EnvGen/BARM_web_server

Name: BARM_web_server

Owner: Environmental Genomics Group SciLifeLab/KTH Stockholm

Description: Baltic sea Reference Metagenome web server

Created: 2015-11-06 09:11:23.0

Updated: 2016-01-11 15:51:37.0

Pushed: 2017-11-22 15:17:49.0

Homepage: null

Size: 7375

Language: Python

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README

BARM_web_server

Baltic sea Reference Metagenome web server

running at https://barm.scilifelab.se

Dev note

I always forget this, to log in to psql on local mac:

sudo -u postgres /Library/PostgreSQL/9.4/bin/psql

The first password it asks for is for the sudo. The second password is postgres psql password.

When creating a new database:

sudo -u postgres /Library/PostgreSQL/9.4/bin/createdb -U $USER --locale=en_US.utf-8 -E utf-8 -O $USER barm_web_dev -T template0

The first password is for sudo, the second is for user $USER (not postgres) for psql.

Drop stage database and recreate it with new data:

Drop the stage database with all the tables:

sudo -u postgres /Library/PostgreSQL/9.4/bin/psql
postgres=# DROP DATABASE barm_web_dev;
postgres=# \q

Recreate the empty stage database:

sudo -u postgres /Library/PostgreSQL/9.4/bin/createdb -U $USER --locale=en_US.utf-8 -E utf-8 -O $USER barm_web_dev -T template0

Recreate all the tables:

source activate BARM_web
source local_variables.sh
python manage.py db upgrade

Populate the tables:

time python populate_db.py --sample_info data/stage/samples.csv --all_annotations data/stage/all_annotations.tsv --annotation_source_info data/stage/annotation_source_info.csv --gene_annotations_cog data/stage/megahit_coassembly.0.COG.tsv --gene_annotations_pfam data/stage/megahit_coassembly.0.PFAM.tsv --gene_annotations_tigrfam data/stage/megahit_coassembly.0.TIGR.tsv --reference_assembly "megahit_coassembly.0" --gene_counts data/stage/rpkm_table.tsv --metadata_reference data/stage/metadata_reference.tsv --tmp_file /Users/johannesalneberg/repos/BARM_web_server/data/stage/tmp_file.csv

Export database to the server:

pg_dump dbname >file.sql

scp file.sql username.login@barm.scilifelab.se:~/

On the actual server

Loading in a new databse:

createdb -U db_user -O db_owner barm_web_prod -T template0
psql -U db_user -d barm_web_prod -f file.sql

Shutdown current process:

pkill -f runserver

Start running the server manually:

bash /home/<user>/starta_barm.sh  >>  /var/log/barm.log  2>&1 &