HTS Bioinf - Deployment of vcpipe for production
Scope
This document describes how to update the software modules part of the variant calling pipeline on TSD and NSC. This assumes that a software package has been created and is available for deployment. The development, testing and documentation are described in HTS Bioinf - Process for updates to production pipelines.
Responsibility
The bioinformatician responsible for pipeline release.
Note that "Endringskontroll for bioinformatiske endringer" should be filled in and approved by a manager prior to deploying any major or minor versions (does not apply to hotfixes).
Platforms
All production paths (starting with production/
) are given relative to the base path for the system in question.
System | Directory | Location |
---|---|---|
TSD | production | /ess/p22/data/durable/production |
NSC | production | /boston/diag/ |
As the system can run on different production platforms, the setup can vary slightly.
On NSC the relevant servers are beta
, diag-executor
and diag-webui
and on TSD the servers are p22-submit
, p22-submit2
or p22-submit-dev
.
1. Copy and archive the deployable package to the production platforms
Transfer the artifact to TSD using the data transfer API. The files will end up in /ess/p22/data/durable/file-import
.
Make a copy of the transferred files into in /ess/p22/data/durable/file-export
(in order to get files to NSC).
For TSD
-
Log in to
p22-submit
(orp22-submit-dev
if using the backup server): -
Copy the package to the
{production}/sw/archive
directory. - For singularity, copy the image to
/ess/p22/cluster/singularity
.
For NSC
- Log in to
sleipnir
. - Use
tacl
to transfer files fromfile-export
on TSD to/boston/diag/transfer
. - On
beta
, copy the files to{production}/sw/archive
. - Singularity images go into/boston/diag/singularity
.
2. Stop production processes
Refer to Execution and monitoring of pipeline section "Finish production" for instructions on how to stop executor
and webui
on TSD and NSC.
3. Extract the package
or, for Python modules:
Verify that the version of the deployed package matches the one intended
Note! The deploy is always run on both NSC/beta
and TSD.
4. Start production processes
Refer to Execution and monitoring of pipeline section "Start production" for instructions on how to start executor
and webui
on TSD and NSC under {serviceuser}.