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Swap out fishpond for eds #772

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merged 5 commits into from
Jun 6, 2024
Merged

Swap out fishpond for eds #772

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6637a75
Swap out fishpond for eds
jashapiro Jun 5, 2024
42abac0
RSamtools broken package fix
jashapiro Jun 5, 2024
7016a59
No, this is the fix...
jashapiro Jun 5, 2024
a248c2a
capitalization
jashapiro Jun 5, 2024
888397a
use Rscript
jashapiro Jun 5, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/build-docker.yml
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Original file line number Diff line number Diff line change
@@ -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
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10 changes: 8 additions & 2 deletions Dockerfile
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Expand Up @@ -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')"
Comment on lines +78 to +79
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ooof what happened to RSamtools?

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I'm not sure... something in an interaction between the Bioc docker image, renv and Rsamtools means that the package it downloads is corrupted and fails to untar properly. Ally ran into it in her Docker image a week or so ago. I'm expecting it to be resolved at some point when things rebuild somewhere.


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*
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2 changes: 1 addition & 1 deletion components/dependencies.R
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Expand Up @@ -7,7 +7,7 @@ library(markdown)
library(magick)

# Recommended by tximport
library(fishpond)
library(eds)

# Required for DESeq2::lfcShrink()
library(apeglm)
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50 changes: 11 additions & 39 deletions renv.lock
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
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