From 4f8902adc9e6eef2e98b7f9961edea4b2e90aedb Mon Sep 17 00:00:00 2001 From: labkey-jony Date: Fri, 6 Oct 2023 15:00:57 -0700 Subject: [PATCH 1/5] Adding additional packages (R and Bioconductor) for testing --- images/labkey/rstudio/Dockerfile | 2 +- images/labkey/rstudio/install.R | 20 ++++++++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/images/labkey/rstudio/Dockerfile b/images/labkey/rstudio/Dockerfile index 4d9bb89..102c752 100644 --- a/images/labkey/rstudio/Dockerfile +++ b/images/labkey/rstudio/Dockerfile @@ -5,7 +5,7 @@ RUN apt-get update && \ apt-get install -y --no-install-recommends \ curl libcurl4-openssl-dev \ libgd-dev libcairo2 libcairo2-dev libxt-dev pandoc \ - libssl-dev openssl && \ + libssl-dev openssl cmake libnlopt-dev && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* diff --git a/images/labkey/rstudio/install.R b/images/labkey/rstudio/install.R index b43f3dc..5c25ae2 100644 --- a/images/labkey/rstudio/install.R +++ b/images/labkey/rstudio/install.R @@ -33,3 +33,23 @@ install.packages(c( "rsconnect" ), repos='https://cran.rstudio.com/') +install.packages(c( + "latticeExtra", + "lme4", + "lmtest", + "openssl", + "plotly", + "plyr", + "png", + "readxl", + "reshape2", + "RSQLite", + "stringr", + "stringi", + "tidyverse", + "tibble", + "tidyr" + ), + repos='https://cran.rstudio.com/') +install.packages("BiocManager", repos = "https://cloud.r-project.org") +BiocManager::install(c("flowWorkspace", "CytoML")) From 48da97bcb1e82074d281924ce1b2b3e492ea7761 Mon Sep 17 00:00:00 2001 From: labkey-jony Date: Mon, 9 Oct 2023 15:14:14 -0700 Subject: [PATCH 2/5] Retrying Bioconductor package install based on GitHub install instructions --- images/labkey/rstudio/install.R | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/images/labkey/rstudio/install.R b/images/labkey/rstudio/install.R index 5c25ae2..d762df0 100644 --- a/images/labkey/rstudio/install.R +++ b/images/labkey/rstudio/install.R @@ -48,8 +48,17 @@ install.packages(c( "stringi", "tidyverse", "tibble", - "tidyr" + "tidyr", + "devtools" ), repos='https://cran.rstudio.com/') install.packages("BiocManager", repos = "https://cloud.r-project.org") -BiocManager::install(c("flowWorkspace", "CytoML")) + + +library(BiocManager) +library(devtools) + +BiocManager::install("openCyto") + +install_github("RGLab/flowWorkspace") +install_github("RGLab/openCyto") \ No newline at end of file From 0b67398ffd8c5fa556f99925c88b3de08eab3ae1 Mon Sep 17 00:00:00 2001 From: labkey-jony Date: Tue, 10 Oct 2023 13:01:41 -0700 Subject: [PATCH 3/5] Split up install of packages, added more dev packages via apt --- images/labkey/rstudio/Dockerfile | 10 ++++++-- images/labkey/rstudio/extra.R | 43 ++++++++++++++++++++++++++++++++ images/labkey/rstudio/install.R | 29 --------------------- 3 files changed, 51 insertions(+), 31 deletions(-) create mode 100644 images/labkey/rstudio/extra.R diff --git a/images/labkey/rstudio/Dockerfile b/images/labkey/rstudio/Dockerfile index 102c752..6654c7f 100644 --- a/images/labkey/rstudio/Dockerfile +++ b/images/labkey/rstudio/Dockerfile @@ -3,9 +3,10 @@ FROM labkey/rstudio-base:${VERSION} RUN apt-get update && \ apt-get install -y --no-install-recommends \ - curl libcurl4-openssl-dev \ + curl libcurl4-openssl-dev \ libgd-dev libcairo2 libcairo2-dev libxt-dev pandoc \ - libssl-dev openssl cmake libnlopt-dev && \ + libssl-dev openssl cmake libnlopt-dev libgit2-dev libfontconfig1-dev \ + libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* @@ -13,3 +14,8 @@ COPY install.R / RUN dos2unix install.R && \ R --no-site-file -f install.R && \ chmod -R 755 /usr/local/lib/R/site-library + +COPY extra.R / +RUN dos2unix extra.R && \ + R --no-site-file -f extra.R && \ + chmod -R 755 /usr/local/lib/R/site-library diff --git a/images/labkey/rstudio/extra.R b/images/labkey/rstudio/extra.R new file mode 100644 index 0000000..69582b8 --- /dev/null +++ b/images/labkey/rstudio/extra.R @@ -0,0 +1,43 @@ +## +# Copyright (c) 2017 LabKey Corporation +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +## +install.packages("BiocManager", repos = "https://cloud.r-project.org") +install.packages("devtools", repos = "https://cloud.r-project.org/") +install.packages(c( + "latticeExtra", + "lme4", + "lmtest", + "openssl", + "plotly", + "plyr", + "png", + "readxl", + "reshape2", + "RSQLite", + "stringr", + "stringi", + "tidyverse", + "tibble", + "tidyr" + ), + repos='https://cran.rstudio.com/') + +library(BiocManager) +library(devtools) + +BiocManager::install("openCyto") + +install_github("RGLab/flowWorkspace") +install_github("RGLab/openCyto") \ No newline at end of file diff --git a/images/labkey/rstudio/install.R b/images/labkey/rstudio/install.R index d762df0..b43f3dc 100644 --- a/images/labkey/rstudio/install.R +++ b/images/labkey/rstudio/install.R @@ -33,32 +33,3 @@ install.packages(c( "rsconnect" ), repos='https://cran.rstudio.com/') -install.packages(c( - "latticeExtra", - "lme4", - "lmtest", - "openssl", - "plotly", - "plyr", - "png", - "readxl", - "reshape2", - "RSQLite", - "stringr", - "stringi", - "tidyverse", - "tibble", - "tidyr", - "devtools" - ), - repos='https://cran.rstudio.com/') -install.packages("BiocManager", repos = "https://cloud.r-project.org") - - -library(BiocManager) -library(devtools) - -BiocManager::install("openCyto") - -install_github("RGLab/flowWorkspace") -install_github("RGLab/openCyto") \ No newline at end of file From 7274600e7c188d8b31c32bff90e772b7a66e3331 Mon Sep 17 00:00:00 2001 From: labkey-jony Date: Wed, 11 Oct 2023 14:29:35 -0700 Subject: [PATCH 4/5] Split out bioConductor further, updated Dockerfile --- images/labkey/rstudio/Dockerfile | 5 +++++ images/labkey/rstudio/bioConductor.R | 3 +++ images/labkey/rstudio/extra.R | 8 -------- 3 files changed, 8 insertions(+), 8 deletions(-) create mode 100644 images/labkey/rstudio/bioConductor.R diff --git a/images/labkey/rstudio/Dockerfile b/images/labkey/rstudio/Dockerfile index 6654c7f..ed79b2f 100644 --- a/images/labkey/rstudio/Dockerfile +++ b/images/labkey/rstudio/Dockerfile @@ -19,3 +19,8 @@ COPY extra.R / RUN dos2unix extra.R && \ R --no-site-file -f extra.R && \ chmod -R 755 /usr/local/lib/R/site-library + +COPY bioConductor.R / +RUN dos2unix bioConductor.R && \ + R --no-site-file -f bioConductor.R && \ + chmod -R 755 /usr/local/lib/R/site-library \ No newline at end of file diff --git a/images/labkey/rstudio/bioConductor.R b/images/labkey/rstudio/bioConductor.R new file mode 100644 index 0000000..1a51088 --- /dev/null +++ b/images/labkey/rstudio/bioConductor.R @@ -0,0 +1,3 @@ +#!/usr/bin/env Rscript +BiocManager::install("flowWorkspace") +BiocManager::install("CytoML") diff --git a/images/labkey/rstudio/extra.R b/images/labkey/rstudio/extra.R index 69582b8..3821ba6 100644 --- a/images/labkey/rstudio/extra.R +++ b/images/labkey/rstudio/extra.R @@ -33,11 +33,3 @@ install.packages(c( "tidyr" ), repos='https://cran.rstudio.com/') - -library(BiocManager) -library(devtools) - -BiocManager::install("openCyto") - -install_github("RGLab/flowWorkspace") -install_github("RGLab/openCyto") \ No newline at end of file From 8a97452dc79ee11eeb10b72ed22334c0eda5e8b1 Mon Sep 17 00:00:00 2001 From: labkey-jony Date: Fri, 13 Oct 2023 10:34:39 -0700 Subject: [PATCH 5/5] Added more packages and revised version of R to newer one --- images/labkey/rstudio-base/Dockerfile | 2 +- images/labkey/rstudio-singleuser/Dockerfile | 2 +- images/labkey/rstudio/bioConductor.R | 6 +++++- images/labkey/rstudio/extra.R | 9 +++++++++ images/labkey/rstudio/make | 2 +- 5 files changed, 17 insertions(+), 4 deletions(-) diff --git a/images/labkey/rstudio-base/Dockerfile b/images/labkey/rstudio-base/Dockerfile index e1bea03..213ad95 100644 --- a/images/labkey/rstudio-base/Dockerfile +++ b/images/labkey/rstudio-base/Dockerfile @@ -1,4 +1,4 @@ -ARG VERSION=4.0.5 +ARG VERSION=4.3.1 FROM rocker/rstudio:${VERSION} RUN apt-get update && \ diff --git a/images/labkey/rstudio-singleuser/Dockerfile b/images/labkey/rstudio-singleuser/Dockerfile index e92b27c..28bb769 100644 --- a/images/labkey/rstudio-singleuser/Dockerfile +++ b/images/labkey/rstudio-singleuser/Dockerfile @@ -1,4 +1,4 @@ -ARG VERSION=4.0.5 +ARG VERSION=4.3.1 FROM rocker/rstudio:${VERSION} COPY rstudio-singleuser / diff --git a/images/labkey/rstudio/bioConductor.R b/images/labkey/rstudio/bioConductor.R index 1a51088..c554dd4 100644 --- a/images/labkey/rstudio/bioConductor.R +++ b/images/labkey/rstudio/bioConductor.R @@ -1,3 +1,7 @@ #!/usr/bin/env Rscript +BiocManager::install("flowCore") +BiocManager::install("flowViz") +BiocManager::install("cytolib") +BiocManager::install("ncdfFlow") BiocManager::install("flowWorkspace") -BiocManager::install("CytoML") +BiocManager::install("CytoML") \ No newline at end of file diff --git a/images/labkey/rstudio/extra.R b/images/labkey/rstudio/extra.R index 3821ba6..d0777bb 100644 --- a/images/labkey/rstudio/extra.R +++ b/images/labkey/rstudio/extra.R @@ -15,6 +15,15 @@ ## install.packages("BiocManager", repos = "https://cloud.r-project.org") install.packages("devtools", repos = "https://cloud.r-project.org/") +install.packages(c( + "locfit", + "ks", + "hdrcde", + "rainbow", + "fds", + "fda" + ), + repos='https://cran.rstudio.com/') install.packages(c( "latticeExtra", "lme4", diff --git a/images/labkey/rstudio/make b/images/labkey/rstudio/make index e4b1131..0d4e368 100755 --- a/images/labkey/rstudio/make +++ b/images/labkey/rstudio/make @@ -2,7 +2,7 @@ echo requires docker 17.05.0 or greater -export VERSION=${1-4.0.5} +export VERSION=${1-4.3.1} shift echo build VERSION=${VERSION}