From 86fe153eacda7916485dfce1c270ddff6a0421c9 Mon Sep 17 00:00:00 2001 From: Hendrik Schultheis Date: Fri, 26 Jun 2020 14:18:20 +0200 Subject: [PATCH 1/3] Add logging to convert_*_overview rules --- snakefiles/wilson.snake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/snakefiles/wilson.snake b/snakefiles/wilson.snake index f0fbb6e..1dc2ee8 100644 --- a/snakefiles/wilson.snake +++ b/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: From b01a311bc5583573ccdc306aa125b922c5370ca8 Mon Sep 17 00:00:00 2001 From: Hendrik Schultheis Date: Fri, 26 Jun 2020 14:20:05 +0200 Subject: [PATCH 2/3] Updated howto text --- snakefiles/wilson.snake | 1 - 1 file changed, 1 deletion(-) diff --git a/snakefiles/wilson.snake b/snakefiles/wilson.snake index 1dc2ee8..ab60ddf 100644 --- a/snakefiles/wilson.snake +++ b/snakefiles/wilson.snake @@ -90,7 +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) From bf8a3808fd7b956b79a5a50051651676006af54d Mon Sep 17 00:00:00 2001 From: Hendrik Schultheis Date: Fri, 26 Jun 2020 14:56:15 +0200 Subject: [PATCH 3/3] Add missing dependency to avoid error when env is used while also a package is installed --- environments/wilson.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/environments/wilson.yaml b/environments/wilson.yaml index 409376c..60a20ce 100644 --- a/environments/wilson.yaml +++ b/environments/wilson.yaml @@ -28,3 +28,4 @@ dependencies: - r-car - r-rjson - r-circlize==0.4.8 + - r-optparse