Mercurial > repos > gga > chado_feature_load_fasta
changeset 13:313a27d7d64a draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
| author | gga |
|---|---|
| date | Thu, 11 Jul 2019 08:33:47 -0400 |
| parents | 5a1a37db2784 |
| children | 86589f36dfad |
| files | feature_load_fasta.xml macros.xml |
| diffstat | 2 files changed, 16 insertions(+), 18 deletions(-) [+] |
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--- a/feature_load_fasta.xml Mon Jul 08 05:30:24 2019 -0400 +++ b/feature_load_fasta.xml Thu Jul 11 08:33:47 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="feature_load_fasta" name="Chado load fasta" version="@WRAPPER_VERSION@.0"> +<tool id="feature_load_fasta" name="Chado load fasta" version="@WRAPPER_VERSION@.1"> <description></description> <macros> <import>macros.xml</import> @@ -45,7 +45,7 @@ | jq -S . > '$results' -&& @ZIP_PSQL@ +@ZIP_PSQL@ ]]></command> <inputs> <expand macro="psql_target"/>
--- a/macros.xml Mon Jul 08 05:30:24 2019 -0400 +++ b/macros.xml Thu Jul 11 08:33:47 2019 -0400 @@ -89,32 +89,29 @@ </conditional> </xml> - <token name="@AUTH@"><![CDATA[ - if [ -z "$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