diff --git a/carlisle b/carlisle index 21ab605..e1f4663 100755 --- a/carlisle +++ b/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 diff --git a/config/config.yaml b/config/config.yaml index c6566a5..036b1a7 100644 --- a/config/config.yaml +++ b/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" \ No newline at end of file diff --git a/config/rpackages.csv b/config/rpackages.csv new file mode 100644 index 0000000..1dc64df --- /dev/null +++ b/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 \ No newline at end of file