Merge pull request #284 from galaxyproject/update_samples

Update samples and cleanup unused
galaxyproject · May 24, 2024 · dca5e0c · dca5e0c
2 parents 2326217 + 0533f8c
commit dca5e0c
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Showing 12 changed files with 27 additions and 140 deletions.
diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@ The `kubectl` program is only required when bootstrapping a new Galaxy instance,
 
 ### Credentials
 
-You will need an [API key](https://training.galaxyproject.org/training-material/faqs/galaxy/preferences_admin_api_key.html) for every Galaxy instance you would like to intereact with. You will also need the *kubeconfig* file for each Kubernetes cluster.  The `abm` script loads the Galaxy server URLs, API keys, and the location of the *kubeconfig* files from a Yaml configuration file that it expects to find in `$HOME/.abm/profile.yml` or `.abm-profile.yml` in the current directory.  You can use the `profile-sample.yml` file as a starting point and it includes the URLs for all Galaxy instances we have used to date (December 22, 2021 as of this writing). 
+You will need an [API key](https://training.galaxyproject.org/training-material/faqs/galaxy/preferences_admin_api_key.html) for every Galaxy instance you would like to intereact with. You will also need the *kubeconfig* file for each Kubernetes cluster.  The `abm` script loads the Galaxy server URLs, API keys, and the location of the *kubeconfig* files from a Yaml configuration file that it expects to find in `$HOME/.abm/profile.yml` or `.abm-profile.yml` in the current directory.  You can use the `samples/profile.yml` file as a starting point and it includes the URLs for all Galaxy instances we have used to date (December 22, 2021 as of this writing). 
 
 :bulb: It is now possible (>=2.0.0) to create Galaxy users and their API keys directly with `abm`.
 

diff --git a/abm/lib/experiment.py b/abm/lib/experiment.py
@@ -45,7 +45,6 @@ def run(context: Context, args: list):
     print(f"Starting with run number {argv.run_number}")
 
     profiles = load_profiles()
-    # latch = CountdownLatch(len(config['cloud']))
     threads = []
     start = perf_counter()
     for cloud in config['cloud']:

diff --git a/abm/lib/history.py b/abm/lib/history.py
@@ -214,7 +214,7 @@ def error_message(msg='Invalid command'):
         else:
             datasets = None
             config = f'{os.path.dirname(os.path.abspath(__file__))}/histories.yml'
-            # First load the histories.yml file that is pacakged with abm
+            # First load the histories.yml file that is packaged with abm
             if os.path.exists(config):
                 with open(config, 'r') as f:
                     datasets = yaml.safe_load(f)

diff --git a/abm/lib/threads/Latch.py b/abm/lib/threads/Latch.py
diff --git a/bootstrap-config/test.yaml b/bootstrap-config/test.yaml
diff --git a/rules/default.yml b/rules/default.yml
diff --git a/benchmarks/dna-named-2.yml → samples/benchmarks/dna-named.yml b/benchmarks/dna-named-2.yml → samples/benchmarks/dna-named.yml
diff --git a/benchmarks/example.yml → samples/benchmarks/example.yml b/benchmarks/example.yml → samples/benchmarks/example.yml
diff --git a/samples/benchmarks/rna-named.yml b/samples/benchmarks/rna-named.yml
@@ -0,0 +1,14 @@
+- workflow_id: d6d3c2119c4849e4
+  output_history_base_name: RNA-seq
+  reference_data:
+    - name: Reference Transcript (FASTA)
+      dataset_id: 50a269b7a99356aa
+  runs:
+    - history_name: 1
+      inputs:
+      - name: FASTQ RNA Dataset
+        dataset_id: 28fa757e56346a34
+    - history_name: 2
+      inputs:
+      - name: FASTQ RNA Dataset
+        dataset_id: 1faa2d3b2ed5c436
diff --git a/samples/benchmarks/rules/4x8.yml b/samples/benchmarks/rules/4x8.yml
diff --git a/samples/benchmarks/rules/8x16.yml b/samples/benchmarks/rules/8x16.yml
diff --git a/samples/experiment.yaml b/samples/experiment.yaml
@@ -0,0 +1,11 @@
+name: Benchmarking DNA
+runs: 3
+workflow_conf:
+  - benchmarks/example.yml
+  - benchmarks/dna-named.yml
+  - benchmarks/rna-named.yml
+cloud:
+  - iu2
+job_configs:
+  - rules/4x8.yml
+  - rules/8x16.yml