# HG changeset patch # User gga # Date 1562578594 14400 # Node ID ae5af24183a6249da7c20f931ef7e4de04aa7729 # Parent 46b3ccaa24ca92313270ecb4b0247cc059b62032 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea diff -r 46b3ccaa24ca -r ae5af24183a6 feature_load_featureprops.xml --- a/feature_load_featureprops.xml Tue Mar 05 05:15:15 2019 -0500 +++ b/feature_load_featureprops.xml Mon Jul 08 05:36:34 2019 -0400 @@ -7,7 +7,7 @@ '$results' + +&& @ZIP_PSQL@ ]]> + @@ -39,6 +42,9 @@ + + psql_target['method'] == "pgtools" + Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value) diff -r 46b3ccaa24ca -r ae5af24183a6 macros.xml --- a/macros.xml Tue Mar 05 05:15:15 2019 -0500 +++ b/macros.xml Mon Jul 08 05:36:34 2019 -0400 @@ -2,12 +2,16 @@ - python-chado + python-chado jq + postgresql + pglite + 11.2 + @@ -16,7 +20,7 @@ - 2.2.5 + 2.2.6 @@ -32,19 +36,6 @@ - '.auth.yml' && - echo "local:" >> '.auth.yml' && - echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' && - echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' && - echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' && - echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' && - echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' && - echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' && - - CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml' - ]]> - @@ -83,4 +74,63 @@ label="Sequence type of the parent" help="this should be a Sequence Ontology term" /> + + + + + + + + + + + + + + + + '.auth.yml' && + echo "local:" >> '.auth.yml' && + echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' && + echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' && + echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' && + echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' && + echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' && + echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' && + + export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml' + ; fi + ]]> + + /dev/null && + . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema' + #else + @AUTH@ + #end if + ]]> + + + + /dev/null + ; + ## Make sure psql is stopped even if loading script failed + pglite stop -d ./postgresql || true + #end if + ]]> diff -r 46b3ccaa24ca -r ae5af24183a6 prepare_psql.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_psql.sh Mon Jul 08 05:36:34 2019 -0400 @@ -0,0 +1,23 @@ +#!/bin/bash + +export PWD=`pwd` && +sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '$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'