Mercurial > repos > gga > chado_feature_load_gff

annotate prepare_psql.sh @ 21:23f9585a5cd7 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 73142be24a0462a3aeb303401e8fcbc72f1cd4f5"
author gga
date Mon, 14 Mar 2022 14:51:05 +0000
parents 1282f881e3bf
children
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1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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1 #!/bin/bash
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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3 export PWD=`pwd` &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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4 sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '$PWD/postgresql/'|" ./postgresql/db/postgresql.conf &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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5
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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6 pglite start -d ./postgresql &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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7
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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8 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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9 pglite status -d ./postgresql &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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10 timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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11 pglite status -d ./postgresql &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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12
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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13 echo "__default: local" > '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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14 echo "local:" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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15 echo " dbhost: \"xxx\"" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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16 echo " dbname: \"xxx\"" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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17 echo " dbpass: \"xxx\"" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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18 echo " dbuser: \"xxx\"" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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19 echo " dbschema: \"$1\"" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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20 echo " dbport: \"xxx\"" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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21 echo " dburl: \"$(pglite url -d ./postgresql)\"" >> '.auth.yml' &&
1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents:
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1282f881e3bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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23 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'