From 326f666af979bc73d5cd506dcd565c6f1fa4a997 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 24 Jul 2020 13:41:05 +0200 Subject: [PATCH 01/27] Create lrz.config Config file for LRZ CoolMuc2 --- conf/lrz.config | 64 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 conf/lrz.config diff --git a/conf/lrz.config b/conf/lrz.config new file mode 100644 index 0000000..6f1fbf8 --- /dev/null +++ b/conf/lrz.config @@ -0,0 +1,64 @@ +/* +Copyright (C) 2019-2020 Patrick Hüther, Niklas Schandry + +This file is part of araDeepopsis. +araDeepopsis 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, +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 . +*/ + +/* ------------------------------------------------- + * Nextflow config file for LRZ Linux Cluster (CM2) + * ------------------------------------------------- + */ + +/* Requires miniconda3 module. + This can be created using spack + $ module load user_spack + $ spack install miniconda3 + $ spack module tcl refresh miniconda3 + */ + +process { + module = 'miniconda3' + executor = 'slurm' + queue = 'cm2_std' + clusterOptions = "--clusters cm2 --qos cm2_std" + errorStrategy = { task.exitStatus in [104,134,135,137,139,140,143] ? 'retry' : 'finish' } + maxRetries = 3 + + withName: build_records { + cpus = { 1 * task.attempt } + memory = { 1.GB * task.attempt } + time = { 1.h * task.attempt } + } + withName: run_predictions { + cpus = { 4 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } + } + withName: run_predictions_DPP { + cpus = { 4 * task.attempt } + memory = { 16.GB * task.attempt } + time = { 2.h * task.attempt } + } + withName: extract_traits { + cpus = { 1 * task.attempt } + memory = { 1.GB * task.attempt } + time = { 1.h * task.attempt } + } + withName: draw_diagnostics { + cpus = { 1 * task.attempt } + memory = { 2.GB * task.attempt } + time = { 1.h * task.attempt } + } +} From 57eaa46edc83db2a7913db4dcebac4cbab10711c Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 24 Jul 2020 13:42:05 +0200 Subject: [PATCH 02/27] Update nextflow.config Add lrzcm2 profile for CoolMuc2 --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 64ca493..9206af6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,6 +71,7 @@ profiles { test { includeConfig 'conf/test.config' } // cluster specific profiles cbe { includeConfig 'conf/cbe.config' } + lrzcm2 { includeConfig 'conf/lrz.config' } } manifest { From 5e5a9504acbdd42a41c431014409f4fff15d01ac Mon Sep 17 00:00:00 2001 From: phue Date: Sun, 26 Jul 2020 15:34:59 +0200 Subject: [PATCH 03/27] bump tags to dev --- conf/base.config | 12 ++++++------ containers/addons/dpp/Dockerfile | 2 +- containers/addons/dpp/environment.yml | 2 +- containers/base/Dockerfile | 2 +- containers/base/environment.yml | 2 +- containers/shiny/Dockerfile | 2 +- containers/shiny/environment.yml | 2 +- docs/parameters.md | 2 +- nextflow.config | 2 +- 9 files changed, 14 insertions(+), 14 deletions(-) diff --git a/conf/base.config b/conf/base.config index 3ddaf0a..174411c 100644 --- a/conf/base.config +++ b/conf/base.config @@ -28,36 +28,36 @@ env { process { withName: build_records { - container = 'beckerlab/aradeepopsis-base:1.2.1' + container = 'beckerlab/aradeepopsis-base:dev' cpus = 1 memory = 2.GB time = 1.h } withName: run_predictions { - container = 'beckerlab/aradeepopsis-base:1.2.1' + container = 'beckerlab/aradeepopsis-base:dev' cpus = 2 memory = params.multiscale ? 12.GB : 6.GB time = 4.h } withName: run_predictions_DPP { - container = 'beckerlab/aradeepopsis-dpp:1.2.1' + container = 'beckerlab/aradeepopsis-dpp:dev' cpus = 2 memory = 2.GB time = 4.h } withName: extract_traits { - container = 'beckerlab/aradeepopsis-base:1.2.1' + container = 'beckerlab/aradeepopsis-base:dev' cpus = 1 memory = 2.GB time = 1.h } withName: draw_diagnostics { - container = 'beckerlab/aradeepopsis-base:1.2.1' + container = 'beckerlab/aradeepopsis-base:dev' cpus = 1 memory = 2.GB time = 1.h } withName: launch_shiny { - container = 'beckerlab/aradeepopsis-shiny:1.2.1' + container = 'beckerlab/aradeepopsis-shiny:dev' } } diff --git a/containers/addons/dpp/Dockerfile b/containers/addons/dpp/Dockerfile index c0f51c9..693ebee 100644 --- a/containers/addons/dpp/Dockerfile +++ b/containers/addons/dpp/Dockerfile @@ -6,4 +6,4 @@ 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-v1.2.1/bin:$PATH +ENV PATH /opt/conda/envs/aradeepopsis-dpp-dev/bin:$PATH diff --git a/containers/addons/dpp/environment.yml b/containers/addons/dpp/environment.yml index 2022c67..e1151ab 100644 --- a/containers/addons/dpp/environment.yml +++ b/containers/addons/dpp/environment.yml @@ -1,4 +1,4 @@ -name: aradeepopsis-dpp-v1.2.1 +name: aradeepopsis-dpp-dev channels: - conda-forge - defaults diff --git a/containers/base/Dockerfile b/containers/base/Dockerfile index 30ae3d4..a353c76 100644 --- a/containers/base/Dockerfile +++ b/containers/base/Dockerfile @@ -6,4 +6,4 @@ 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-v1.2.1/bin:$PATH \ No newline at end of file +ENV PATH /opt/conda/envs/aradeepopsis-base-dev/bin:$PATH \ No newline at end of file diff --git a/containers/base/environment.yml b/containers/base/environment.yml index 66414fa..94a5004 100644 --- a/containers/base/environment.yml +++ b/containers/base/environment.yml @@ -1,4 +1,4 @@ -name: aradeepopsis-base-v1.2.1 +name: aradeepopsis-base-dev channels: - conda-forge - defaults diff --git a/containers/shiny/Dockerfile b/containers/shiny/Dockerfile index 2dbd0e1..a5ad267 100644 --- a/containers/shiny/Dockerfile +++ b/containers/shiny/Dockerfile @@ -6,6 +6,6 @@ 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-shiny-v1.2.1/bin:$PATH +ENV PATH /opt/conda/envs/aradeepopsis-shiny-dev/bin:$PATH EXPOSE 44333 \ No newline at end of file diff --git a/containers/shiny/environment.yml b/containers/shiny/environment.yml index ea30a9c..47fbe33 100644 --- a/containers/shiny/environment.yml +++ b/containers/shiny/environment.yml @@ -1,4 +1,4 @@ -name: aradeepopsis-shiny-v1.2.1 +name: aradeepopsis-shiny-dev channels: - conda-forge - r diff --git a/docs/parameters.md b/docs/parameters.md index 8cdf697..85ea75c 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:1.2.1 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 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. diff --git a/nextflow.config b/nextflow.config index b27056e..64ca493 100644 --- a/nextflow.config +++ b/nextflow.config @@ -77,7 +77,7 @@ manifest { homePage = 'https://github.com/Gregor-Mendel-Institute/aradeepopsis' description = "Nextflow pipeline to run semantic segmentation on plant rosette images with DeepLab V3+" name = 'aradeepopsis' - version = '1.2.1' + version = 'dev' mainScript = 'main.nf' nextflowVersion = '>=20.01.0' } From 50704029184e262107c17f89b429cb94595e8c82 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Mon, 27 Jul 2020 13:44:24 +0200 Subject: [PATCH 04/27] Update lrz.config Added information on how to install nextflow via spack --- conf/lrz.config | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/conf/lrz.config b/conf/lrz.config index 6f1fbf8..2b5756d 100644 --- a/conf/lrz.config +++ b/conf/lrz.config @@ -16,18 +16,23 @@ You should have received a copy of the GNU General Public License along with araDeepopsis. If not, see . */ -/* ------------------------------------------------- - * Nextflow config file for LRZ Linux Cluster (CM2) - * ------------------------------------------------- - */ - -/* Requires miniconda3 module. +/* Requires miniconda3 module and nextflow > v20. This can be created using spack $ module load user_spack $ spack install miniconda3 $ spack module tcl refresh miniconda3 + $ spack repo create ~/spack/repos/nextflow + $ spack create --repo ~/spack/repos/nextflow/ https://github.com/nextflow-io/nextflow/releases/download/v20.07.1/nextflow + $ spack repo add ~/spack/repos/nextflow/ + $ spack install nextflow@20.07.1 + $ spack module tcl refresh nextflow */ +/* ------------------------------------------------- + * Nextflow config file for LRZ Linux Cluster (CM2) + * ------------------------------------------------- + */ + process { module = 'miniconda3' executor = 'slurm' From bb9777961f6fc64afd84c8d5f0b042a8217d683b Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Mon, 27 Jul 2020 14:13:35 +0200 Subject: [PATCH 05/27] Update CHANGELOG.md --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3de7a0b..f68a88e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ## Unreleased +* Added config for LRZ coolmuc2 * updated pipeline to fetch trained models from the deposited [Zenodo record](https://doi.org/10.5281/zenodo.3946321) instead of Dropbox * fixed an issue where the DPP addon produced sub-par segmentation results compared to the [tools](https://deep-plant-phenomics.readthedocs.io/en/latest/Tools/#vegetation-segmentation-network) implementation in Deep Plant Phenomics. * updated shiny app to show visualizations sorted by filename @@ -30,4 +31,4 @@ ## [v1.0](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.0) - 2020-04-02 -Initial pipeline release \ No newline at end of file +Initial pipeline release From 84089805769d9d99c5a8b77aa9d2783b7a385801 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Mon, 27 Jul 2020 17:47:06 +0200 Subject: [PATCH 06/27] Update CHANGELOG.md --- CHANGELOG.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 48a7a73..7099764 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,11 @@ # Changelog -## [v1.2.1](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.2.1) - 2020-07-23 +## Unreleased * Added config for LRZ coolmuc2 + +## [v1.2.1](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.2.1) - 2020-07-23 + * updated pipeline to fetch trained models from the deposited [Zenodo record](https://doi.org/10.5281/zenodo.3946321) instead of Dropbox * fixed an issue where the DPP addon produced sub-par segmentation results compared to the [tools](https://deep-plant-phenomics.readthedocs.io/en/latest/Tools/#vegetation-segmentation-network) implementation in Deep Plant Phenomics. * updated shiny app to show visualizations sorted by filename From 8a38c825b3c86a3f261bf4dc8dd3565e94b6f484 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 10 Aug 2020 21:55:29 +0200 Subject: [PATCH 07/27] Shiny app: fix invalid join key and facet by grouping variable --- CHANGELOG.md | 3 ++- assets/shiny/app.R | 5 +++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7099764..55ec093 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,8 @@ ## Unreleased -* Added config for LRZ coolmuc2 +* fixed plotting of leaf states over time in Shiny app (when appropriate metadata are provided) +* added config for LRZ coolmuc2 ## [v1.2.1](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.2.1) - 2020-07-23 diff --git a/assets/shiny/app.R b/assets/shiny/app.R index c500ed4..c02b638 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -222,9 +222,9 @@ server <- function(input, output, session) { }) output$leafstates <- renderPlot({ joined() %>% - select(file_name,groupVar,dateVar,matches("norm_area|antho_area|senesc_area")) %>% + select(file,groupVar,dateVar,matches("norm_area|antho_area|senesc_area")) %>% pivot_longer(starts_with("class_"),names_to = "state") %>% - group_by(groupVar,dateVar,file_name) %>% + group_by(groupVar,dateVar,file) %>% mutate(relativeFrac=value/sum(value)) %>% ggplot(aes(x = dateVar, y = relativeFrac, colour=state)) + stat_summary(geom="line") + @@ -234,6 +234,7 @@ server <- function(input, output, session) { "class_senesc_area" = rgb(253,231,37, maxColorValue = 255))) + scale_y_continuous(labels = scales::percent) + labs(x="time",y="% of plant area",colour=element_blank()) + + facet_wrap(~groupVar) + theme_bw() }) # show a description if Rosette Experiment is selected From d6c0baf09f533f8905807aeea85a2f8a92540f83 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Patrick=20H=C3=BCther?= Date: Wed, 25 Nov 2020 18:15:21 +0100 Subject: [PATCH 08/27] add profile for charliecloud container engine requires atleast charliecloud version 0.19 and current nextflow master PR pending https://github.com/nextflow-io/nextflow/pull/1809 Test run with: ``` nextflow run Gregor-Mendel-Institute/aradeepopsis -profile test,charliecloud ``` --- conf/charliecloud.config | 31 +++++++++++++++++++++++++++++++ conf/lrz.config | 13 ------------- main.nf | 4 ++-- nextflow.config | 1 + 4 files changed, 34 insertions(+), 15 deletions(-) create mode 100644 conf/charliecloud.config diff --git a/conf/charliecloud.config b/conf/charliecloud.config new file mode 100644 index 0000000..11ce89f --- /dev/null +++ b/conf/charliecloud.config @@ -0,0 +1,31 @@ +/* +Copyright (C) 2019-2020 Patrick Hüther + +This file is part of araDeepopsis. +araDeepopsis 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, +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 . +*/ + +/* ------------------------------------------------- + * Nextflow config file for araDeepopsis + * ------------------------------------------------- + */ + +env { + //for charliecloud, the PATH environment within the Docker image needs to be passed explicitly + PATH = "/opt/conda/envs/aradeepopsis-dpp-dev/bin:/opt/conda/envs/aradeepopsis-shiny-dev/bin:/opt/conda/envs/aradeepopsis-base-dev/bin:$PATH" +} + +charliecloud { + enabled = true +} diff --git a/conf/lrz.config b/conf/lrz.config index 2b5756d..2ce7ca3 100644 --- a/conf/lrz.config +++ b/conf/lrz.config @@ -16,25 +16,12 @@ You should have received a copy of the GNU General Public License along with araDeepopsis. If not, see . */ -/* Requires miniconda3 module and nextflow > v20. - This can be created using spack - $ module load user_spack - $ spack install miniconda3 - $ spack module tcl refresh miniconda3 - $ spack repo create ~/spack/repos/nextflow - $ spack create --repo ~/spack/repos/nextflow/ https://github.com/nextflow-io/nextflow/releases/download/v20.07.1/nextflow - $ spack repo add ~/spack/repos/nextflow/ - $ spack install nextflow@20.07.1 - $ spack module tcl refresh nextflow - */ - /* ------------------------------------------------- * Nextflow config file for LRZ Linux Cluster (CM2) * ------------------------------------------------- */ process { - module = 'miniconda3' executor = 'slurm' queue = 'cm2_std' clusterOptions = "--clusters cm2 --qos cm2_std" diff --git a/main.nf b/main.nf index 3ac7211..68a8b5b 100644 --- a/main.nf +++ b/main.nf @@ -457,7 +457,7 @@ ch_results .set {ch_resultfile} process launch_shiny { - containerOptions { workflow.profile.contains('singularity') ? '' : '-p 44333:44333' } + containerOptions { workflow.profile.contains('singularity') || workflow.profile.contains('charliecloud') ? '' : '-p 44333:44333' } executor 'local' cache false @@ -487,4 +487,4 @@ workflow.onError { The current pipeline configuration requires at least ${params.multiscale ? '12GB' : '6GB'} of RAM. """.stripIndent() } -} \ No newline at end of file +} diff --git a/nextflow.config b/nextflow.config index 9206af6..12225f2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -67,6 +67,7 @@ profiles { docker { docker.enabled = true } podman { podman.enabled = true } singularity { singularity.enabled = true } + charliecloud { includeConfig 'conf/charliecloud.config' } conda { includeConfig 'conf/conda.config' } test { includeConfig 'conf/test.config' } // cluster specific profiles From 43fd95d2f2ac4bd11d519cf91fda8692b201b6ee Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Thu, 17 Dec 2020 12:58:10 +0100 Subject: [PATCH 09/27] Update lrz.config added queuesize to lrz config to comply with max number of jobs on cm2_std --- conf/lrz.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/lrz.config b/conf/lrz.config index 2ce7ca3..a35beec 100644 --- a/conf/lrz.config +++ b/conf/lrz.config @@ -24,6 +24,7 @@ along with araDeepopsis. If not, see . process { executor = 'slurm' queue = 'cm2_std' + queueSize = 50 clusterOptions = "--clusters cm2 --qos cm2_std" errorStrategy = { task.exitStatus in [104,134,135,137,139,140,143] ? 'retry' : 'finish' } maxRetries = 3 From ac3f327040b91d2f2e767630e26db8df3ff1cf2e Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 6 Jan 2021 21:09:18 +0100 Subject: [PATCH 10/27] require nextflow 20.12.0-edge for charliecloud --- CHANGELOG.md | 1 + conf/charliecloud.config | 4 ++++ 2 files changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 55ec093..143d1f1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ## Unreleased +* added charliecloud profile (needs nextflow >= 20.12.0-edge) * fixed plotting of leaf states over time in Shiny app (when appropriate metadata are provided) * added config for LRZ coolmuc2 diff --git a/conf/charliecloud.config b/conf/charliecloud.config index 11ce89f..e910f46 100644 --- a/conf/charliecloud.config +++ b/conf/charliecloud.config @@ -29,3 +29,7 @@ env { charliecloud { enabled = true } + +manifest { + nextflowVersion = '>=20.12.0-edge' +} \ No newline at end of file From f81c5613c0afc24f8bb2d3e83aa8eea1a0a1c56f Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 6 Jan 2021 21:36:16 +0100 Subject: [PATCH 11/27] shiny: make slickR carousel responsive to screen width bonus: now looks good on mobile too --- assets/shiny/app.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/shiny/app.R b/assets/shiny/app.R index c02b638..aa92dfc 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -42,7 +42,7 @@ traitcount <- ncol(data) - 2 # exclude filename and suffix imagecount <- nrow(data) # Define UI -ui <- navbarPage(title="aradeepopsis", id="nav", theme = shinytheme("flatly"), +ui <- navbarPage(title=a("aradeepopsis", href="https://github.com/Gregor-Mendel-Institute/aradeepopsis", target="_blank"), windowTitle = "ARADEEPOPSIS", id="nav", theme = shinytheme("flatly"), collapsible=TRUE, tabPanel("Rosette Carousel", sliderInput("chunk", label = "Select chunk:", min = 1, max = ceiling(imagecount/60), value = 1, width = '100%', step = 1), slickROutput("slickr",width='100%',height='400px') %>% withSpinner() @@ -263,7 +263,7 @@ server <- function(input, output, session) { # this drastically improves page loading time chunks <- if (imagecount > 60) split(imagenames$file, ceiling(seq_along(imagenames$file)/60)) else split(imagenames$file, 1) - opts <- settings(slidesToShow = 6, slidesToScroll = 6) + opts <- settings(slidesToShow=6, slidesToScroll=6, responsive = htmlwidgets::JS("[{breakpoint: 1440,settings: {slidesToShow: 3,slidesToScroll: 3}},{breakpoint: 680,settings: {slidesToShow: 1,slidesToScroll: 1}}]")) overlay <- slickR(glue::glue("diagnostics/overlay/overlay_{chunks[[input$chunk]]}.jpeg"), height = 200) + opts mask <- slickR(glue::glue("diagnostics/mask/mask_{chunks[[input$chunk]]}.png"), height = 200) + opts + settings(arrows = F) From e8872c026c02c1c63a568ff8b676596636c1bd57 Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 6 Jan 2021 22:27:45 +0100 Subject: [PATCH 12/27] shiny: fix distorted display of images previously, images were forced to dimensions 400x400. Changing height to 'auto' should keep the aspect ratio --- assets/shiny/app.R | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/assets/shiny/app.R b/assets/shiny/app.R index aa92dfc..1414c53 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -45,7 +45,7 @@ imagecount <- nrow(data) ui <- navbarPage(title=a("aradeepopsis", href="https://github.com/Gregor-Mendel-Institute/aradeepopsis", target="_blank"), windowTitle = "ARADEEPOPSIS", id="nav", theme = shinytheme("flatly"), collapsible=TRUE, tabPanel("Rosette Carousel", sliderInput("chunk", label = "Select chunk:", min = 1, max = ceiling(imagecount/60), value = 1, width = '100%', step = 1), - slickROutput("slickr",width='100%',height='400px') %>% withSpinner() + slickROutput("slickr", width='auto', height='auto') %>% withSpinner() ), tabPanel("Rosette Explorer", sidebarPanel( @@ -129,16 +129,16 @@ server <- function(input, output, session) { updateSelectizeInput(session, "explorer_files", choices = c(imagenames), server = TRUE) output$mask <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/mask/mask_{input$explorer_files}.png"),width=400,height=400) + list(src = glue::glue("diagnostics/mask/mask_{input$explorer_files}.png"),width=400,height="auto") }) output$hull <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/convex_hull/hull_{input$explorer_files}.png"),width=400,height=400) + list(src = glue::glue("diagnostics/convex_hull/hull_{input$explorer_files}.png"),width=400,height="auto") }) output$rosette <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg"),width=400,height=400) + list(src = glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg"),width=400,height="auto") }) output$overlay <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/overlay/overlay_{input$explorer_files}.jpeg"),width=400,height=400) + list(src = glue::glue("diagnostics/overlay/overlay_{input$explorer_files}.jpeg"),width=400,height="auto") }) output$color <- renderPlot({ img <- readJPEG(glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg")) @@ -263,7 +263,7 @@ server <- function(input, output, session) { # this drastically improves page loading time chunks <- if (imagecount > 60) split(imagenames$file, ceiling(seq_along(imagenames$file)/60)) else split(imagenames$file, 1) - opts <- settings(slidesToShow=6, slidesToScroll=6, responsive = htmlwidgets::JS("[{breakpoint: 1440,settings: {slidesToShow: 3,slidesToScroll: 3}},{breakpoint: 680,settings: {slidesToShow: 1,slidesToScroll: 1}}]")) + opts <- settings(slidesToShow=6, slidesToScroll=6, responsive=htmlwidgets::JS("[{breakpoint: 1440,settings: {slidesToShow: 3,slidesToScroll: 3}},{breakpoint: 680,settings: {slidesToShow: 1,slidesToScroll: 1}}]")) overlay <- slickR(glue::glue("diagnostics/overlay/overlay_{chunks[[input$chunk]]}.jpeg"), height = 200) + opts mask <- slickR(glue::glue("diagnostics/mask/mask_{chunks[[input$chunk]]}.png"), height = 200) + opts + settings(arrows = F) From 0061afaebaeb3cdeb07431a8e2b67bab18a16b1f Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 6 Jan 2021 22:33:42 +0100 Subject: [PATCH 13/27] Revert "fetch models from their zenodo record instead of dropbox" This reverts commit f7566a0d49cd4f36ab39816aa206368d1ecb4ac7. See https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/53 --- main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 68a8b5b..3886621 100644 --- a/main.nf +++ b/main.nf @@ -110,19 +110,19 @@ Pipeline parameters switch(params.model) { case 'A': - model = "https://zenodo.org/record/3946618/files/1_class_${params.multiscale ? 'multiscale' : 'singlescale'}.pb" + model = params.multiscale ? 'https://www.dropbox.com/s/19eeq3yog975otz/1_class_multiscale.pb?dl=1' : 'https://www.dropbox.com/s/ejpkgnvsv9p9s5d/1_class_singlescale.pb?dl=1' labels = "class_background=0,class_norm=1" ignore_label = "None" max_dimension = 602 break case 'B': - model = "https://zenodo.org/record/3946618/files/2_class_${params.multiscale ? 'multiscale' : 'singlescale'}.pb" + model = params.multiscale ? 'https://www.dropbox.com/s/9m4wy990ajv7cmg/2_class_multiscale.pb?dl=1' : 'https://www.dropbox.com/s/s808kcq9jgiyko9/2_class_singlescale.pb?dl=1' labels = "class_background=0,class_norm=1,class_senesc=2" ignore_label = params.ignore_senescence ? "2" : "None" max_dimension = 602 break case 'C': - model = "https://zenodo.org/record/3946618/files/3_class_${params.multiscale ? 'multiscale' : 'singlescale'}.pb" + model = params.multiscale ? 'https://www.dropbox.com/s/xwnqytcf6xzdumq/3_class_multiscale.pb?dl=1' : 'https://www.dropbox.com/s/1axmww7cqor6i7x/3_class_singlescale.pb?dl=1' labels = "class_background=0,class_norm=1,class_senesc=2,class_antho=3" ignore_label = params.ignore_senescence ? "2" : "None" max_dimension = 602 From 55041d9a3147e76c68a2ba0c195ec4da9fa26442 Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 6 Jan 2021 23:12:52 +0100 Subject: [PATCH 14/27] add publication doi to pipeline manuscript doi field requires nextflow 20.07.1 --- README.md | 2 +- nextflow.config | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index cd53180..0e254b9 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ![Latest Release](https://img.shields.io/github/v/release/Gregor-Mendel-Institute/aradeepopsis?sort=semver) ![License](https://img.shields.io/github/license/Gregor-Mendel-Institute/aradeepopsis) [![DOI](https://zenodo.org/badge/240287274.svg)](https://zenodo.org/badge/latestdoi/240287274) -[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.01.0-important.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.0-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 | diff --git a/nextflow.config b/nextflow.config index 12225f2..0b4b199 100644 --- a/nextflow.config +++ b/nextflow.config @@ -81,7 +81,8 @@ manifest { name = 'aradeepopsis' version = 'dev' mainScript = 'main.nf' - nextflowVersion = '>=20.01.0' + nextflowVersion = '>=20.07.1' + doi = '10.1105/tpc.20.00318' } timeline { From d1799d6769715ba4c2ab5a2f3c119db41a5e96c0 Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 6 Jan 2021 23:14:04 +0100 Subject: [PATCH 15/27] update CHANGELOG.md --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 143d1f1..7b88078 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,11 @@ ## Unreleased + +* added publication doi to pipeline manifest +* changed (back) download links in pipeline to fetch pretrained models from Dropbox instead of Zenodo ([#53](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/53#issue-779431868)) +* changed rosette carousel in Shiny app to be responsive to screen width ([#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) +* fixed distorted display of images in Shiny app rosette explorer ([#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) * added charliecloud profile (needs nextflow >= 20.12.0-edge) * fixed plotting of leaf states over time in Shiny app (when appropriate metadata are provided) * added config for LRZ coolmuc2 From 82b2587400c644b323c1e70577f28720512e90e2 Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 6 Jan 2021 23:29:59 +0100 Subject: [PATCH 16/27] bump dependency versions --- CHANGELOG.md | 5 ++++- README.md | 2 +- containers/base/environment.yml | 4 ++-- containers/shiny/environment.yml | 5 +++-- 4 files changed, 10 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b88078..e5eefef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,10 @@ ## Unreleased - +* updated `scikit-image` `0.17.2` > `0.18.1` +* updated `imagemagick` dependency `7.0.10_23` > `7.0.10_28` +* updated `shinycssloaders` dependency `0.3` > `1.0.0` +* updated `slickr` dependency `0.4.9` > `0.5.0` * added publication doi to pipeline manifest * changed (back) download links in pipeline to fetch pretrained models from Dropbox instead of Zenodo ([#53](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/53#issue-779431868)) * changed rosette carousel in Shiny app to be responsive to screen width ([#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) diff --git a/README.md b/README.md index 0e254b9..2411069 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ![Latest Release](https://img.shields.io/github/v/release/Gregor-Mendel-Institute/aradeepopsis?sort=semver) ![License](https://img.shields.io/github/license/Gregor-Mendel-Institute/aradeepopsis) [![DOI](https://zenodo.org/badge/240287274.svg)](https://zenodo.org/badge/latestdoi/240287274) -[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.0-important.svg)](https://www.nextflow.io/) +[![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 | diff --git a/containers/base/environment.yml b/containers/base/environment.yml index 94a5004..1d1ef63 100644 --- a/containers/base/environment.yml +++ b/containers/base/environment.yml @@ -5,5 +5,5 @@ channels: dependencies: - anaconda::tensorflow-base=2.0.0 - anaconda::tensorflow-estimator=2.0.0 - - conda-forge::scikit-image=0.17.2 - - conda-forge::imagemagick=7.0.10_23 + - conda-forge::scikit-image=0.18.1 + - conda-forge::imagemagick=7.0.10_28 diff --git a/containers/shiny/environment.yml b/containers/shiny/environment.yml index 47fbe33..62c136f 100644 --- a/containers/shiny/environment.yml +++ b/containers/shiny/environment.yml @@ -7,8 +7,9 @@ dependencies: - conda-forge::r-tidyverse=1.3.0 - conda-forge::r-shiny=1.5.0 - conda-forge::r-shinythemes=1.1.2 - - conda-forge::r-shinycssloaders=0.3 - - conda-forge::r-slickr=0.4.9 + - conda-forge::r-shinycssloaders=1.0.0 + - conda-forge::r-slickr=0.5.0 - conda-forge::r-corrplot=0.84 - conda-forge::r-jpeg=0.1_8.1 - r::r-radarchart=0.3.1 + From 5dc448a85b6187cd5e48446d88b80761280c4a74 Mon Sep 17 00:00:00 2001 From: phue Date: Thu, 7 Jan 2021 21:12:34 +0100 Subject: [PATCH 17/27] shiny: make size of visualizations more consistent --- assets/shiny/app.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/assets/shiny/app.R b/assets/shiny/app.R index 1414c53..23465c6 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -129,18 +129,18 @@ server <- function(input, output, session) { updateSelectizeInput(session, "explorer_files", choices = c(imagenames), server = TRUE) output$mask <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/mask/mask_{input$explorer_files}.png"),width=400,height="auto") + list(src = glue::glue("diagnostics/mask/mask_{input$explorer_files}.png"),width=600,height="auto") }) output$hull <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/convex_hull/hull_{input$explorer_files}.png"),width=400,height="auto") + list(src = glue::glue("diagnostics/convex_hull/hull_{input$explorer_files}.png"),width=600,height="auto") }) output$rosette <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg"),width=400,height="auto") + list(src = glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg"),width=600,height="auto") }) output$overlay <- renderImage(deleteFile=FALSE,{ - list(src = glue::glue("diagnostics/overlay/overlay_{input$explorer_files}.jpeg"),width=400,height="auto") + list(src = glue::glue("diagnostics/overlay/overlay_{input$explorer_files}.jpeg"),width=600,height="auto") }) - output$color <- renderPlot({ + output$color <- renderPlot(width=600,height=600,{ img <- readJPEG(glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg")) r <- img[,,1] %>% as_tibble() %>% pivot_longer(everything()) %>% mutate(name=1) From ffdc1dae58ddbaa75cc4fce1dba782131fd0fef7 Mon Sep 17 00:00:00 2001 From: phue Date: Thu, 7 Jan 2021 22:50:54 +0100 Subject: [PATCH 18/27] shiny: improve description of metadata feature --- assets/shiny/app.R | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/assets/shiny/app.R b/assets/shiny/app.R index 23465c6..5f3354d 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -92,7 +92,7 @@ ui <- navbarPage(title=a("aradeepopsis", href="https://github.com/Gregor-Mendel- div(style = "overflow-x:scroll;", tableOutput("meta")), varSelectizeInput("file","Select column containing the filename", data = NULL), varSelectizeInput("date","Select column containing the timestamp", data = NULL), - textInput("date_format","Enter timestamp format",value="%y-%m-%d"), + textInput("date_format",HTML('Enter timestamp format'),value="%y-%m-%d"), varSelectizeInput("groupvar","Select column to group by", data = NULL), actionButton("merge_data", "Analyze!"), conditionalPanel( @@ -244,12 +244,14 @@ server <- function(input, output, session) { modalDialog( title="Experimental feature!", HTML("This feature is meant to add metadata to the pipeline result, allowing to visualize traits over time.
- It requires a table with metadata in csv format.
- Such metadata has to contain one row per input image and columns with the following information:
- - filename of the original image
- - timestamp when the image was recorded
- - format of the timestamp
- - variable by which the result should be grouped (such as a genotype ID)") + It requires a csv table with metadata that is then joined with the pipeline result.
+
+ Such metadata has to contain one row per input image and the following columns:
+ - Filenames of the original images
+ - Timestamps when the images were recorded
+ - Variable(s) by which the result should be grouped (such as genotype or accession ID)
+
+ Note: If the 'file' column of aradeepopsis_traits.csv is used to extract such metadata, trait columns should be removed before uploading") ) ) } From 4f374e2aa4d4c60bdb5b8788a5b4623117031441 Mon Sep 17 00:00:00 2001 From: phue Date: Thu, 7 Jan 2021 22:53:08 +0100 Subject: [PATCH 19/27] shiny: improve rendering of timeseries plots --- assets/shiny/app.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/shiny/app.R b/assets/shiny/app.R index 5f3354d..a3d7e67 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -214,9 +214,9 @@ server <- function(input, output, session) { joined() %>% select(dateVar,groupVar,trait := !!input$exp_traits) %>% ggplot(aes(x=dateVar,y=trait,colour=groupVar)) + - stat_summary(geom="line") + + stat_summary(geom="line", size=1.5) + stat_summary(geom="pointrange") + - scale_color_viridis_d(option="A") + + scale_color_viridis_d(option="A", end=0.9) + labs(x="time",y="trait value",colour=element_blank()) + theme_bw() }) @@ -227,7 +227,7 @@ server <- function(input, output, session) { group_by(groupVar,dateVar,file) %>% mutate(relativeFrac=value/sum(value)) %>% ggplot(aes(x = dateVar, y = relativeFrac, colour=state)) + - stat_summary(geom="line") + + stat_summary(geom="line", size=1.5) + stat_summary(geom="pointrange") + scale_color_manual(values = c("class_norm_area" = rgb(31,158,137, maxColorValue = 255), "class_antho_area" = rgb(72,40,120, maxColorValue = 255), From ebf897bead9a742a0d85445fdf881996883cad4e Mon Sep 17 00:00:00 2001 From: phue Date: Thu, 7 Jan 2021 23:00:40 +0100 Subject: [PATCH 20/27] minor cleanup --- Jenkinsfile | 3 --- assets/shiny/app.R | 2 +- conf/charliecloud.config | 2 +- containers/addons/dpp/Dockerfile | 1 - containers/base/Dockerfile | 1 - containers/shiny/Dockerfile | 1 - main.nf | 2 +- nextflow.config | 2 +- 8 files changed, 4 insertions(+), 10 deletions(-) delete mode 100644 Jenkinsfile diff --git a/Jenkinsfile b/Jenkinsfile deleted file mode 100644 index 408d8c5..0000000 --- a/Jenkinsfile +++ /dev/null @@ -1,3 +0,0 @@ -buildDockerImage([imageName: "aradeepopsis", - pushRegistryNamespace: "becker", - pushBranches:["master","dev","next"]]) diff --git a/assets/shiny/app.R b/assets/shiny/app.R index a3d7e67..3690913 100755 --- a/assets/shiny/app.R +++ b/assets/shiny/app.R @@ -1,4 +1,4 @@ -# Copyright (C) 2019-2020 Patrick Hüther +# Copyright (C) 2019-2021 Patrick Hüther # # This file is part of araDeepopsis. # araDeepopsis free software: you can redistribute it and/or modify diff --git a/conf/charliecloud.config b/conf/charliecloud.config index e910f46..e807b6e 100644 --- a/conf/charliecloud.config +++ b/conf/charliecloud.config @@ -1,5 +1,5 @@ /* -Copyright (C) 2019-2020 Patrick Hüther +Copyright (C) 2019-2021 Patrick Hüther This file is part of araDeepopsis. araDeepopsis free software: you can redistribute it and/or modify diff --git a/containers/addons/dpp/Dockerfile b/containers/addons/dpp/Dockerfile index 693ebee..611163a 100644 --- a/containers/addons/dpp/Dockerfile +++ b/containers/addons/dpp/Dockerfile @@ -1,5 +1,4 @@ FROM continuumio/miniconda3 -MAINTAINER Patrick Hüther LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ description="Container image containing DPP dependencies for araDeepopsis" diff --git a/containers/base/Dockerfile b/containers/base/Dockerfile index a353c76..70b9741 100644 --- a/containers/base/Dockerfile +++ b/containers/base/Dockerfile @@ -1,5 +1,4 @@ FROM continuumio/miniconda3 -MAINTAINER Patrick Hüther LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ description="Container image containing base dependencies for araDeepopsis" diff --git a/containers/shiny/Dockerfile b/containers/shiny/Dockerfile index a5ad267..1951a6a 100644 --- a/containers/shiny/Dockerfile +++ b/containers/shiny/Dockerfile @@ -1,5 +1,4 @@ FROM continuumio/miniconda3 -MAINTAINER Patrick Hüther LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ description="Container image containing shiny dependencies for araDeepopsis" diff --git a/main.nf b/main.nf index 3886621..fcf8225 100644 --- a/main.nf +++ b/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow /* -Copyright (C) 2019-2020 Patrick Hüther +Copyright (C) 2019-2021 Patrick Hüther This file is part of araDeepopsis. araDeepopsis free software: you can redistribute it and/or modify diff --git a/nextflow.config b/nextflow.config index 0b4b199..f8918d9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,5 +1,5 @@ /* -Copyright (C) 2019-2020 Patrick Hüther +Copyright (C) 2019-2021 Patrick Hüther This file is part of araDeepopsis. araDeepopsis free software: you can redistribute it and/or modify From 2cc00c6de9160e44db7f91fb2d6ffea064af4cf7 Mon Sep 17 00:00:00 2001 From: phue Date: Thu, 7 Jan 2021 23:24:53 +0100 Subject: [PATCH 21/27] update CHANGELOG.md --- CHANGELOG.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e5eefef..61a7467 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,14 +2,13 @@ ## Unreleased +* 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` * updated `shinycssloaders` dependency `0.3` > `1.0.0` * updated `slickr` dependency `0.4.9` > `0.5.0` * added publication doi to pipeline manifest * changed (back) download links in pipeline to fetch pretrained models from Dropbox instead of Zenodo ([#53](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/53#issue-779431868)) -* changed rosette carousel in Shiny app to be responsive to screen width ([#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) -* fixed distorted display of images in Shiny app rosette explorer ([#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) * added charliecloud profile (needs nextflow >= 20.12.0-edge) * fixed plotting of leaf states over time in Shiny app (when appropriate metadata are provided) * added config for LRZ coolmuc2 From 3e3c3aad43c18b7adfbe63be279514656f4013d9 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 11 Jan 2021 17:50:50 +0100 Subject: [PATCH 22/27] v1.3: set release date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 61a7467..76df3da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## Unreleased +## [v1.3](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.3) - 2021-01-11 * 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` From b0d043c661c5ca6b9c4d90306b8e8cc09057af28 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 11 Jan 2021 17:52:35 +0100 Subject: [PATCH 23/27] set version tags for v1.3 release --- conf/base.config | 12 ++++++------ conf/charliecloud.config | 2 +- containers/addons/dpp/Dockerfile | 2 +- containers/addons/dpp/environment.yml | 2 +- containers/base/Dockerfile | 2 +- containers/base/environment.yml | 2 +- containers/shiny/Dockerfile | 2 +- containers/shiny/environment.yml | 2 +- docs/parameters.md | 2 +- nextflow.config | 2 +- 10 files changed, 15 insertions(+), 15 deletions(-) diff --git a/conf/base.config b/conf/base.config index 174411c..7042dcc 100644 --- a/conf/base.config +++ b/conf/base.config @@ -28,36 +28,36 @@ env { process { withName: build_records { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'beckerlab/aradeepopsis-base:1.3' cpus = 1 memory = 2.GB time = 1.h } withName: run_predictions { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'beckerlab/aradeepopsis-base:1.3' cpus = 2 memory = params.multiscale ? 12.GB : 6.GB time = 4.h } withName: run_predictions_DPP { - container = 'beckerlab/aradeepopsis-dpp:dev' + container = 'beckerlab/aradeepopsis-dpp:1.3' cpus = 2 memory = 2.GB time = 4.h } withName: extract_traits { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'beckerlab/aradeepopsis-base:1.3' cpus = 1 memory = 2.GB time = 1.h } withName: draw_diagnostics { - container = 'beckerlab/aradeepopsis-base:dev' + container = 'beckerlab/aradeepopsis-base:1.3' cpus = 1 memory = 2.GB time = 1.h } withName: launch_shiny { - container = 'beckerlab/aradeepopsis-shiny:dev' + container = 'beckerlab/aradeepopsis-shiny:1.3' } } diff --git a/conf/charliecloud.config b/conf/charliecloud.config index e807b6e..120b6f7 100644 --- a/conf/charliecloud.config +++ b/conf/charliecloud.config @@ -23,7 +23,7 @@ along with araDeepopsis. If not, see . env { //for charliecloud, the PATH environment within the Docker image needs to be passed explicitly - PATH = "/opt/conda/envs/aradeepopsis-dpp-dev/bin:/opt/conda/envs/aradeepopsis-shiny-dev/bin:/opt/conda/envs/aradeepopsis-base-dev/bin:$PATH" + PATH = "/opt/conda/envs/aradeepopsis-dpp-v1.3/bin:/opt/conda/envs/aradeepopsis-shiny-v1.3/bin:/opt/conda/envs/aradeepopsis-base-v1.3/bin:$PATH" } charliecloud { diff --git a/containers/addons/dpp/Dockerfile b/containers/addons/dpp/Dockerfile index 611163a..f4a4151 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:$PATH +ENV PATH /opt/conda/envs/aradeepopsis-dpp-v1.3/bin:$PATH diff --git a/containers/addons/dpp/environment.yml b/containers/addons/dpp/environment.yml index e1151ab..71b1279 100644 --- a/containers/addons/dpp/environment.yml +++ b/containers/addons/dpp/environment.yml @@ -1,4 +1,4 @@ -name: aradeepopsis-dpp-dev +name: aradeepopsis-dpp-v1.3 channels: - conda-forge - defaults diff --git a/containers/base/Dockerfile b/containers/base/Dockerfile index 70b9741..37f27fa 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:$PATH \ No newline at end of file +ENV PATH /opt/conda/envs/aradeepopsis-base-v1.3/bin:$PATH \ No newline at end of file diff --git a/containers/base/environment.yml b/containers/base/environment.yml index 1d1ef63..ee0d468 100644 --- a/containers/base/environment.yml +++ b/containers/base/environment.yml @@ -1,4 +1,4 @@ -name: aradeepopsis-base-dev +name: aradeepopsis-base-v1.3 channels: - conda-forge - defaults diff --git a/containers/shiny/Dockerfile b/containers/shiny/Dockerfile index 1951a6a..5ea148b 100644 --- a/containers/shiny/Dockerfile +++ b/containers/shiny/Dockerfile @@ -5,6 +5,6 @@ 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-shiny-dev/bin:$PATH +ENV PATH /opt/conda/envs/aradeepopsis-shiny-v1.3/bin:$PATH EXPOSE 44333 \ No newline at end of file diff --git a/containers/shiny/environment.yml b/containers/shiny/environment.yml index 62c136f..7922263 100644 --- a/containers/shiny/environment.yml +++ b/containers/shiny/environment.yml @@ -1,4 +1,4 @@ -name: aradeepopsis-shiny-dev +name: aradeepopsis-shiny-v1.3 channels: - conda-forge - r diff --git a/docs/parameters.md b/docs/parameters.md index 85ea75c..3b983bf 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 beckerlab/aradeepopsis-shiny:v1.3 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. diff --git a/nextflow.config b/nextflow.config index f8918d9..6280275 100644 --- a/nextflow.config +++ b/nextflow.config @@ -79,7 +79,7 @@ manifest { homePage = 'https://github.com/Gregor-Mendel-Institute/aradeepopsis' description = "Nextflow pipeline to run semantic segmentation on plant rosette images with DeepLab V3+" name = 'aradeepopsis' - version = 'dev' + version = '1.3' mainScript = 'main.nf' nextflowVersion = '>=20.07.1' doi = '10.1105/tpc.20.00318' 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 24/27] 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 $(pwd):/mnt/shiny -p 44333:44333 quay.io/beckerlab/aradeepopsis-shiny:dev R -e "shiny::runApp('/mnt/shiny/app.R', port=44333, host='0.0.0.0')" > ``` > The shiny app can then be opened in a browser by typing localhost:44333 in the address bar. It will terminate when the browser window is closed. From bb41e5919e9139a09479664e2f0512c319cc3d35 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 11 Jan 2021 20:01:03 +0100 Subject: [PATCH 25/27] update CHANGELOG.md --- CHANGELOG.md | 1 + containers/base/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 76df3da..5adfb0d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ## [v1.3](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.3) - 2021-01-11 +* changed container registry from docker.io to quay.io * improved image visualization and plot rendering in Shiny app (see [#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) thanks @dschneiderch for input * updated `scikit-image` `0.17.2` > `0.18.1` * updated `imagemagick` dependency `7.0.10_23` > `7.0.10_28` diff --git a/containers/base/Dockerfile b/containers/base/Dockerfile index 70b9741..d8bf7f7 100644 --- a/containers/base/Dockerfile +++ b/containers/base/Dockerfile @@ -5,4 +5,4 @@ LABEL authors="patrick.huether@gmi.oeaw.ac.at" \ COPY environment.yml / RUN apt-get update && apt-get install -y procps graphviz && apt-get clean -y RUN conda env create -f /environment.yml && conda clean -afy -ENV PATH /opt/conda/envs/aradeepopsis-base-dev/bin:$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 26/27] 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 27/27] 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. */