# HG changeset patch # User gga # Date 1562578578 14400 # Node ID b739fe763fcc2d16eeeb2ef183be00feea4920ca # Parent 4211d5d719ee017e2b8df10293ca28255d11eb8c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea diff -r 4211d5d719ee -r b739fe763fcc export_export_gff3.xml --- a/export_export_gff3.xml Tue Mar 05 05:15:00 2019 -0500 +++ b/export_export_gff3.xml Mon Jul 08 05:36:18 2019 -0400 @@ -7,15 +7,17 @@


      '$results'
 
- > '$results'
+ && @STOP_PSQL@
     ]]>
     
+        
         
         
     
         
-            python-chado
+            python-chado
             jq
+            postgresql
+            pglite
             
         
     
 
+    11.2
+
     
         
             
@@ -16,7 +20,7 @@
         
     
 
-    2.2.5
+    2.2.6
 
     
         
@@ -32,19 +36,6 @@
     
 
-     '.auth.yml' &&
-        echo "local:" >> '.auth.yml' &&
-        echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
-        echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
-        echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
-        echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
-        echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
-        echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
-
-        CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
-    ]]>
-
     
         
             
@@ -83,4 +74,63 @@
                label="Sequence type of the parent"
                help="this should be a Sequence Ontology term" />
     
+
+    
+      
+         
+              
+              
+          
+          
+          
+            
+            
+          
+      
+    
+
+     '.auth.yml' &&
+          echo "local:" >> '.auth.yml' &&
+          echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
+          echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
+          echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
+          echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
+          echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
+          echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
+
+          export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
+        ; fi
+    ]]>
+
+     /dev/null &&
+            . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
+        #else
+            @AUTH@
+        #end if
+    ]]>
+
+    
+
+     /dev/null
+            ;
+            ## Make sure psql is stopped even if loading script failed
+            pglite stop -d ./postgresql || true
+        #end if
+    ]]>
 
diff -r 4211d5d719ee -r b739fe763fcc prepare_psql.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prepare_psql.sh	Mon Jul 08 05:36:18 2019 -0400
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+export PWD=`pwd` &&
+sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '$PWD/postgresql/'|" ./postgresql/db/postgresql.conf &&
+
+pglite start  -d ./postgresql &&
+
+timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' &&
+pglite status -d ./postgresql &&
+timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done' &&
+pglite status -d ./postgresql &&
+
+echo "__default: local" > '.auth.yml' &&
+echo "local:" >> '.auth.yml' &&
+echo "    dbhost: \"xxx\"" >> '.auth.yml' &&
+echo "    dbname: \"xxx\"" >> '.auth.yml' &&
+echo "    dbpass: \"xxx\"" >> '.auth.yml' &&
+echo "    dbuser: \"xxx\"" >> '.auth.yml' &&
+echo "    dbschema: \"$1\"" >> '.auth.yml' &&
+echo "    dbport: \"xxx\"" >> '.auth.yml' &&
+echo "    dburl: \"$(pglite url -d ./postgresql)\"" >> '.auth.yml' &&
+
+export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'