From a51dec5c0158a2275ca9c1aca0715666b4cd2aac Mon Sep 17 00:00:00 2001
From: Aris Paschalidis <aris.paschalidis@gmail.com>
Date: Mon, 9 May 2022 12:52:21 -0400
Subject: [PATCH] Combine the two `nohup.out` files and force the mv command

* Combine the nohup files to simplify the logs

* Force the mv command so that the app can still run even if there is a previous run. The app will overwrite the needed files.
---
 docs/guides/analysis-pipeline.rst |  8 ++++----
 src/generate_wrangler_scripts.py  | 16 ++++++----------
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/docs/guides/analysis-pipeline.rst b/docs/guides/analysis-pipeline.rst
index b02fbd7..667e75f 100644
--- a/docs/guides/analysis-pipeline.rst
+++ b/docs/guides/analysis-pipeline.rst
@@ -77,10 +77,10 @@ Next, we can run the :ref:`wrangler app <wrangler-app>`:
     -s ${sample_sets_used} -c ${cpu_number} -m ${min_capture_length}
 
 The :ref:`wrangler app <wrangler-app>` will save the main outputs as compressed
-files in the :code:`wrangler` directory. There will additionally be two
-:code:`nohup` files that contain errors and warning messages logged by the
-:ref:`wrangler app <wrangler-app>`. These files should be empty if the all went
-well. In our example run, both :code:`nohup` files were empty and the main
+files in the :code:`wrangler` directory. There will additionally be a
+:code:`nohup` file that contains errors and warning messages logged by the
+:ref:`wrangler app <wrangler-app>`. This file should be empty if the all went
+well. In our example run, the :code:`nohup` file was empty and the main
 outputs were aggregated into the three files:
 
 * :code:`run_test_run_wrangled_20220314.txt.gz`
diff --git a/src/generate_wrangler_scripts.py b/src/generate_wrangler_scripts.py
index 0bc367b..5bacaea 100644
--- a/src/generate_wrangler_scripts.py
+++ b/src/generate_wrangler_scripts.py
@@ -326,17 +326,13 @@
         str(server_num),
         str(cpu_count),
         str(args["population_fraction_cutoff"]),
+        ">>",
+        os.path.join(analysis_dir, "nohup.out"),
     ],
-    ["mv", os.path.join(analysis_dir, "analysis/logs"), analysis_dir],
-    ["mv", os.path.join(analysis_dir, "analysis/scripts"), analysis_dir],
-    ["mv", os.path.join(analysis_dir, "analysis/resources"), analysis_dir],
-    [
-        "mv",
-        os.path.join(analysis_dir, "analysis/nohup.out"),
-        os.path.join(analysis_dir, "nohup2.out"),
-        "2>/dev/null ||true",
-    ],
-    ["mv", info_file, renamed_info],
+    ["mv -f", os.path.join(analysis_dir, "analysis/logs"), analysis_dir],
+    ["mv -f", os.path.join(analysis_dir, "analysis/scripts"), analysis_dir],
+    ["mv -f", os.path.join(analysis_dir, "analysis/resources"), analysis_dir],
+    ["mv -f", info_file, renamed_info],
     ["pigz", "-9", "-p", str(cpu_count), renamed_info],
 ]
 extraction_summary_file = "extractInfoSummary.txt"