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Consolidate R package install and see if that speeds things up
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@jaclyn-taroni
jaclyn-taroni committed May 20, 2022
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233 changes: 80 additions & 153 deletions Dockerfile
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Expand Up @@ -36,16 +36,18 @@ RUN pip3 install \
"six==1.14.0" \
"wheel==0.34.2"


# Install java
RUN apt-get update && apt-get -y --no-install-recommends install \
default-jdk


# Required for running matplotlib in Python in an interactive session
RUN apt-get -y --no-install-recommends install \
python3-tk

# gmp, dependency for signature.tools.lib
RUN apt-get -y --no-install-recommends install \
libgmp-dev

# Standalone tools and libraries
################################

Expand Down Expand Up @@ -77,142 +79,102 @@ RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar
#### R packages
###############

# Commonly used R packages
# From CRAN and Bioconductor
RUN ./install_bioc.r \
annotatr \
BSgenome.Hsapiens.UCSC.hg19 \
BSgenome.Hsapiens.UCSC.hg38 \
caret \
class \
cluster \
cmprsk \
ComplexHeatmap \
corrplot \
d3r \
data.table \
deconstructSigs \
DT \
e1071 \
EnsDb.Hsapiens.v86 \
ensembldb \
EnvStats \
flextable \
foreign \
gdalUtils \
GenVisR \
GGally \
ggbio \
ggforce \
ggfortify \
ggpubr \
ggrepel \
ggsci \
ggsignif \
glmnet \
glmnetUtils \
gplots \
gridGraphics \
GSVA \
hexbin \
janitor \
lattice \
leafem \
leafpop \
lsa \
lwgeom \
mapview \
MASS \
Matrix \
mgcv \
MM2S \
msigdbr \
multipanelfigure \
nlme \
nnet \
openxlsx \
optparse \
org.Hs.eg.db \
pheatmap \
plainview \
preprocessCore \
qdapRegex \
R.utils \
RColorBrewer \
rJava \
rpart \
rprojroot \
survival \
viridis \
openxlsx


# Required for interactive sample distribution plots
# map view is needed to create HTML outputs of the interactive plots
RUN ./install_bioc.r \
gdalUtils \
leafem \
leafpop \
lwgeom \
mapview \
plainview \
sf \
stars

# Installs packages needed for plottings
# treemap, interactive plots, and hex plots
# Rtsne and umap are required for dimension reduction analyses
RUN ./install_bioc.r \
corrplot \
d3r \
ggfortify \
ggpubr \
ggrepel \
ggsci \
ggsignif \
gridGraphics \
hexbin \
pheatmap \
rtracklayer \
Rtsne \
sf \
spatial \
survival \
survMisc \
survminer \
stars \
treemap \
TxDb.Hsapiens.UCSC.hg38.knownGene \
umap \
UpSetR \
VennDiagram

# Install rjava
RUN ./install_bioc.r \
rJava

# Need for survminer for doing survival analysis
RUN ./install_bioc.r \
cmprsk \
survMisc \
survminer

# maftools for proof of concept in create-subset-files
RUN R -e "remotes::install_github('PoisonAlien/maftools', ref = '9719868262f946e0b8eb2e7ec2510ee18c6cafa3')"

# ComplexHeatmap
RUN ./install_bioc.r \
ComplexHeatmap

# This is needed for the CNV frequency and proportion aberration plots
RUN ./install_bioc.r \
GenVisR

# These packages are for the genomic region analysis for snv-callers
RUN ./install_bioc.r \
annotatr \
TxDb.Hsapiens.UCSC.hg38.knownGene \
org.Hs.eg.db \
BSgenome.Hsapiens.UCSC.hg19 \
BSgenome.Hsapiens.UCSC.hg38

# Packages for expression normalization and batch correction
RUN ./install_bioc.r \
preprocessCore \
sva


## This is deprecated
# # These packages are for single-sample GSEA analysis
# RUN ./install_bioc.r 'GSEABase', 'GSVA'

# Required for sex prediction from RNA-seq data
RUN ./install_bioc.r \
glmnet \
glmnetUtils \
caret \
e1071
VennDiagram \
viridis

### Install R packages from GitHub ###

# Need to explicitly check via loading
# bedr package & check to make sure binaries are available by loading
RUN ./install_bioc.r \
bedr \
&& Rscript -e "library(bedr)"

# Also install for mutation signature analysis
# qdapRegex is for the fusion analysis
RUN ./install_bioc.r \
deconstructSigs \
qdapRegex

# packages required for collapsing RNA-seq data by removing duplicated gene symbols
RUN ./install_bioc.r \
rtracklayer
# maftools for proof of concept in create-subset-files
RUN R -e "remotes::install_github('PoisonAlien/maftools', ref = '9719868262f946e0b8eb2e7ec2510ee18c6cafa3')"

# TCGAbiolinks for TMB compare analysis
RUN R -e "remotes::install_github('RDocTaskForce/parsetools', ref = '1e682a9f4c5c7192d22e8985ce7723c09e98d62b', dependencies = TRUE)" \
&& R -e "remotes::install_github('RDocTaskForce/testextra', ref = '4e5dfac8853c08d5c2a8790a0a1f8165f293b4be', dependencies = TRUE)" \
&& R -e "remotes::install_github('halpo/purrrogress', ref = '54f2130477f161896e7b271ed3ea828c7e4ccb1c', dependencies = TRUE)" \
&& ./install_bioc.r TCGAbiolinks

# Install for mutation signature analysis
RUN ./install_bioc.r \
ggbio

# CRAN package msigdbr and GSVA for gene-set-enrichment-analysis
RUN ./install_bioc.r \
msigdbr \
GSVA


# package required for immune deconvolution
RUN R -e "remotes::install_github('icbi-lab/immunedeconv', ref = '493bcaa9e1f73554ac2d25aff6e6a7925b0ea7a6', dependencies = TRUE)"

Expand All @@ -233,11 +195,6 @@ RUN R -e "remotes::install_github('NNoureen/EXTEND', ref = '467c2724e1324ef05ad9
# package required for shatterseek
RUN R -e "withr::with_envvar(c(R_REMOTES_NO_ERRORS_FROM_WARNINGS='true'), remotes::install_github('parklab/ShatterSeek', ref = '83ab3effaf9589cc391ecc2ac45a6eaf578b5046', dependencies = TRUE))"

# Packages required for rna-seq-composition
RUN ./install_bioc.r \
EnvStats \
janitor

# Patchwork for plot compositions
RUN R -e "remotes::install_github('thomasp85/patchwork', ref = 'c67c6603ba59dd46899f17197f9858bc5672e9f4')"

Expand All @@ -247,6 +204,24 @@ RUN R -e "remotes::install_github('wilkox/treemapify', ref = 'e70adf727f4d13223d
# Need this specific version of circlize so it has hg38
RUN R -e "remotes::install_github('jokergoo/circlize', ref = 'b7d86409d7f893e881980b705ba1dbc758df847d', dependencies = TRUE)"

# More recent version of sva required for molecular subtyping MB
RUN R -e "remotes::install_github('jtleek/sva-devel@123be9b2b9fd7c7cd495fab7d7d901767964ce9e', dependencies = FALSE, upgrade = FALSE)"

# To install sigfit, we need a more recent version of rstantools than we can obtain via the MRAN snapshot route
# We're using the ref for the most recent release on GitHub (2.0.0)
RUN R -e "remotes::install_github('stan-dev/rstantools', ref = 'd43bf9fb6120d40a60e708853e4b80cdb4689d19', dependencies = TRUE)"

# Build arguments are according to the sigfit instructions
RUN R -e "remotes::install_github('kgori/sigfit', ref = '209776ee1d2193ad4b682b2e2472f848bd7c67a6', build_vignettes = TRUE, build_opts = c('--no-resave-data', '--no-manual'), dependencies = TRUE)"

RUN R -e "remotes::install_github('d3b-center/annoFuse',ref = 'c6a2111b5949ca2aae3853f7f34de3d0db4ffa33', dependencies = TRUE)"

# CNS signatures can be obtained from signature.tools.lib
RUN R -e "remotes::install_github('Nik-Zainal-Group/signature.tools.lib', ref = '73e899c9090a215a76a307480bda76c241a4a489')"

# Patterned geoms
RUN R -e "remotes::install_github('coolbutuseless/ggpattern', ref = '390e13fead028ba240eae9293a5ef422df02bc8e')"

# Install python packages
##########################

Expand Down Expand Up @@ -370,54 +345,6 @@ RUN mkdir -p gistic_install && \
chmod 755 /home/rstudio/gistic_install
WORKDIR /rocker-build/

# Install multipanelfigure, required for transcriptomic overview figure
# gplots for gistic comparison
RUN ./install_bioc.r \
multipanelfigure \
gplots

# Molecular subtyping MB
RUN R -e "remotes::install_github('d3b-center/medullo-classifier-package', ref = 'e3d12f64e2e4e00f5ea884f3353eb8c4b612abe8', dependencies = TRUE, upgrade = FALSE)" \
&& ./install_bioc.r MM2S \
&& Rscript -e "library(medulloPackage)"

# More recent version of sva required for molecular subtyping MB
RUN R -e "remotes::install_github('jtleek/sva-devel@123be9b2b9fd7c7cd495fab7d7d901767964ce9e', dependencies = FALSE, upgrade = FALSE)"

# Packages required for de novo mutational signatures
RUN install2.r --error --deps TRUE \
lsa

# To install sigfit, we need a more recent version of rstantools than we can obtain via the MRAN snapshot route
# We're using the ref for the most recent release on GitHub (2.0.0)
RUN R -e "remotes::install_github('stan-dev/rstantools', ref = 'd43bf9fb6120d40a60e708853e4b80cdb4689d19', dependencies = TRUE)"

# Build arguments are according to the sigfit instructions
RUN R -e "remotes::install_github('kgori/sigfit', ref = '209776ee1d2193ad4b682b2e2472f848bd7c67a6', build_vignettes = TRUE, build_opts = c('--no-resave-data', '--no-manual'), dependencies = TRUE)"

# Package for kinase domain retention for fusions
RUN ./install_bioc.r \
EnsDb.Hsapiens.v86 \
ensembldb

RUN R -e "remotes::install_github('d3b-center/annoFuse',ref = 'c6a2111b5949ca2aae3853f7f34de3d0db4ffa33', dependencies = TRUE)"


# gmp, dependency for signature.tools.lib
RUN apt-get -y --no-install-recommends install \
libgmp-dev

# CNS signatures can be obtained from signature.tools.lib
RUN R -e "remotes::install_github('Nik-Zainal-Group/signature.tools.lib', ref = '73e899c9090a215a76a307480bda76c241a4a489')"

# Patterned geoms
RUN R -e "remotes::install_github('coolbutuseless/ggpattern', ref = '390e13fead028ba240eae9293a5ef422df02bc8e')"


# ggforce for mutational-signatures sina plots
RUN ./install_bioc.r \
ggforce


#### Please install your dependencies immediately above this comment.
#### Add a comment to indicate what analysis it is required for
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