Rehousing CaeNDR-specific changes back to AndersenLab

env/Dockerfile

@@ -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

env/conda.yml

@@ -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

heritability-nxf.sh

@@ -6,7 +6,7 @@
 
 DEFAULT_DATA_DIR="gs://nf-pipelines/heritability/"
 DEFAULT_VCF_VERSION="20220216"
-DEFAULT_SPECIES='c_elegans'
+DEFAULT_SPECIES="c_elegans"
 DEFAULT_GOOGLE_PROJECT="andersen-lab"
 DEFAULT_GOOGLE_ZONE="us-central1-a"
 DEFAULT_GOOGLE_SERVICE_ACCOUNT_EMAIL="nscalc-201573431837@andersen-lab.iam.gserviceaccount.com"

main.nf

@@ -10,10 +10,14 @@ nextflow.enable.dsl=2
 
 date = new Date().format( 'yyyyMMdd' )
 params.binDir = "${workflow.projectDir}"
-params.species = "c_elegans"
 params.fix = "fix"
 params.maf = 0.05
 
+// default to C. elegans if no species given
+if(!params.species) {
+    params.species = "c_elegans"
+}
+
 /*
 ~ ~ ~ > * Parameters
 */

nextflow.config

@@ -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 {