feat: add rpackage config

carlisle

@@ -27,7 +27,7 @@ tools_specific_yaml="tools_biowulf.yaml"
 # essential files
 # these are relative to the workflows' base folder
 # these are copied into the WORKDIR
-ESSENTIAL_FILES="config/config.yaml config/samples.tsv config/contrasts.tsv config/fqscreen_config.conf config/multiqc_config.yaml"
+ESSENTIAL_FILES="config/config.yaml config/samples.tsv config/contrasts.tsv config/fqscreen_config.conf config/multiqc_config.yaml config/rpackages.csv"
 ESSENTIAL_FOLDERS="workflow/scripts annotation"
 # set extra singularity bindings
 EXTRA_SINGULARITY_BINDS="-B /data/CCBR_Pipeliner/,/lscratch"
@@ -222,6 +222,9 @@ function runlocal() {
 }
 
 function runtest() {
+  module load $PYTHON_VERSION
+  module load $SNAKEMAKE_VERSION
+  module load $SINGULARITY_VERSION
   check_essential_files
   sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" ${PIPELINE_HOME}/.test/samples.test.tsv > $WORKDIR/config/samples.tsv
   cp ${PIPELINE_HOME}/.test/contrasts.test.tsv $WORKDIR/config/contrasts.tsv

config/config.yaml

@@ -147,3 +147,9 @@ spikein_reference:
     fa: "PIPELINE_HOME/resources/spikein/S_cer_S288C_R64.fna"
 
 adapters: "PIPELINE_HOME/resources/other/adapters.fa"
+
+#####################################################################################
+# R Packages
+#####################################################################################
+Rlib_dir: "/data/CCBR_Pipeliner/db/PipeDB/Rlibrary_4.3_carlisle/"
+Rpkg_config: "WORKDIR/config//Rpack.config"

config/rpackages.csv

@@ -0,0 +1,31 @@
+package,source,version,gh_name,diff,spike_in,go
+DT,cr,0.29,NA,Y,Y,N
+RColorBrewer,cr,,NA,Y,N,N
+dplyr,cr,,NA,Y,N,N
+ggfortify,cr,,NA,Y,N,N
+ggplot2,cr,3.4.2,NA,Y,Y,N
+ggrepel,cr,,NA,Y,N,N
+pander,cr,,NA,Y,N,N
+plotly,cr,,NA,Y,N,N
+reshape2,cr,,NA,Y,N,N
+stringr,cr,1.5.0,NA,Y,N,N
+tidyverse,cr,,NA,Y,N,N
+yaml,cr,,NA,Y,N,N
+BiocManager,cr,3.17,NA,Y,N,N
+ChIPseeker,bc,,NA,Y,N,N
+DESeq2,bc,,NA,Y,N,N
+ELBOW,bc,,NA,Y,N,N
+EnhancedVolcano,bc,,NA,Y,N,N
+GenomicFeatures,bc,,NA,Y,N,N
+HTSFilter,bc,,NA,Y,N,N
+TxDb.Hsapiens.UCSC.hg19.knownGene,bc,,NA,Y,N,N
+TxDb.Hsapiens.UCSC.hg38.knownGene,bc,,NA,Y,N,N
+TxDb.Mmusculus.UCSC.mm10.knownGene,bc,,NA,Y,N,N
+edgeR,bc,,NA,Y,N,N
+org.Hs.eg.db,bc,3.17.0,NA,Y,N,N
+org.Mm.eg.db,bc,3.17.0,NA,Y,N,N
+rtracklayer,bc,,NA,Y,N,N
+BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0,bc,,NA,Y,N,Y
+chipenrich,bc,,NA,N,Y,Y
+latticeExtra,cr,,NA,N,N,Y
+pdp,cr,,NA,N,N,Y