Revert required version

[dnil]

This PR adds | fixes:

• Currently pip updates on hasta etc fail.

[daniel.nilsson@hasta:~/sandbox/liquidprompt] [S_loqusdb] stable 45s ± us
[daniel.nilsson@hasta:~/sandbox/liquidprompt] [S_main] stable 6s ± cg deploy loqusdb
/home/proj/bin/conda/envs/S_main/lib/python3.7/site-packages/sqlalchemy/orm/relationships.py:2231: SAWarning: Cascade settings "delete, merge, save-update" should not be combined with a viewonly=True relationship.  This configuration will raise an error in version 1.4. Note that in versions prior to 1.4, these cascade settings may still produce a mutating effect even though this relationship is marked as viewonly=True.
 "viewonly=True." % (", ".join(sorted(non_viewonly)))
Running CG DEPLOY
Set dry run to False
Deploying LoqusDB with CG
Deploying the loqusdb software
Running command /home/proj/bin/conda/envs/S_shipping/bin/shipping --host-config /home/proj/stage/servers/config/hasta.scilifelab.se/host_config_stage.yaml --tool-name loqusdb deploy
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.cli.base[6191] INFO Hello shipper daniel.nilsson
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.cli.base[6191] INFO Sailing on [hasta.scilifelab.se](http://hasta.scilifelab.se/)
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.cli.deploy[6191] INFO Running shipping deploy
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] INFO Locating base to /home/proj/bin/conda
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.commands[6191] DEBUG Initialising Process with binary: /home/proj/bin/conda/envs/S_loqusdb/bin/python
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.commands[6191] DEBUG Use base call ['/home/proj/bin/conda/envs/S_loqusdb/bin/python']
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.package[6191] INFO Fetch current version for package loqusdb
2022-05-25 10:54:49 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.commands[6191] INFO Running command /home/proj/bin/conda/envs/S_loqusdb/bin/python -m pip show loqusdb
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.cli.deploy[6191] INFO daniel.nilsson wants to deploy loqusdb on host [hasta.scilifelab.se](http://hasta.scilifelab.se/) in environment S_loqusdb
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.deploy.conda[6191] INFO Check if conda is available on your system
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] INFO Locating base to /home/proj/bin/conda
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Conda is available: /home/proj/bin/conda
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.deploy.conda[6191] INFO You are in conda environment S_main
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] INFO Locating base to /home/proj/bin/conda
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.deploy.conda[6191] INFO You want to install in conda environment /home/proj/bin/conda/envs/S_loqusdb
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Check if conda environment S_loqusdb exists
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] INFO Locating base to /home/proj/bin/conda
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Conda env: S_loqusdb exists: True
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.environment[6191] INFO Locating base to /home/proj/bin/conda
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.commands[6191] DEBUG Initialising Process with binary: /home/proj/bin/conda/envs/S_loqusdb/bin/python
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.commands[6191] DEBUG Use base call ['/home/proj/bin/conda/envs/S_loqusdb/bin/python']
2022-05-25 10:55:24 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.commands[6191] INFO Running command /home/proj/bin/conda/envs/S_loqusdb/bin/python -m pip install -U loqusdb
2022-05-25 10:55:53 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.cli.deploy[6191] INFO Tool was successfully deployed
2022-05-25 10:55:53 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.package[6191] INFO Fetch current version for package loqusdb
2022-05-25 10:55:53 [hasta.scilifelab.se](http://hasta.scilifelab.se/) shipping.commands[6191] INFO Running command /home/proj/bin/conda/envs/S_loqusdb/bin/python -m pip show loqusdb
θ61° [daniel.nilsson@hasta:~/sandbox/liquidprompt] [S_main] stable 3m38s ± loqusdb --version
loqusdb, version 2.5.2

It seems likely pip doesn't find a version compatible with the local python 3.7.

How to prepare for test:

• ssh to ...
• Install on stage:
  bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]

How to test:

Expected outcome:

• [ ]

Review:

• Code approved by
• Tests executed by
• "Merge and deploy" approved by

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[dnil]

Indeed!
🆗 Deploy to stage

[daniel.nilsson@hasta:~/sandbox/liquidprompt] [S_main] stable ± cg deploy loqusdb
/home/proj/bin/conda/envs/S_main/lib/python3.7/site-packages/sqlalchemy/orm/relationships.py:2231: SAWarning: Cascade settings "delete, merge, save-update" should not be combined with a viewonly=True relationship.   This configuration will raise an error in version 1.4.  Note that in versions prior to 1.4, these cascade settings may still produce a mutating effect even though this relationship is marked as viewonly=True.
  "viewonly=True." % (", ".join(sorted(non_viewonly)))
Running CG DEPLOY
Set dry run to False
Deploying LoqusDB with CG
Deploying the loqusdb software
Running command /home/proj/bin/conda/envs/S_shipping/bin/shipping --host-config /home/proj/stage/servers/config/hasta.scilifelab.se/host_config_stage.yaml --tool-name loqusdb deploy
2022-05-25 12:15:32 hasta.scilifelab.se shipping.cli.base[87249] INFO Hello shipper daniel.nilsson
2022-05-25 12:15:32 hasta.scilifelab.se shipping.cli.base[87249] INFO Sailing on hasta.scilifelab.se
2022-05-25 12:15:32 hasta.scilifelab.se shipping.cli.deploy[87249] INFO Running shipping deploy
2022-05-25 12:15:32 hasta.scilifelab.se shipping.environment[87249] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 12:15:32 hasta.scilifelab.se shipping.environment[87249] INFO Locating base to /home/proj/bin/conda
2022-05-25 12:15:32 hasta.scilifelab.se shipping.commands[87249] DEBUG Initialising Process with binary: /home/proj/bin/conda/envs/S_loqusdb/bin/python
2022-05-25 12:15:32 hasta.scilifelab.se shipping.commands[87249] DEBUG Use base call ['/home/proj/bin/conda/envs/S_loqusdb/bin/python']
2022-05-25 12:15:32 hasta.scilifelab.se shipping.package[87249] INFO Fetch current version for package loqusdb
2022-05-25 12:15:32 hasta.scilifelab.se shipping.commands[87249] INFO Running command /home/proj/bin/conda/envs/S_loqusdb/bin/python -m pip show loqusdb
2022-05-25 12:16:11 hasta.scilifelab.se shipping.cli.deploy[87249] INFO daniel.nilsson wants to deploy loqusdb on host hasta.scilifelab.se in environment S_loqusdb
2022-05-25 12:16:11 hasta.scilifelab.se shipping.deploy.conda[87249] INFO Check if conda is available on your system
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] INFO Locating base to /home/proj/bin/conda
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] DEBUG Conda is available: /home/proj/bin/conda
2022-05-25 12:16:11 hasta.scilifelab.se shipping.deploy.conda[87249] INFO You are in conda environment S_main
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] INFO Locating base to /home/proj/bin/conda
2022-05-25 12:16:11 hasta.scilifelab.se shipping.deploy.conda[87249] INFO You want to install in conda environment /home/proj/bin/conda/envs/S_loqusdb
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] DEBUG Check if conda environment S_loqusdb exists
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] INFO Locating base to /home/proj/bin/conda
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] DEBUG Conda env: S_loqusdb exists: True
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] DEBUG Found conda env path: /home/proj/bin/conda/envs/S_shipping
2022-05-25 12:16:11 hasta.scilifelab.se shipping.environment[87249] INFO Locating base to /home/proj/bin/conda
2022-05-25 12:16:11 hasta.scilifelab.se shipping.commands[87249] DEBUG Initialising Process with binary: /home/proj/bin/conda/envs/S_loqusdb/bin/python
2022-05-25 12:16:11 hasta.scilifelab.se shipping.commands[87249] DEBUG Use base call ['/home/proj/bin/conda/envs/S_loqusdb/bin/python']
2022-05-25 12:16:11 hasta.scilifelab.se shipping.commands[87249] INFO Running command /home/proj/bin/conda/envs/S_loqusdb/bin/python -m pip install -U loqusdb
2022-05-25 12:23:48 hasta.scilifelab.se shipping.cli.deploy[87249] INFO Tool was successfully deployed
2022-05-25 12:23:48 hasta.scilifelab.se shipping.package[87249] INFO Fetch current version for package loqusdb
2022-05-25 12:23:48 hasta.scilifelab.se shipping.commands[87249] INFO Running command /home/proj/bin/conda/envs/S_loqusdb/bin/python -m pip show loqusdb
[daniel.nilsson@hasta:~/sandbox/liquidprompt] [S_main] stable 12m0s ± loqusdb --version
loqusdb, version 2.6.8

[dnil]

🆗 Quick test on stage, since this was likely not done since 2.5.2:

[daniel.nilsson@hasta:~/tmp] [S_main] $ loqusdb export -o loqusdb_stage_dump.sv.vcf -t sv -f
θ66° [daniel.nilsson@hasta:~/tmp] [S_main] 1m19s $ grep BND loqusdb_stage_dump.sv.vcf |wc -l 
15781
θ66° [daniel.nilsson@hasta:~/tmp] [S_main] $ wc -l loqusdb_stage_dump.sv.vcf 
74456 loqusdb_stage_dump.sv.vcf

No new ˆL00 contigs in prod since the script for reverting them (2.6.6), so no need to rerun.

🆗 Deploy to prod

θ70° [daniel.nilsson@hasta:~/tmp] [P_main] 130 $ cg deploy loqusdb
Running CG DEPLOY
Set dry run to False
Deploying LoqusDB with CG
Deploying the loqusdb software
Running command /home/proj/bin/conda/envs/P_shipping/bin/shipping --host-config /home/proj/production/servers/config/hasta.scilifelab.se/host_config_prod.yaml --tool-name loqusdb deploy
2022-05-25 13:58:17 hasta.scilifelab.se shipping.cli.base[193179] INFO Hello shipper daniel.nilsson
2022-05-25 13:58:17 hasta.scilifelab.se shipping.cli.base[193179] INFO Sailing on hasta.scilifelab.se
2022-05-25 13:58:17 hasta.scilifelab.se shipping.cli.deploy[193179] INFO Running shipping deploy
2022-05-25 13:58:17 hasta.scilifelab.se shipping.environment[193179] DEBUG Found conda env path: /home/proj/bin/conda/envs/P_shipping
2022-05-25 13:58:17 hasta.scilifelab.se shipping.environment[193179] INFO Locating base to /home/proj/bin/conda
2022-05-25 13:58:17 hasta.scilifelab.se shipping.commands[193179] DEBUG Initialising Process with binary: /home/proj/bin/conda/envs/P_loqusdb/bin/python
2022-05-25 13:58:17 hasta.scilifelab.se shipping.commands[193179] DEBUG Use base call ['/home/proj/bin/conda/envs/P_loqusdb/bin/python']
2022-05-25 13:58:17 hasta.scilifelab.se shipping.package[193179] INFO Fetch current version for package loqusdb
2022-05-25 13:58:17 hasta.scilifelab.se shipping.commands[193179] INFO Running command /home/proj/bin/conda/envs/P_loqusdb/bin/python -m pip show loqusdb
2022-05-25 13:58:53 hasta.scilifelab.se shipping.cli.deploy[193179] INFO daniel.nilsson wants to deploy loqusdb on host hasta.scilifelab.se in environment P_loqusdb
2022-05-25 13:58:53 hasta.scilifelab.se shipping.deploy.conda[193179] INFO Check if conda is available on your system
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] DEBUG Found conda env path: /home/proj/bin/conda/envs/P_shipping
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] INFO Locating base to /home/proj/bin/conda
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] DEBUG Conda is available: /home/proj/bin/conda
2022-05-25 13:58:53 hasta.scilifelab.se shipping.deploy.conda[193179] INFO You are in conda environment P_main
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] DEBUG Found conda env path: /home/proj/bin/conda/envs/P_shipping
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] INFO Locating base to /home/proj/bin/conda
2022-05-25 13:58:53 hasta.scilifelab.se shipping.deploy.conda[193179] INFO You want to install in conda environment /home/proj/bin/conda/envs/P_loqusdb
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] DEBUG Check if conda environment P_loqusdb exists
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] DEBUG Found conda env path: /home/proj/bin/conda/envs/P_shipping
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] INFO Locating base to /home/proj/bin/conda
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] DEBUG Conda env: P_loqusdb exists: True
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] DEBUG Found conda env path: /home/proj/bin/conda/envs/P_shipping
2022-05-25 13:58:53 hasta.scilifelab.se shipping.environment[193179] INFO Locating base to /home/proj/bin/conda
2022-05-25 13:58:53 hasta.scilifelab.se shipping.commands[193179] DEBUG Initialising Process with binary: /home/proj/bin/conda/envs/P_loqusdb/bin/python
2022-05-25 13:58:53 hasta.scilifelab.se shipping.commands[193179] DEBUG Use base call ['/home/proj/bin/conda/envs/P_loqusdb/bin/python']
2022-05-25 13:58:53 hasta.scilifelab.se shipping.commands[193179] INFO Running command /home/proj/bin/conda/envs/P_loqusdb/bin/python -m pip install -U loqusdb
2022-05-25 14:03:06 hasta.scilifelab.se shipping.cli.deploy[193179] INFO Tool was successfully deployed
2022-05-25 14:03:06 hasta.scilifelab.se shipping.package[193179] INFO Fetch current version for package loqusdb
2022-05-25 14:03:06 hasta.scilifelab.se shipping.commands[193179] INFO Running command /home/proj/bin/conda/envs/P_loqusdb/bin/python -m pip show loqusdb
[daniel.nilsson@hasta:~/tmp] [P_main] 9m3s $ loqusdb --version
loqusdb, version 2.6.8