modification de fichiers

src/tp1.R

@@ -2,7 +2,7 @@ options(repos = c(CRAN = "https://cloud.r-project.org"))
 output_dir = "results/tp1"
 dir.create(output_dir, showWarnings = F, recursive = T)
 
-<<<<<<< HEAD
+
 # if (!require("BiocManager", quietly = TRUE))
 #  install.packages("BiocManager")
 
@@ -18,8 +18,6 @@ dir.create(output_dir, showWarnings = F, recursive = T)
 #library(devtools)
 #library(plyr)
 
-=======
->>>>>>> main
 # Les données analysées nécessitant beaucoup de RAM, nous allons sélectionner aléatoirement 250000 SNPs et réecrire des fichiers bed, bim, fam
 penncath_bed_path = "results/data/penncath.bed"
 penncath_bim_path = "results/data/penncath.bim"
@@ -46,8 +44,8 @@ rm(geno)
 rdata_path = file.path(output_dir, "TP1_asbvg.RData")
 save.image(rdata_path)
 
-<<<<<<< HEAD
-=======
 
 
->>>>>>> main
+
+
+

src/tp3.R

@@ -12,13 +12,13 @@ if (!require("BiocManager", quietly = TRUE))
 if (!require("snpStats", quietly = TRUE))
   BiocManager::install("snpStats")
 
-if (!require("doParallel", quietly = TRUE))
-  BiocManager::install("doParallel")
+#if (!require("doParallel", quietly = TRUE))
+ # BiocManager::install("doParallel")
 
 library(snpStats)
 library(plyr)
 library(GenABEL)
-library(doParallel)
+#library(doParallel)
 
 rdata_path = file.path(output_dir,"TP3_asbvg.RData")
 save.image(rdata_path)

src/tp4.R

@@ -6,14 +6,14 @@ output_dir = "results/tp4"
 dir.create(output_dir, showWarnings = F, recursive = T)
 
 #Library
-if(!require("dplyr",quietly = T))
-  install.packages("dplyr")
+#if(!require("dplyr",quietly = T))
+ # install.packages("dplyr")
 
-if(!require("plyr",quietly = T))
-  install.packages("plyr")
+#if(!require("plyr",quietly = T))
+  #install.packages("plyr")
 
-if(!require("GenABEL",quietly = T))
-  install.packages("GenABEL")
+#if(!require("GenABEL",quietly = T))
+  #install.packages("GenABEL")
 
 rdata_path = file.path(output_dir,"TP4_asbvg.RData")
 save.image(rdata_path)

workflow/makefile

 all:results/tp4/TP4_asbvg.RData
-	
-results/tp4/TP4_asbvg.RData: results/tp3/TP3_asbvg.RData
 	Rscript src/tp4.R
 
-results/tp3/TP3_asbvg.RData: results/tp2/TP2_asbvg.RData
+results/tp4/TP4_asbvg.RData:results/tp3/TP3_asbvg.RData
 	Rscript src/tp3.R
 
-results/tp2/TP2_asbvg.RData: results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData
+results/tp3/TP3_asbvg.RData:results/tp2/TP2_asbvg.RData
 	Rscript src/tp2.R
 
-results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData: results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam
+results/tp2/TP2_asbvg.RData:results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData
 	Rscript src/tp1.R
 
-results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam:
+results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData:results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam
 	Rscript src/download_data.R
 
-clean:
-	rm -rf results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam results/data/penncath.csv results/penncath.tar.gz results/data
-