecks.groovy index 1572646..2a26730 100644 --- a/lib/ParameterChecks.groovy +++ b/lib/ParameterChecks.groovy @@ -1,19 +1,19 @@ /* Copyright (C) 2019-2020 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ class ParameterChecks { diff --git a/main.nf b/main.nf index fcf8225..18848c9 100644 --- a/main.nf +++ b/main.nf @@ -3,19 +3,19 @@ /* Copyright (C) 2019-2021 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* diff --git a/nextflow.config b/nextflow.config index f8918d9..b949f41 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,24 +1,24 @@ /* Copyright (C) 2019-2021 Patrick Hüther -This file is part of araDeepopsis. -araDeepopsis free software: you can redistribute it and/or modify +This file is part of ARADEEPOPSIS. +ARADEEPOPSIS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -araDeepopsis is distributed in the hope that it will be useful, +ARADEEPOPSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License -along with araDeepopsis. If not, see . +along with ARADEEPOPSIS. If not, see . */ /* * ------------------------------------------------- - * araDeepopsis Nextflow config file + * ARADEEPOPSIS Nextflow config file * ------------------------------------------------- * Default config options for all environments. */