remove conda channel setup

README.md

@@ -63,8 +63,6 @@ cd plague-phylogeography
 conda install -c conda-forge mamba
 mamba env create -f workflow/envs/default.yaml
 conda activate default
-conda config --add channels bioconda
-conda config --add channels conda-forge
 ```
 
 ## Usage
@@ -74,7 +72,7 @@ snakemake \
   --use-conda \
   --conda-frontend mamba \
   --profile profiles/gh-actions \
-  --report workflow/report/report.html  \
+  --log_handler_script workflow/scripts/slack_log.py \
   help
 ```
 

profiles/graham/config.yaml

@@ -1,3 +1,3 @@
 cores : "4"
 default-resources: [cpus=1, mem_mb=2000, time_min=60]
-resources: [cpus=4, mem_mb=8000, load=100]
+resources: [cpus=4, mem_mb=4000, load=100]

workflow/scripts/slack_test.py

@@ -0,0 +1,47 @@
+import os
+from slack import WebClient
+import platform  # Get system name
+from dotenv import load_dotenv  # Reading env files
+from datetime import datetime  # Logging time
+
+# import logging
+# logging.basicConfig(level=logging.DEBUG)
+
+# --------------------------------------------------------------------------#
+# General Setup
+# --------------------------------------------------------------------------#
+load_dotenv()
+token = os.getenv("SLACK_TOKEN")
+
+if not token:
+    print(
+        "Please create an API token for your Slack App and",
+        "export SLACK_TOKEN='yourtoken' to a .env file.",
+    )
+    exit(-1)
+
+client = WebClient(token=token)
+node_name = platform.node()
+now = datetime.now()
+current_time = now.strftime("%H:%M")
+
+
+if __name__ == "__main__":
+    client.chat_postMessage(
+        channel="snakemake",
+        blocks=[
+            {"type": "divider"},
+            {
+                "type": "section",
+                "text": {
+                    "type": "mrkdwn",
+                    "text": ":exclamation: *"
+                    + node_name
+                    + "* is testing slack integration at "
+                    + "*"
+                    + current_time
+                    + "*.",
+                },
+            },
+        ],
+    )