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Resolve conflicts with biocommons #46

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merged 6 commits into from
Aug 26, 2024
Merged

Resolve conflicts with biocommons #46

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6a6a4eb
docs: update readme instructions for installing db dumps
korikuzma Jan 19, 2024
9a2ea1b
Merge branch 'main' into docs-install-db-dump
korikuzma Jan 22, 2024
ac8e34e
Merge pull request #250 from biocommons/docs-install-db-dump
reece Mar 2, 2024
feedaa6
Fix uta container search path (#256)
b0d0nne11 Mar 26, 2024
53243ea
Update README.md
reece Jul 8, 2024
6d5e252
Merge remote-tracking branch 'upstream/main' into biocommons-sync-2
bsgiles73 Aug 26, 2024
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6 changes: 4 additions & 2 deletions README.md
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Expand Up @@ -10,7 +10,7 @@ aligning the same transcript to multiple references using multiple
alignment methods. Specifically, it facilitates the following:

- Querying for multiple transcript sources through a single interface
- Interpretating variants reported in literature against obsolete
- Interpreting variants reported in literature against obsolete
transcript records
- Identifying regions where transcript and reference genome sequence
assemblies disagree
Expand Down Expand Up @@ -243,11 +243,13 @@ the installation environment.*
uta_admin are likely to ease installation.

$ createuser -U postgres uta_admin
$ createuser -U postgres anonymous
$ createdb -U postgres -O uta_admin uta

3. Restore the database.

$ gzip -cdq uta_20150827.pgd.gz | psql -U uta_admin -1 -v ON_ERROR_STOP=1 -d uta -Eae
$ uta_v=uta_20210129b
$ gzip -cdq $uta_v.pgd.gz | psql -U uta_admin -1 -v ON_ERROR_STOP=1 -d uta -Eae

## Developer Setup

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2 changes: 1 addition & 1 deletion misc/docker/load-uta.sh
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Expand Up @@ -50,7 +50,7 @@ gzip -cdq < "${UTA_PGD_FN}" \

gzip -cdq < "${UTA_PGD_FN}" \
| perl -n \
-e 'm/CREATE SCHEMA (uta_\d+)/ && print("ALTER DATABASE :DBNAME SET search_path=$1;\n");' \
-e 'm/CREATE SCHEMA (uta_[\d\w]+)/ && print("ALTER DATABASE :DBNAME SET search_path=$1;\n");' \
-e 'print if s/CREATE MATERIALIZED VIEW (.\S+) AS/REFRESH MATERIALIZED VIEW $1;/' \
| psql -1e -U uta_admin -d uta -v ON_ERROR_STOP=1

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