Include avian run script

builds/avian/run_avian.py

@@ -0,0 +1,39 @@
+import os
+
+def build(
+    segments = ['pb2', 'pb1', 'pa', 'ha', 'np', 'na', 'mp', 'ns'],
+    system="local"
+    ):
+    call = ['python',
+        'avian.prepare.py',
+        '--segments', ' '.join(segments)
+        ]
+    print(' '.join(call))
+    os.system(' '.join(call))
+    for segment in segments:
+        call = [
+            'avian.process.py',
+            '--json', 'prepared/avian_h7n9_%s.json'%(segment)]
+        if (system == "qsub"):
+            call = ['qsub', 'submit_script.sh'] + call
+        elif (system == "sbatch"):
+            call = ['python'] + call
+            concat = '"' + ' '.join(call) + '"'
+            call = ['sbatch', '-n', '1', '-c', '2', '--mem', '16192', '--time', '12:00:00', '--wrap', concat]
+        elif (system == "local"):
+            call = ['python'] + call
+        print(' '.join(call))
+        os.system(' '.join(call))
+
+if __name__ == '__main__':
+    import argparse
+
+    parser = argparse.ArgumentParser(description='Run flu builds')
+    parser.add_argument('-s', '--system', type = str, default = 'local', help='where to run, local, qsub or sbatch')
+    parser.add_argument('--segments', nargs='+', type = str,  help ="segments to include")
+    params = parser.parse_args()
+
+    if params.segments is None:
+        params.segments = ['pb2', 'pb1', 'pa', 'ha', 'np', 'na', 'mp', 'ns']
+
+    build(segments = params.segments)