From 3f03c5d303fbdd9e05aa13a4d93bce08cade32b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Wed, 16 Mar 2022 13:14:05 +0100
Subject: [PATCH] fix: do not skip local conda env creation per se when having
 no shared FS, because it is still needed for local jobs. Instead, decide for
 each env whether it is needed locally or not. (#1490)

* fix: do not skip local conda env creation per se when having no shared FS, because it is still needed for local jobs. Instead, decide for each env whether it is needed locally or not.

* extend test case to cover this issue
---
 snakemake/workflow.py        |  9 +++----
 tests/test_tibanna/Snakefile | 49 +++++++++++++++++++++++-------------
 2 files changed, 36 insertions(+), 22 deletions(-)

diff --git a/snakemake/workflow.py b/snakemake/workflow.py
index c78df2c3c..d15dec62a 100644
--- a/snakemake/workflow.py
+++ b/snakemake/workflow.py
@@ -968,11 +968,10 @@ def files(items):
                 dryrun=dryrun or list_conda_envs, quiet=list_conda_envs
             )
         if self.use_conda:
-            if self.assume_shared_fs:
-                dag.create_conda_envs(
-                    dryrun=dryrun or list_conda_envs or conda_cleanup_envs,
-                    quiet=list_conda_envs,
-                )
+            dag.create_conda_envs(
+                dryrun=dryrun or list_conda_envs or conda_cleanup_envs,
+                quiet=list_conda_envs,
+            )
             if conda_create_envs_only:
                 return True
 
diff --git a/tests/test_tibanna/Snakefile b/tests/test_tibanna/Snakefile
index 8717edc58..61faeb810 100644
--- a/tests/test_tibanna/Snakefile
+++ b/tests/test_tibanna/Snakefile
@@ -9,73 +9,88 @@
 # Output of step2 is set remote.
 
 from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
+
 S3 = S3RemoteProvider()
 
-#envvars:
+# envvars:
 #    "TEST_ENVVAR1",
 #    "TEST_ENVVAR2"
 
+
+localrules:
+    all,
+
+
 rule all:
+    conda:
+        "env.yml"
     input:
-        final = S3.remote("snakemake-tibanna-test/1/final_message"),
+        final=S3.remote("snakemake-tibanna-test/1/final_message"),
         # final = "snakemake-tibanna-test/1/final_message"
-        final2 = S3.remote("snakemake-tibanna-test2/1/final_message")
+        final2=S3.remote("snakemake-tibanna-test2/1/final_message"),
+    shell:
+        "echo test"
 
 
 rule step1:
     conda:
         "env.yml"
-    group: "mygroup"
+    group:
+        "mygroup"
     input:
-        S3.remote("snakemake-tibanna-test/1/somefile")
+        S3.remote("snakemake-tibanna-test/1/somefile"),
     output:
-        message = "message1"
+        message="message1",
     shell:
         """
         echo {config[message]} > message1
         cat snakemake-tibanna-test/1/somefile >> message1
         """
 
+
 rule step1a:
     conda:
         "env.yml"
-    group: "mygroup"
+    group:
+        "mygroup"
     input:
-        message = "message1"
+        message="message1",
     output:
-        next_message = "next_message"
+        next_message="next_message",
     shell:
         """
         cat message1 message1 > next_message
         """
 
+
 rule step1b:
     conda:
         "env.yml"
     input:
-        S3.remote("snakemake-tibanna-test/1/somefile2")
+        S3.remote("snakemake-tibanna-test/1/somefile2"),
     output:
-        message = "message2"
+        message="message2",
     log:
-        "log.txt"
+        "log.txt",
     benchmark:
         "benchmark.txt"
     threads: 1
     resources:
-        mem_mb=1024
+        mem_mb=1024,
     shell:
         """
         echo "abcdefg" > message2
         cat snakemake-tibanna-test/1/somefile2 >> message2
         """
 
+
 rule step2:
     input:
-        message1 = "next_message",
-        message2 = "message2"
+        message1="next_message",
+        message2="message2",
     output:
-        final = S3.remote("snakemake-tibanna-test/1/final_message"),
+        final=S3.remote("snakemake-tibanna-test/1/final_message"),
         # final = "snakemake-tibanna-test/1/final_message"
-        final2 = S3.remote("snakemake-tibanna-test2/1/final_message")
+        final2=S3.remote("snakemake-tibanna-test2/1/final_message"),
     script:
         "scripts/step2.py"