bbtools v39.91

[RaheelSyedAhmed]

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

PR Details:
Updated BBTOOLSVER to 39.91 in the Dockerfile. The main README.md has version 39.91 of bbtools added to the versions dropdown list. The program specific README.md has been maintained from the prior version, except for the reformatting and copying of the live table of contents on the bbtools website. The release logs indicate only database additions have been made. The program license remains non-standard.

[erinyoung]

@staphb-dockerbuilds-diff bbtools 39.84 39.91

[github-actions]

Dockerfile Diff: bbtools

Comparing: 39.84 -> 39.91

--- build-files/bbtools/39.84/Dockerfile	2026-06-26 18:46:30.658634284 +0000
+++ build-files/bbtools/39.91/Dockerfile	2026-06-26 18:46:30.658727312 +0000
@@ -8,7 +8,7 @@
 FROM ubuntu:noble AS app
 
 ARG SAMBAMBAVER=1.0.1
-ARG BBTOOLSVER=39.84
+ARG BBTOOLSVER=39.91
 
 LABEL base.image="ubuntu:noble"
 LABEL dockerfile.version="1"

[erinyoung]

Tests worked

#22 [test 3/3] RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam &&     streamsam.sh in='SRR13957123.primertrim.sorted.bam' out='test_SRR13957123.primertrim.sorted.fastq.gz' &&     test -f test_SRR13957123.primertrim.sorted.fastq.gz
#22 0.279 java -ea  --add-modules jdk.incubator.vector -Xmx2g -Xms2g -cp /bbmap/bbtools.jar stream.SamStreamerWrapper in=SRR13957123.primertrim.sorted.bam out=test_SRR13957123.primertrim.sorted.fastq.gz
#22 0.335 WARNING: Using incubator modules: jdk.incubator.vector
#22 1.584 Time:                         	1.225 seconds.
#22 1.587 Reads Processed:    153310 	125.13k reads/sec
#22 1.587 Bases Processed:    21265977 	17.36 Mbp/sec
#22 1.587 Reads Out:          153310
#22 1.587 Bases Out:          21265977
#22 DONE 1.6s

[erinyoung]

I have no changes to recommend. Let's get this merged and deployed!

[erinyoung]

Thank you for putting this together! You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/28259265134