test r...

config/config_final.yml

@@ -30,6 +30,7 @@ conda:
   STAR: $envsdir/STAR.yml
   stringtie: $envsdir/stringtie.yml
   salmon: $envsdir/salmon.yml
+  r: $envsdir/R.yml
 
 # reference files, genome indices and data
 reference:

workflow/R/R_custom.R

@@ -1,17 +1,8 @@
 ### Create and load vector of packages
 #setwd(final_output)
 source("workflow/R/config_all.R")
-new.packages <- my_packages_cran[!(my_packages_cran %in% installed.packages()[,"Package"])]
-if(length(new.packages)) install.packages(new.packages)
-# Load BiocManager
-if (!requireNamespace("BiocManager", quietly = TRUE))
-    install.packages("BiocManager")
-# Check and install missing packages
-missing_packages <- my_packages_bioconductor[!(my_packages_bioconductor %in% installed.packages()[,"Package"])]
-if (length(missing_packages))
-    BiocManager::install(missing_packages)
-lapply(my_packages_cran, require, character.only = TRUE) 
-lapply(mmy_packages_bioconductor, require, character.only = TRUE) 
+lapply(my_packages, require, character.only = TRUE) 
+
 ### Create a list with all txt files containing the samples for each tissues
 ### Extract all samples from the txt list files for each tissues
 setwd(txt_files_dir)

workflow/R/config_all.R

@@ -20,9 +20,8 @@ BRAF_ids <- c("ENST00000288602.11","ENST00000469930.2","ENST00000479537.6","ENST
               "ENST00000647434.1")
 
 ## libraries
-my_packages_cran <- c("dplyr","ggplot2","tidyr","ggsignif","ggpubr","patchwork","stringr","ggrepel","tibble")
-my_packages_bioconductor <- c("GenomicAlignments","tximport","tximeta")
-my_packages_github <- c("bedtoolsr")
+my_packages <- c("dplyr","ggplot2","tidyr","ggsignif","ggpubr","patchwork","stringr",
+                 "ggrepel","GenomicAlignments","bedtoolsr","tximport","tximeta","tibble")
 
 ## Sample typologies
 samples_typologies <-  c("Lung")

workflow/envs/R.yml

@@ -0,0 +1,11 @@
+name: my_r_env
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults  ## block user/system channels
+dependencies:
+  - r-base=4.2  ## always specify the R version (faster solve; more stable)
+  - r-essentials
+  - bioconductor-GenomicAlignments
+  - bioconductor-tximport
+  - bioconductor-tibble

workflow/snakefile_final.smk

@@ -402,6 +402,8 @@ rule polyA_r_script:
     output:
         polyA_204 = config['datadirs']['r'] + "polyA_filtered_3UTR204.csv",
         polyA_220 = config['datadirs']['r'] + "polyA_filtered_3UTR220.csv"
+    conda:
+        config['conda']['r']
     shell:
         "Rscript {params.r_polya}"
 
@@ -412,6 +414,8 @@ rule custom_r_script:
         r_custom = config['scripts']['r_custom']
     output:
         boxplot_custom = config['datadirs']['r'] + "ratio_BRAF.pdf"
+    conda:
+        config['conda']['r']
     shell:
         "Rscript {params.r_custom}"
 
@@ -424,5 +428,7 @@ rule salmon_r_script:
         boxplot_salmon = config['datadirs']['r'] + "ratio_salmon.pdf",
         piecharts_salmon = config['datadirs']['r'] + "pie_charts.pdf",
         total_salmon = config['datadirs']['r'] + "total_salmon.pdf"
+    conda:
+        config['conda']['r']
     shell:
         "Rscript {params.r_salmon}"