Merge branch 'master' into jashapiro/gsvaParams-update

AlexsLemonade · Jun 17, 2024 · 8ad545e · 8ad545e
2 parents aef1d22 + 31bf431
commit 8ad545e
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diff --git a/.github/workflows/build-docker.yml b/.github/workflows/build-docker.yml
@@ -1,4 +1,4 @@
-name: Build Docker Image and Push to Dockerhub
+name: Build Docker Image
 
 # Every time something is merged to master or a tag is pushed, we build and push
 # the Docker image

diff --git a/Dockerfile b/Dockerfile
@@ -68,12 +68,18 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
 COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt
 
+
+
 # Use renv for R packages
 WORKDIR /usr/local/renv
 ENV RENV_CONFIG_CACHE_ENABLED=FALSE
+RUN Rscript -e "install.packages('renv')"
+
+# Temporary fix for broken(?) RSamtools package
+RUN Rscript -e "install.packages('BiocManager'); BiocManager::install('Rsamtools')"
+
 COPY renv.lock renv.lock
-RUN R -e "install.packages('renv')"
-RUN R -e "renv::restore()" \
+RUN Rscript -e "renv::restore()" \
     rm -rf ~/.cache/R/renv && \
     rm -rf /tmp/downloaded_packages && \
     rm -rf /tmp/Rtmp*

diff --git a/components/dependencies.R b/components/dependencies.R
@@ -7,7 +7,7 @@ library(markdown)
 library(magick)
 
 # Recommended by tximport
-library(fishpond)
+library(eds)
 
 # Required for DESeq2::lfcShrink()
 library(apeglm)

diff --git a/renv.lock b/renv.lock
@@ -2378,6 +2378,17 @@
       ],
       "Hash": "20783ecb7e7cea3f351e8b21153e3eb8"
     },
+    "eds": {
+      "Package": "eds",
+      "Version": "1.6.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "Matrix",
+        "Rcpp"
+      ],
+      "Hash": "ab19d02b3418e44d6f32ffb8060427d2"
+    },
     "ellipsis": {
       "Package": "ellipsis",
       "Version": "0.3.2",
@@ -2631,31 +2642,6 @@
       ],
       "Hash": "192053c276525c8495ccfd523aa8f2d1"
     },
-    "fishpond": {
-      "Package": "fishpond",
-      "Version": "2.10.0",
-      "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.19",
-      "Requirements": [
-        "GenomicRanges",
-        "IRanges",
-        "Matrix",
-        "S4Vectors",
-        "SingleCellExperiment",
-        "SummarizedExperiment",
-        "abind",
-        "graphics",
-        "gtools",
-        "jsonlite",
-        "matrixStats",
-        "methods",
-        "qvalue",
-        "stats",
-        "svMisc",
-        "utils"
-      ],
-      "Hash": "9091a296b5cdb86da7c4c35f958c67f6"
-    },
     "flexmix": {
       "Package": "flexmix",
       "Version": "2.3-19",
@@ -5008,20 +4994,6 @@
       ],
       "Hash": "184d7799bca4ba8c3be72ea396f4b9a3"
     },
-    "svMisc": {
-      "Package": "svMisc",
-      "Version": "1.2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods",
-        "stats",
-        "tools",
-        "utils"
-      ],
-      "Hash": "b13f5680860f67c32ccb006ad38f24f4"
-    },
     "sys": {
       "Package": "sys",
       "Version": "3.4.2",