diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/add_missing_columns.sh | 24 | ||||
| -rwxr-xr-x | scripts/run_debug.sh | 20 |
2 files changed, 44 insertions, 0 deletions
diff --git a/scripts/add_missing_columns.sh b/scripts/add_missing_columns.sh new file mode 100644 index 00000000..70d5fdeb --- /dev/null +++ b/scripts/add_missing_columns.sh @@ -0,0 +1,24 @@ + #! /bin/bash + # + # Add missing columns to test db downloaded from: + # https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip + + QUERY=" + ALTER TABLE InbredSet + ADD Family varchar(20) AFTER FullName, + ADD FamilyOrder varchar(20) AFTER Family, + ADD MenuOrderId smallint(6) AFTER FamilyOrder, + ADD InbredSetCode varchar(5) AFTER MenuOrderId; + + ALTER TABLE PublishXRef + ADD mean double AFTER DataId; + + -- This takes some time + ALTER TABLE ProbeSet + ADD UniProtID varchar(20) AFTER ProteinName; + " + + USER=gn2 + DBNAME=db_webqtl_s + PASS=mysql_password + mysql -u"$USER" -p"$PASS" -h localhost -D "$DBNAME" -e "$QUERY" diff --git a/scripts/run_debug.sh b/scripts/run_debug.sh new file mode 100755 index 00000000..be7ecdb8 --- /dev/null +++ b/scripts/run_debug.sh @@ -0,0 +1,20 @@ +#! /bin/bash +# +# PLEASE DO NOT CHANGE THIS FILE - copy it elsewhere to run +# +# Run with GN2_PROFILE and SERVER_PORT overrides, e.g. +# +# env GN2_PROFILE=/usr/local/guix-profiles/gn-latest SERVER_PORT=5010 scripts/run_debug.sh + +[ -z $GN2_PROFILE ] && export GN2_PROFILE=/usr/local/guix-profiles/gn-latest +[ -z $SERVER_PORT ] && export SERVER_PORT=5010 + +echo Running on port $SERVER_PORT from $GN2_PROFILE + +cwd=`pwd` +echo Running source from $cwd + +mkdir -p ~/tmp + +env TMPDIR=~/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG GENENETWORK_FILES=/export/data/genenetwork/genotype_files/ SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev + |