Merge pull request #890 from sjspielman/sjspielman/866-update-renv-do…

…cker Add zellkonverter to wilms-06 environment
AlexsLemonade · Nov 18, 2024 · a275005 · a275005
2 parents 59d0d79 + e563242
commit a275005
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Showing 4 changed files with 78 additions and 4 deletions.
diff --git a/.github/workflows/docker_cell-type-wilms-tumor-06.yml b/.github/workflows/docker_cell-type-wilms-tumor-06.yml
@@ -16,6 +16,7 @@ on:
   pull_request:
     branches:
       - main
+      - feature/*
     paths:
       - "analyses/cell-type-wilms-tumor-06/Dockerfile"
       - "analyses/cell-type-wilms-tumor-06/.dockerignore"
@@ -24,6 +25,7 @@ on:
   push:
     branches:
       - main
+      - feature/*
     paths:
       - "analyses/cell-type-wilms-tumor-06/Dockerfile"
       - "analyses/cell-type-wilms-tumor-06/.dockerignore"

diff --git a/analyses/cell-type-wilms-tumor-06/Dockerfile b/analyses/cell-type-wilms-tumor-06/Dockerfile
@@ -29,3 +29,9 @@ RUN Rscript -e 'renv::restore()' && \
   rm -rf ~/.cache/R/renv && \
   rm -rf /tmp/downloaded_packages && \
   rm -rf /tmp/Rtmp*
+
+# Complete installation of zellkonverter conda env
+ENV BASILISK_EXTERNAL_DIR /usr/local/renv/basilisk
+RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
+  basilisk::basiliskStop(proc); \
+  basilisk.utils::cleanConda()"
diff --git a/analyses/cell-type-wilms-tumor-06/components/dependencies.R b/analyses/cell-type-wilms-tumor-06/components/dependencies.R
@@ -1,11 +1,9 @@
 # Tidyverse
-library(tidyverse)
 library(assertthat)
 
 # Single-cell packages
-library(Azimuth) # remotes::install_github("satijalab/azimuth")
-library(SCpubr)
 library(ggplotify)
 library(edgeR)
 library(ggdist)
 library(fetusref.SeuratData)
+library(zellkonverter)
diff --git a/analyses/cell-type-wilms-tumor-06/renv.lock b/analyses/cell-type-wilms-tumor-06/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.4.1",
+    "Version": "4.4.0",
     "Repositories": [
       {
         "Name": "BioCsoft",
@@ -1540,6 +1540,34 @@
       ],
       "Hash": "543776ae6848fde2f48ff3816d0628bc"
     },
+    "basilisk": {
+      "Package": "basilisk",
+      "Version": "1.16.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "basilisk.utils",
+        "dir.expiry",
+        "methods",
+        "parallel",
+        "reticulate",
+        "utils"
+      ],
+      "Hash": "0402cc833c4fa37a80b44deffce28fe6"
+    },
+    "basilisk.utils": {
+      "Package": "basilisk.utils",
+      "Version": "1.16.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "dir.expiry",
+        "methods",
+        "tools",
+        "utils"
+      ],
+      "Hash": "39d6ecdea862d961c3dfe4d4d7c57920"
+    },
     "beachmat": {
       "Package": "beachmat",
       "Version": "2.20.0",
@@ -1973,6 +2001,17 @@
       ],
       "Hash": "33698c4b3127fc9f506654607fb73676"
     },
+    "dir.expiry": {
+      "Package": "dir.expiry",
+      "Version": "1.12.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "filelock",
+        "utils"
+      ],
+      "Hash": "41bd784b988874bccef2d4df2a69fd1a"
+    },
     "distributional": {
       "Package": "distributional",
       "Version": "0.5.0",
@@ -2276,6 +2315,16 @@
       ],
       "Hash": "ead409e5a973cd285681c3bb0ade49a7"
     },
+    "filelock": {
+      "Package": "filelock",
+      "Version": "1.0.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "192053c276525c8495ccfd523aa8f2d1"
+    },
     "findpython": {
       "Package": "findpython",
       "Version": "1.0.8",
@@ -5184,6 +5233,25 @@
       ],
       "Hash": "367554cd9602e69616660580c820b3bf"
     },
+    "zellkonverter": {
+      "Package": "zellkonverter",
+      "Version": "1.14.1",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "DelayedArray",
+        "Matrix",
+        "S4Vectors",
+        "SingleCellExperiment",
+        "SummarizedExperiment",
+        "basilisk",
+        "cli",
+        "methods",
+        "reticulate",
+        "utils"
+      ],
+      "Hash": "656ccd4d9874cf077f9a688b38d03a63"
+    },
     "zlibbioc": {
       "Package": "zlibbioc",
       "Version": "1.50.0",