annotate prepare_psql.sh @ 7:10629751e10b draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit fa25d58f87bfe8b12dc9a497c08855ee5d8ff641"
author gga
date Thu, 24 Jun 2021 09:09:32 +0000
parents 1daff3b60f39
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
1 #!/bin/bash
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
2
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
3 export PWD=`pwd` &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
4 sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '$PWD/postgresql/'|" ./postgresql/db/postgresql.conf &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
5
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
6 pglite start -d ./postgresql &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
7
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
8 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
9 pglite status -d ./postgresql &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
10 timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
11 pglite status -d ./postgresql &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
12
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
13 echo "__default: local" > '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
14 echo "local:" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
15 echo " dbhost: \"xxx\"" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
16 echo " dbname: \"xxx\"" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
17 echo " dbpass: \"xxx\"" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
18 echo " dbuser: \"xxx\"" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
19 echo " dbschema: \"$1\"" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
20 echo " dbport: \"xxx\"" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
21 echo " dburl: \"$(pglite url -d ./postgresql)\"" >> '.auth.yml' &&
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
22
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
23 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'