Merge pull request #2 from loosolab/wilson

Wilson

environments/wilson.yaml

@@ -28,3 +28,4 @@ dependencies:
   - r-car
   - r-rjson
   - r-circlize==0.4.8
+  - r-optparse

snakefiles/wilson.snake

@@ -45,8 +45,10 @@ rule convert_individual_overview:
 		"../environments/wilson.yaml"
 	output:
 		os.path.join(OUTPUTDIR, "wilson", "data", "{TF}_overview.clarion")
+	log:
+		os.path.join(OUTPUTDIR, "logs", "wilson", "{TF}_convert_individual_overview.log")
 	shell:
-		"Rscript {params.scripts}/convert_data.R --input {input.overview} --output {output} --condition_names {input.condition_names} &> /dev/null "
+		"Rscript {params.scripts}/convert_data.R --input {input.overview} --output {output} --condition_names {input.condition_names} &> {log} "
 
 #Convert global bindetect-output:
 rule convert_global_overview:
@@ -56,13 +58,15 @@ rule convert_global_overview:
 		app = os.path.join(OUTPUTDIR, "wilson", "app.R")
 	output:
 		os.path.join(OUTPUTDIR, "wilson", "data", "bindetect_results.clarion")
+	log:
+		os.path.join(OUTPUTDIR, "logs", "wilson", "convert_global_overview.log")
 	params: 
 		overview = os.path.join(OUTPUTDIR, "overview", "*_results.txt"),
 		scripts = scripts_dir
 	conda:
 		"../environments/wilson.yaml"
 	shell:
-		"Rscript {params.scripts}/convert_data.R --input {params.overview} --output {output} --condition_names {input.condition_names} &> /dev/null "
+		"Rscript {params.scripts}/convert_data.R --input {params.overview} --output {output} --condition_names {input.condition_names} &> {log} "
 
 rule wilson_howto:
 	input:	
@@ -86,7 +90,6 @@ if (!require(shiny)) install.packages("shiny"); library(shiny)
 Now your browser will open and you can start using the app. If this is not the case try opening the link displayed in your console manually.
 
 Note that unlike normal scripts the app will not terminate on its own so please make sure to close the respective process after you are done.
-Furthermore, Windows users should install Rtools (https://cran.r-project.org/bin/windows/Rtools/) to enable plot downloading.
 """
 
 		f.write(howto)