fix amrfinderplus pinning in abritamr

[rpetit3]

abritamr packages a prebuilt database that is locked to a specific ncbi-amrfinderplus version. Added a note to review this every new release, and which file to review

Database directory: '/usr/local/lib/python3.12/site-packages/abritamr/db/amrfinderplus/data/2024-01-31.1'
Database version: 2024-01-31.1

ESC[1;31m*** ERROR ***ESC[0m
Database requires sofware version at least 3.12.1

HOSTNAME: ?
SHELL: ?
PWD: /home/robert_petit/pytest_workflow_a9fmmcy8/abritamr-test/work/43/5c9ff0c6ef49be3520c78e6dcff64c
PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Progam name:  amrfinder
Command line: amrfinder -n GCF_001682305.fna -o results/amrfinder.out --plus --threads 4 -d /usr/local/lib/python3.12/site-packages/abritamr/db/amrfinderplus/data/2024-01-31.1

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semantic versioning	{{ pin_subpackage("myrecipe", max_pin="x") }}
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[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Azure

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	abritamr-1.0.17-pyh5707d69_1.tar.bz2	LinuxArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

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Docker image(s) built (images for Azure are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
abritamr	1.0.17--pyh5707d69_1	show gzip -dc LinuxArtifacts/images/abritamr:1.0.17--pyh5707d69_1.tar.gz | docker load

[rpetit3]

Working now

[INFO:03/24/2024 12:01:15 AM] The input file seems to be in the correct format. Thank you.
[INFO:03/24/2024 12:01:15 AM] Checking if file GCF_001682305.fna exists
[INFO:03/24/2024 12:01:15 AM] GCF_001682305.fna is present. abritamr can proceed.
[INFO:03/24/2024 12:01:15 AM] Checking for amrfinder DB: /usr/local/lib/python3.12/site-packages/abritamr/db/amrfinderplus/data/2024-01-31.1 and comparing it to 2024-01-31.1
[INFO:03/24/2024 12:01:15 AM] You seem to have the correct AMRfinder DB setup. Well done!
[INFO:03/24/2024 12:01:15 AM] All check complete now running AMRFinder
[INFO:03/24/2024 12:01:15 AM] You are running abritamr in assembly mode. Now executing : mkdir -p results && amrfinder -n GCF_001682305.fna -o results/amrfinder.out --plus  --threads 4 -d /usr/local/lib/python3.12/site-packages/abritamr/db/amrfinderplus/data/2024-01-31.1
[INFO:03/24/2024 12:02:46 AM] AMRfinder completed successfully. Will now move on to collation.
[INFO:03/24/2024 12:02:46 AM] This is a single sample run.
[INFO:03/24/2024 12:02:46 AM] Opened amrfinder output for results
[INFO:03/24/2024 12:02:46 AM] Saving files now.
[INFO:03/24/2024 12:02:46 AM] Saving results/summary_matches.txt
[INFO:03/24/2024 12:02:46 AM] Saving results/summary_partials.txt
[INFO:03/24/2024 12:02:46 AM] Saving results/summary_virulence.txt
[INFO:03/24/2024 12:02:46 AM] Saving combined file : results/abritamr.txt

[rpetit3]

Thank you @thanhleviet !