Mercurial > repos > gga > chado_organism_delete_organisms

comparison macros.xml @ 11:c09cee3486a4 draft

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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 08:34:35 -0400
parents 87df7adce77e
children 80dc4a25db97
comparison
equal deleted inserted replaced
10:87df7adce77e 11:c09cee3486a4
87 <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/> 87 <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/>
88 </when> 88 </when>
89 </conditional> 89 </conditional>
90 </xml> 90 </xml>
91 91
92 <token name="@AUTH@"><![CDATA[
93 if [ -z "$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
94 echo "__default: local" > '.auth.yml' &&
95 echo "local:" >> '.auth.yml' &&
96 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
97 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
98 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
99 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
100 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
101 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
102
103 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
104 ; fi
105 ]]></token>
106
107 <token name="@START_PSQL@"><![CDATA[ 92 <token name="@START_PSQL@"><![CDATA[
108 #if $psql_target.method == 'pgtools' 93 #if $psql_target.method == 'pgtools'
109 tar -xjvf '$psql_target.infile' > /dev/null && 94 tar -xjvf '$psql_target.infile' > /dev/null &&
110 . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema' 95 . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
111 #else 96 #else
112 @AUTH@ 97 if [ -z "\$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
98 echo "__default: local" > '.auth.yml' &&
99 echo "local:" >> '.auth.yml' &&
100 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
101 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
102 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
103 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
104 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
105 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
106
107 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
108 ; fi
113 #end if 109 #end if
114 ]]></token> 110 ]]></token>
115 111
116 <token name="@STOP_PSQL@"><![CDATA[ 112 <token name="@STOP_PSQL@"><![CDATA[
117 #if $psql_target.method == 'pgtools' 113 #if $psql_target.method == 'pgtools'
114 &&
118 pglite stop -d ./postgresql && 115 pglite stop -d ./postgresql &&
119 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' 116 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
120 ; 117 ;
121 ## Make sure psql is stopped even if loading script failed 118 ## Make sure psql is stopped even if loading script failed
122 pglite stop -d ./postgresql || true 119 pglite stop -d ./postgresql || true
123 #end if 120 #end if
124 ]]></token> 121 ]]></token>
125 122
126 <token name="@ZIP_PSQL@"><![CDATA[ 123 <token name="@ZIP_PSQL@"><![CDATA[
127 #if $psql_target.method == 'pgtools' 124 #if $psql_target.method == 'pgtools'
125 &&
128 pglite stop -d ./postgresql && 126 pglite stop -d ./postgresql &&
129 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' && 127 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
130 tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null 128 tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null
131 ; 129 ;
132 ## Make sure psql is stopped even if loading script failed 130 ## Make sure psql is stopped even if loading script failed