Repository revision
21:a0a0de800749

Repository 'chado_organism_delete_organisms'
hg clone https://toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms

Chado organism delete tool metadata
Miscellaneous
organism_delete_organisms
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.9+galaxy0
2.3.9+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.9+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.8+galaxy0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.7+galaxy0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.6+galaxy0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.5+galaxy0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.4+galaxy0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.3
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.1
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.2.6.0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.2.5.0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.2.3.0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.2.2.0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.1.5.0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.1.4.0
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.1.1.0
organism_delete_organisms
Requirements (dependencies defined in the <requirements> tag set)
name version type
python-chado 2.3.9 package
jq 1.5 package
postgresql 11.2 package
pglite 0.1 package
Additional information about this tool
#if $psql_target.method == 'pgtools'
            tar -xjvf '$psql_target.infile' > /dev/null &&
            . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
        #else
            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
     &&

chakin organism delete_organisms

--organism_id $organism

 > '$results'


        #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
            ;
            ## Make sure psql is stopped even if loading script failed
            pglite stop -d ./postgresql || true
        #end if
    
    
None
False
Functional tests
No functional tests defined