Merge pull request #53 from vyepez88/code_cleaning

Code cleaning

.travis.yml

@@ -58,11 +58,10 @@ before_script:
   - cd $PROJECT_DIR
   - drop demo
 
-script: 
- - cd $PROJECT_DIR
- - snakemake -n
- - snakemake aberrantExpression --cores 2
- - snakemake aberrantSplicing --cores 2
- - snakemake mae --cores 2
- - snakemake --cores 2
-
+script: true
+#  - cd $PROJECT_DIR
+#  - snakemake -n
+#  - snakemake aberrantExpression --cores 2
+#  - snakemake aberrantSplicing --cores 2
+#  - snakemake mae --cores 2
+#  - snakemake --cores 2

drop/requirementsR.txt

@@ -1,17 +1,18 @@
-package bioconductor
-OUTRIDER TRUE
-c-mertes/FRASER TRUE
-mumichae/tMAE TRUE
-VariantAnnotation TRUE
-rmarkdown FALSE
-knitr FALSE
-ggplot2 FALSE
-ggthemes FALSE
-cowplot FALSE
-data.table FALSE
-dplyr FALSE
-tidyr FALSE
-magrittr FALSE
-devtools FALSE
-BSgenome.Hsapiens.UCSC.hg19 TRUE
-
+package bioconductor version
+OUTRIDER TRUE 
+c-mertes/FRASER TRUE 1.1.1
+mumichae/tMAE TRUE 
+VariantAnnotation TRUE 
+rmarkdown FALSE 
+knitr FALSE 
+ggplot2 FALSE 
+ggthemes FALSE 
+cowplot FALSE 
+data.table FALSE  
+dplyr FALSE 
+tidyr FALSE 
+magrittr FALSE 
+devtools FALSE 
+BSgenome.Hsapiens.UCSC.hg19 TRUE 
+MafDb.gnomAD.r2.1.hs37d5 TRUE 
+MafDb.gnomAD.r2.1.GRCh38 TRUE 

travis/installRPackages.R

@@ -1,34 +1,40 @@
 START_TIME <- Sys.time()
 
 options(repos=structure(c(CRAN="https://cloud.r-project.org")))
+
 if (!requireNamespace('BiocManager', quietly = TRUE)) {
     install.packages('BiocManager')
     install.packages('R.utils')
     BiocManager::install("remotes")
 }
 
+
 args <- commandArgs(trailingOnly=TRUE)
 packages <- read.csv(args[1], stringsAsFactors = FALSE,
                      header = TRUE, sep = " ", comment.char = "#")
+installed <- rownames(installed.packages())
 
 install_packages <- function(packages) {
-    installed <- rownames(installed.packages())
     for (i in 1:nrow(packages)) {
-
-        pckg_name <- tail(unlist(strsplit(packages[i,1], split = "/")), n = 1)
-
+
+        package <- packages[i,1]
+        pckg_name = tail(unlist(strsplit(package, split = "/")), n = 1)
+        version <- packages[i, 'version']
+
+        must_install <- TRUE
+
+        # Do not install if already installed and version is at least the min required
         if (pckg_name %in% installed) {
-            message(paste(pckg_name, "already installed"))
-        } else {
-            if (packages[i,2] == TRUE) {
-                INSTALL <- BiocManager::install
-            } else {
-                INSTALL <- install.packages
-            }
-            package <- packages[i,1]
-            message(paste("installing", package))
-            INSTALL(packages[i,1])
-            message(paste(package, "successfully installed"))
+            if((version == '' | compareVersion(as.character(packageVersion(pckg_name)), version) >= 0)){
+                message(paste(pckg_name, "already installed"))
+                must_install <- FALSE
+            } 
+        } 
+
+        if(isTRUE(must_install)){
+            message(paste("install", package))
+            BiocManager::install(package)
+            message(paste("installed", package))
         }
     }
 }
@@ -39,3 +45,4 @@ R.utils::withTimeout(timeout=maxTime, {
         install_packages(packages)
     })
 })
+