| Previous changeset 10:0e5b44c358d1 (2019-07-08) Next changeset 12:6db3135cf337 (2019-08-21) |
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Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d |
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modified:
macros.xml organism_delete_all_organisms.xml |
| b |
| diff -r 0e5b44c358d1 -r 497a82f6a337 macros.xml --- a/macros.xml Mon Jul 08 05:34:50 2019 -0400 +++ b/macros.xml Thu Jul 11 08:35:34 2019 -0400 |
| [ |
| @@ -89,32 +89,29 @@ </conditional> </xml> - <token name="@AUTH@"><![CDATA[ - if [ -z "$CHAKIN_GLOBAL_CONFIG_PATH" ]; then - echo "__default: local" > '.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 - ]]></token> - <token name="@START_PSQL@"><![CDATA[ #if $psql_target.method == 'pgtools' tar -xjvf '$psql_target.infile' > /dev/null && . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema' #else - @AUTH@ + if [ -z "\$CHAKIN_GLOBAL_CONFIG_PATH" ]; then + echo "__default: local" > '.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 #end if ]]></token> <token name="@STOP_PSQL@"><![CDATA[ #if $psql_target.method == 'pgtools' + && pglite stop -d ./postgresql && timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' ; @@ -125,6 +122,7 @@ <token name="@ZIP_PSQL@"><![CDATA[ #if $psql_target.method == 'pgtools' + && pglite stop -d ./postgresql && timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' && tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null |
| b |
| diff -r 0e5b44c358d1 -r 497a82f6a337 organism_delete_all_organisms.xml --- a/organism_delete_all_organisms.xml Mon Jul 08 05:34:50 2019 -0400 +++ b/organism_delete_all_organisms.xml Thu Jul 11 08:35:34 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="organism_delete_all_organisms" name="Chado delete all organisms" version="@WRAPPER_VERSION@.0"> +<tool id="organism_delete_all_organisms" name="Chado delete all organisms" version="@WRAPPER_VERSION@.2"> <description></description> <macros> <import>macros.xml</import> @@ -16,7 +16,7 @@ > '$results' -&& @ZIP_PSQL@ +@ZIP_PSQL@ ]]></command> <inputs> <expand macro="psql_target"/> |