Initial commit

main.py

+from bioblend import galaxy
+import argparse
+
+"""
+
+
+
+"""
+
+parser = argparse.ArgumentParser(description="Input genus, species, strain, version")
+parser.add_argument("--name", help="Sample species name, format: genus-species",type=str, required=True)
+parser.add_argument("--strain", help="Strain of the sample species", type=str, required=True)
+parser.add_argument("--version", help="Data version (e.g 1.0, 1.2, ...)", type=str, required=True)
+parser.add_argument("--common-name", help="Vernacular/common name of the species",type=str, required=False)
+
+user_arguments = parser.parse_args()
+
+genus = user_arguments.name.split('-')[0]
+species = user_arguments.name.split('-')[1]
+strain = user_arguments.strain
+vernacular = user_arguments.common_name
+instance_url = "http://localhost/sp/" + genus + "_" + species + "/galaxy/"
+
+print("Species: " + genus + " " + species + " (Wakame)" +
+      "\nStrain: " + strain +
+      "\nAccessing " + instance_url + "...")
+
+gi = galaxy.GalaxyInstance(url=instance_url,
+                           key="291ec50b48dd1f006985b32e39bc3696",
+                           email="alebars@sb-roscoff.fr",
+                           password="pouet",
+                           verify=True)
+
+# gi = galaxy.GalaxyInstance(url="http://localhost/sp/undaria_pinnatifida/galaxy/",
+#                            # key="291ec50b48dd1f006985b32e39bc3696",
+#                            email="alebars@sb-roscoff.fr",
+#                            password="pouet",
+#                            verify=True)
+
+# gi = galaxy.GalaxyInstance(url="http://localhost/sp/undaria_pinnatifida/galaxy/",
+#                            key="291ec50b48dd1f006985b32e39bc3696",
+#                            email="alebars@sb-roscoff.fr",
+#                            password="pouet",
+#                            verify=True)
+
+# gi = galaxy.GalaxyInstance(url="http://abims-gga.sb-roscoff.fr/sp/ectocarpus_species1/galaxy/",
+#                            key="84dfbee3c0efa9155518f01fbeff57c8",
+#                            email="gga@sb-roscoff.fr",
+#                            password="Mmo,55k")
+
+try:
+    hl = gi.histories.get_histories()
+except ConnectionError:
+    print("Cannot connect to GGA instance @ " + instance_url + "")
+
+
+
+
+