chore: Merge branch 'dev-sovacool'

Author: kelly-sovacool

.codeocean/environment.json

@@ -0,0 +1,10 @@
+{
+	"version": 1,
+	"base_image": "codeocean/mosuite:v0.2.1.9001_a954b69",
+	"post_install": true,
+	"options": {
+		"registry_host_arg": true,
+		"git_ask_pass": true,
+		"mount_secrets": true
+	}
+}

CHANGELOG.md

@@ -1,21 +1,35 @@
 # CodeOcean Capsule - MOSuite - create multiOmicDataset
 
+## development version
+
+- Use MOSuite v0.2.1-dev docker container.
+
 ## v5.0
 
-The output multiOmicDataSet RDS file is now saved to a subdirectory (`results/moo/moo.rds`) for easier re-use as a data asset.
+- The output multiOmicDataSet RDS file is now saved to a subdirectory (`results/moo/moo.rds`) for easier re-use as a data asset.
+
+<https://poc-nci.codeocean.io/capsule/6541445/tree/v5> (`4174472`)
 
 ## v4.0
 
 Report data files found for debugging purposes.
 
+<https://poc-nci.codeocean.io/capsule/6541445/tree/v3> (`37f3c43`)
+
 ## v3.0
 
 Removed counts file & input file parameters -- they are instead found via regex patterns in the data directory.
 
+<https://poc-nci.codeocean.io/capsule/6541445/tree/v3> (`04aa57b`)
+
 ## v2.0
 
 This release is identical to v1.0, except it is a Standard app rather than a No-Code app.
 
+<https://poc-nci.codeocean.io/capsule/6541445/tree/v2> (`a332cc8`)
+
 ## v1.0
 
-First release of MOSuite-create as a No-Code app
+First release of MOSuite-create as a No-Code app.
+
+<https://poc-nci.codeocean.io/capsule/6541445/tree/v1> (`a332cc8`)

README.md

@@ -4,4 +4,4 @@ Code Ocean capsule: MOSuite - create multiOmicDataset
 
 create multiOmicDataset from csv/tsv files
 
-[Code Ocean Capsule](https://poc-nci.codeocean.io/capsule/2543295/tree)
+[Code Ocean Capsule](https://poc-nci.codeocean.io/capsule/2543295/tree) | [Latest Release](https://poc-nci.codeocean.io/capsule/6541445/tree/latest)

environment/Dockerfile

@@ -1,59 +1,11 @@
-# hash:sha256:c9b112f3e66624a69cb708be33c863924c2212d60390363252f0db810ff49f7f
+# hash:sha256:260fa125cd3a5c9a7837cc9845f2662d183f1a2d77599fa149c5cf5e893e1c6d
 ARG REGISTRY_HOST
-FROM $REGISTRY_HOST/codeocean/mosuite:latest
+FROM $REGISTRY_HOST/codeocean/mosuite:v0.2.1.9001_a954b69
 
 ARG DEBIAN_FRONTEND=noninteractive
 ARG GIT_ASKPASS
 COPY git-askpass /
 
-ARG RCACHE_OPTIONS
-RUN echo $RCACHE_OPTIONS >> $(Rscript -e 'cat(R.home())')/etc/Rprofile.site
-ARG R_VERSION=4.3.2
-ENV R_VERSION=${R_VERSION}
-
-SHELL ["/bin/bash", "-lc"]
-
-# install conda packages
-RUN mamba install -y -c conda-forge \
-    r-base=${R_VERSION} \
-    r-argparse \
-    r-amap \
-    r-broom \
-    r-cffr \
-    r-colorspace \
-    r-dendextend \
-    r-devtools \
-    "r-ggplot2 <4.0.0" \
-    r-ggrepel \
-    r-gridExtra \
-    r-matrix \
-    r-mgcv \
-    r-patchwork \
-    r-plotly \
-    r-rcolorbrewer \
-    r-readr \
-    r-rmarkdown \
-    r-survival \
-    r-upsetr \
-    r-viridis \
-    bioconductor-annotationdbi \
-    bioconductor-annotate \
-    bioconductor-complexheatmap \
-    bioconductor-delayedarray \
-    bioconductor-edger \
-    bioconductor-genomicranges \
-    bioconductor-keggrest \
-    bioconductor-limma \
-    bioconductor-s4arrays \
-    bioconductor-summarizedexperiment \
-    bioconductor-sva \
-  && conda clean -afy
-
-# install R package
-RUN R -e 'remotes::install_github("CCBR/MOSuite", dependencies = TRUE, upgrade="never")' && \
-  R -e "library(MOSuite); devtools::test('/opt2/conda/lib/R/library/MOSuite')" && \
-  R -s -e "readr::write_csv(tibble::as_tibble(installed.packages()), '/data2/r-packages.csv')"
-
-# cleanup
-RUN apt-get clean && apt-get purge \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+COPY postInstall /
+RUN --mount=type=secret,id=secrets . /run/secrets/secrets \
+    && /postInstall

environment/postInstall

@@ -0,0 +1,2 @@
+#!/usr/bin/env bash
+set -e