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Documenting problems and fix with 20210728 data release (#450) #456

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merged 1 commit into from Apr 25, 2022
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Documenting problems and fix with 20210728 data release (#450) #456

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4 changes: 4 additions & 0 deletions HISTORY.rst
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Expand Up @@ -10,11 +10,15 @@ End-User Summary
================

- Starting with development of Bollonaster (VarFish v2)
- Documenting problem with extra annotations in ``20210728` data release (#450).
Includes instructions on how to apply patch to get ``20210728b``.

Full Change List
================

- Starting with development of Bollonaster (VarFish v2)
- Documenting problem with extra annotations in ``20210728` data release (#450).
Includes instructions on how to apply patch to get ``20210728b``.

------
v1.2.0
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22 changes: 21 additions & 1 deletion docs_manual/admin_upgrade.rst
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Expand Up @@ -6,6 +6,26 @@ Upgrade Varfish Installation

This section contains upgrade instructions for upgrading your VarFish Server installation using `VarFish Docker Compose <https://github.com/bihealth/varfish-docker-compose>`__.

-------------------------------------------------
Problem with Data Release ``20210728`` and GRCh37
-------------------------------------------------

The data release has a problem with the GRCh37 extra annotations.
If you can then use the updated site data ``20210728b`` release.
If you already have an instance with ``20210728`` background data then you can use the following data file.

- `varfish-server-background-db-20210728-grch37-patch-20210728b.tar.gz <https://file-public.cubi.bihealth.org/transient/varfish/athenea/varfish-server-background-db-20210728-grch37-patch-20210728b.tar.gz>`__

Download and extract the file and mount it as ``/data`` inside the ``varfish-web`` container.
You can then apply the patch to your database with the following command.

::

$ docker exec -it varfish-docker-compose_varfish-web_1 python /usr/src/app/manage.py \
import_tables --tables-path /data --truncate --force

You can find out more details, give feedback, and ask for help `in this Github discussion <https://github.com/bihealth/varfish-server/discussions/451>`__.

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v0.23.0 to v1.2.0
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Expand All @@ -14,7 +34,7 @@ This includes all version in between, v0.23.1, ..., v1.2.0.

**Summary**

This are minor bug fix releases.
This are minor bug fix releases and small added features.
You should be able to upgrade by just updating your ``varfish-docker-compose`` repository clone and calling ``docker-compose up -d``.

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