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Bugfix/missing deps for gls base docker image #2

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Bugfix/missing deps for gls base docker image #2

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7623dd3
changing the GLS base container image
r-vieira Jun 10, 2023
9c890e4
reusing nemascan's GLS base image.
r-vieira Jun 10, 2023
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31 changes: 25 additions & 6 deletions env/Dockerfile
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@@ -1,7 +1,26 @@
FROM rocker/tidyverse:3.6.0
MAINTAINER Katie Evans <katiesevans9@gmail.com>
FROM continuumio/miniconda
MAINTAINER Katie Evans <kathryn.evans@northwestern.edu>

RUN Rscript -e "install.packages(c('futile.logger', 'remotes', 'devtools'), dependencies=TRUE, repos='http://cran.us.r-project.org')"
RUN Rscript -e "remotes::install_github('lme4/lme4', build_vignettes=FALSE)"
RUN Rscript -e "remotes::install_version('sommer', version = '4.0.4', repos = 'http://cran.us.r-project.org')"
RUN Rscript -e "remotes::install_version('boot', version = '1.3-28', repos = 'http://cran.us.r-project.org')"
COPY conda.yml .

RUN conda install mamba -n base -c conda-forge

RUN mamba env update -n root -f conda.yml \
&& mamba clean -a

RUN Rscript -e "install.packages('valr', dependencies=TRUE, repos='http://cran.us.r-project.org')"

# install other tools not avalible on conda cloud
RUN apt-get --allow-releaseinfo-change update && apt-get install -y procps

RUN mamba install -c conda-forge r-fuzzyjoin
RUN mamba install -c bioconda bioconductor-iranges

# RUN Rscript -e "install.packages('roperators',dependencies=TRUE, repos='http://cran.us.r-project.org')"
# RUN Rscript -e "install.packages('tidyverse', dependencies=TRUE, repos='http://cran.us.r-project.org')"
# RUN conda install -c conda-forge r-tidyverse
# RUN conda install r-valr
# RUN Rscript -e "devtools::install_version('tidyverse',version='1.3.1', dependencies = TRUE, repos = 'http://cran.us.r-project.org')"
RUN Rscript -e "remotes::install_version('dplyr', version = '1.0.4', repos = 'http://cran.us.r-project.org')"

RUN mamba install -c conda-forge mscorefonts
40 changes: 40 additions & 0 deletions env/conda.yml
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@@ -0,0 +1,40 @@
name: nemascan
channels:
- defaults
- bioconda
- r
- biobuilds
- conda-forge
dependencies:
- bcftools=1.9
- pandoc=2.12
- plink=1.90b6.12
- bedtools=2.29.2
- libiconv
- r=3.6.0
- r-tidyselect=1.1.0
- r-tidyverse=1.3.0
# - r-dplyr=1.0.8
# - r-tidyr=1.2.0
# - r-readr=2.1.1
# - r-stringr=1.4.0
# - r-glue=1.6.2
# - r-purrr=0.3.2
# - r-ggplot2=3.1.1
- r-devtools=2.0.2
- r-data.table=1.12.2
- r-DT=0.5
- r-genetics=1.3.8.1.2
- r-ggbeeswarm=0.6.0
- r-ggnewscale=0.4.5
- r-ggrepel=0.9.1
- r-knitr=1.22
- r-rmarkdown=1.12
- r-plotly=4.9.0
- r-RSpectra=0.16-0
- r-sommer=4.0.4
- r-coop=0.6-2
# # - r-Rcpp
- r-cowplot=0.9.1

# - bioconductor-ComplexHeatmap=2.4.2
3 changes: 2 additions & 1 deletion nextflow.config
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Expand Up @@ -61,7 +61,8 @@ profiles {

process {
executor = 'google-lifesciences'
container = 'andersenlab/nemascan:20220407173056db3227'
//container = 'andersenlab/nemascan:20220407173056db3227'
container = 'northwesternmti/heritability-gls-base:latest'
//machineType = 'n1-standard-1'

withLabel: medium {
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