microSALT v.5.0.0

[karlnyr]

Description

closes #241

This is a major update to microSALT doing the following:

• Swap to jinja rendering
• Remove Flask dependency
• uv as a package manager
• Transfer project into python 3.12
• Refreshment of test module
• Refactored database management

Primary function of PR

• Hot-fix
• Patch
• Minor functionality improvement
• New type of analysis
• Backward-breaking functionality improvement
• This change requires internal documents to be updated
• This change requires another repository to be updated

Testing

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAME
• us
• conda activate S_microSALT
• microSALT analyse --input /path/to/fastq/ SAMPLEINFO_FILE

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

• Approved to run at Clinical-Genomics by @karlnyr or @Clinical-Genomics/micro

[karlnyr]

testing get-bigsdb-credentials:

# PUBMLST
[10:14] [user@server:~/] [S_microSALT_v5]  (rc5.0.0) $ microsalt utils get-bigsdb-credentials pubmlst
Please log in using your user account at https://pubmlst.org/bigsdb?db=pubmlst_test_seqdef&page=authorizeClient&oauth_token=<SECRET> using a web browser to obtain a verification code.
Please enter verification code: <VERIFICATION_CODE>

Access Token: <ACCESS_TOKEN>
Access Token Secret: <ACCESS?TOKEN_SECRET>
Tokens saved to credentials/pubmlst_credentials.env
# Pasteur
[10:17] [user@server:~/] [S_microSALT_v5]  (rc5.0.0) $ microsalt utils get-bigsdb-credentials --species ecoli pasteur
Please log in using your user account at https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_ecoli_seqdef&page=authorizeClient&oauth_token=<SECRET> using a web browser to obtain a verification code.
Please enter verification code: <VERIFICATION_CODE>

Access Token: <ACCESS_TOKEN>
Access Token Secret: <ACCESS_TOKEN_SECRET>
Tokens saved to credentials/pasteur_credentials.env

✅

[karlnyr]

testing ref update:

# running update command
microsalt utils resync update-refs

This generates the lock:

Now, we seem to have an issue with the container for making the blastdb:

/.singularity.d/actions/exec: 9: exec: makeblastdb: not found
/.singularity.d/actions/exec: 9: exec: makeblastdb: not found
/.singularity.d/actions/exec: 9: exec: makeblastdb: not found
/.singularity.d/actions/exec: 9: exec: makeblastdb: not found
/.singularity.d/actions/exec: 9: exec: makeblastdb: not found
/.singularity.d/actions/exec: 9: exec: makeblastdb: not found
/.singularity.d/actions/exec: 9: exec: makeblastdb: not found

But disregarding that the database is filled with the ST profiles, and once that was finished the lock is released:

2026-03-12 10:32:05 - main_logger - INFO - Reference update lock released

Actions

• Check the container used, and if it is the blast container, check the presence of makeblastdb.