Scripts to query postgres pod and run workflows.

.gitignore

@@ -0,0 +1,2 @@
+.idea/
+.venv/

scripts/config/example.yml

@@ -0,0 +1,32 @@
+# DO NOT RUN
+# This is a non-working example used for discussion purposes only.
+- workflow_id: b94314cb9cb46380
+  comments: DNA testing
+  output_history_base_name: DNA Testing 10 CPU
+  reference_data:
+    - name: FASTQ Reference
+      dataset_id: badfood
+    - name: GTF
+      dataset_id: more
+  runs:
+    - history_name: run one
+      inputs:
+      - name: input one
+        dataset_id: 1f04e612d8649780
+      - name: input two
+        dataset_id: 1f04e612d8649780
+    - history_name: run two
+      inputs:
+      - name: FASTQ Dataset
+        dataset_id: 1f04e612d8649780
+      - name: GTF index
+        dataset_id: 1f04e612d8649780
+- workflow_id: b94314cb9cb46380
+  comments: RNA testing
+  output_history_base_name: RNA Testing 10 CPU
+  runs:
+    - hostory_name: FASTQ Dataset
+      inputs:
+      - name: FASTQ Dataset
+        dataset_ids: 1f04e612d8649780
+

scripts/config/rna-seq.yml

@@ -0,0 +1,29 @@
+- workflow_id: 8557135ce1bff84d
+  output_history_base_name: PairRNA 16C 58G-MEM
+  reference_data:
+    - name: Reference Transcript (FASTA)
+      dataset_id: d61e7f405474c541
+  runs:
+    - history_name: SRS9276533
+      inputs:
+      - name: FASTQ RNA Dataset
+        dataset_id: 28fa757e56346a34
+    - history_name: SRS9276520
+      inputs:
+      - name: FASTQ RNA Dataset
+        dataset_id: 1faa2d3b2ed5c436
+    - history_name: SRS9276534
+      inputs:
+      - name: FASTQ RNA Dataset
+        dataset_id: ec8c5112d867eb82
+- workflow_id: 69906830c7478863
+  output_history_base_name: RNA 16C 58G-MEM
+  reference_data:
+    - name: Reference Transcript (FASTA)
+      dataset_id: d61e7f405474c541
+  runs:
+    - history_name: SRS9551191
+      inputs:
+      - name: FASTQ RNA Dataset
+        dataset_id: 0aedafdec1eb4aeb
+

scripts/paired-dna.yml

@@ -0,0 +1,5 @@
+workflow_id: b94314cb9cb46380
+inputs:
+  - name: FASTQ Dataset
+    dataset_id: e49d4a2f705b9571
+output_history_name: Example Paired DNA Test

scripts/query.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+
+if [[ -z $KUBECONFIG && ! -e $HOME/.kube/config ]] ; then
+	echo "The kubectl program does not apprear to be configured correctly."
+	echo "You can download the required kubeconfig file from Rancher and rename"
+	echo "to $HOME/.kube/config."
+	exit 1
+fi
+
+OPTS=
+if [[ $1 = -c || $1 = --csv ]] ; then
+  OPTS='--csv'
+  shift
+fi
+
+if [[ -z $1 ]] ; then
+	echo "No SQL query provided."
+	exit 1
+fi
+
+if [[ ! -e $1 ]] ; then
+	echo "Unable to find $1"
+	exit 1
+fi
+
+# Note the pod name will change anytime the postgres operator is restarted.
+# POD=$(kubectl get pods -n initial | grep postgres | cut -d\  -f1)
+
+# But this will be faster if we know the pod hasn't been restarted
+POD=galaxy-galaxy-1626291120-galaxy-postgres-0
+kubectl exec -in initial $POD -- sudo -u postgres psql -d galaxy $OPTS < $1