Add upload and update web steps to basic_run

jakelever · Aug 9, 2023 · c5c4fc5 · c5c4fc5
1 parent a2e20e3
commit c5c4fc5
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/basic_run.sh b/basic_run.sh
@@ -5,7 +5,7 @@ set -ex
 bash fetch_last_release.sh
 
 # Download the preprepared term lists from Zenodo
-mkdir pipeline/data
+mkdir -p pipeline/data
 zenodo_get -o pipeline/data -d https://doi.org/10.5281/zenodo.8138562
 
 # Unzip the annotations file
@@ -19,3 +19,12 @@ bash run_update.sh
 cd ../pipeline
 snakemake --cores 1
 
+cd ../database
+bash reload_db.sh
+
+cd ..
+aws_login=`cat aws_login.txt`
+ssh -i aws_time.pem $aws_login ". ~/.bash_profile && cd corona-web && sh redeploy.sh"
+
+bigzenodo --submission submission.json --accessTokenFile zenodo_token.txt --publish
+
diff --git a/database/reload_db.sh b/database/reload_db.sh
@@ -1,9 +1,9 @@
 #!/bin/bash
 set -ex
 
-#db=aws.json
+db=aws.json
 #db=remote.json
-db=local.json
+#db=local.json
 
 python createDB.py --db $db