adding bbtools versions 39.06 (#925)

* adding bbtools versions 39.06

* Adding pigz, pbzip2, lbzip2, bzip2, and bgzip back in

* adding htslib

* adding comment for dependencies

README.md

@@ -118,7 +118,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Auspice](https://hub.docker.com/r/staphb/auspice) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | <ul><li>2.12.0</li></ul> | https://github.com/nextstrain/auspice |
 | [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./bakta/1.9.2/)</li><li>[1.9.2-light](./bakta/1.9.2-5.1-light/)</li><li>[1.9.3](./bakta/1.9.3/)</li></ul> | https://github.com/oschwengers/bakta |
 | [bandage](https://hub.docker.com/r/staphb/bandage) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | <ul><li>[0.8.1](./bandage/0.8.1/)</li></ul> | https://rrwick.github.io/Bandage/ |
-| [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>38.76</li><li>38.86</li><li>38.95</li><li>38.96</li><li>38.97</li><li>38.98</li><li>38.99</li><li>39.00</li><li>39.01</li></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |
+| [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>[38.76](./bbtools/38.76/)</li><li>[38.86](./bbtools/38.86/)</li><li>[38.95](./bbtools/38.95/)</li><li>[38.96](./bbtools/38.96/)</li><li>[38.97](./bbtools/38.97/)</li><li>[38.98](./bbtools/38.98/)</li><li>[38.99](./bbtools/38.99/)</li><li>[39.00](./bbtools/39.00/)</li><li>[39.01](./bbtools/39.01/)</li><li>[39.06](./bbtools/39.06/)</li></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |
 | [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li></ul> | https://github.com/samtools/bcftools |
 | [bedtools](https://hub.docker.com/r/staphb/bedtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | <ul><li>2.29.2</li><li>2.30.0</li><li>[2.31.0](bedtools/2.31.0/)</li><li>[2.31.1](bedtools/2.31.1/)</li></ul> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |
 | [berrywood-report-env](https://hub.docker.com/r/staphb/berrywood-report-env/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | <ul><li>1.0</li></ul> | none |

bbtools/39.06/Dockerfile

@@ -0,0 +1,71 @@
+FROM staphb/samtools:1.19 as samtools
+FROM staphb/htslib:1.19 as htslib
+
+# As a reminder
+# https://github.com/StaPH-B/docker-builds/pull/925#issuecomment-2010553275
+# bbmap/docs/TableOfContents.txt lists additional dependencies
+
+FROM ubuntu:jammy as app
+
+ARG SAMBAMBAVER=1.0.1
+ARG BBTOOLSVER=39.06
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="BBTools"
+LABEL software.version=${BBTOOLSVER}
+LABEL description="A set of tools labeled as \"Bestus Bioinformaticus\""
+LABEL website="https://sourceforge.net/projects/bbmap"
+LABEL documentation="https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
+LABEL license="https://jgi.doe.gov/disclaimer/"
+LABEL maintainer="Abigail Shockey"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Padraic Fanning"
+LABEL maintainer2.email="faninnpm AT miamioh DOT edu"
+
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y \
+    openjdk-8-jre-headless \
+    pigz \
+    pbzip2 \
+    lbzip2 \
+    bzip2 \
+    wget \
+    ca-certificates \
+    procps && \
+    rm -rf /var/lib/apt/lists/* && \
+    apt-get autoclean
+
+# copy samtools to image
+COPY --from=samtools /usr/local/bin/* /usr/local/bin/
+COPY --from=htslib   /usr/local/bin/* /usr/local/bin/
+
+# download and install sambamba
+RUN wget -q https://github.com/biod/sambamba/releases/download/v${SAMBAMBAVER}/sambamba-${SAMBAMBAVER}-linux-amd64-static.gz && \
+    gzip -d sambamba-${SAMBAMBAVER}-linux-amd64-static.gz && \
+    mv sambamba-${SAMBAMBAVER}-linux-amd64-static /usr/local/bin/sambamba && \
+    chmod +x /usr/local/bin/sambamba
+
+# download and install bbtools
+RUN wget -q https://sourceforge.net/projects/bbmap/files/BBMap_${BBTOOLSVER}.tar.gz && \
+    tar -xzf BBMap_${BBTOOLSVER}.tar.gz && \
+    rm BBMap_${BBTOOLSVER}.tar.gz && \
+    mkdir /data
+
+ENV PATH=/bbmap/:$PATH \
+    LC_ALL=C
+
+CMD for tool in $(ls /bbmap/*sh | cut -f 3 -d "/") ; do $tool -h ; done
+
+WORKDIR /data
+
+# testing
+FROM app as test
+
+# testing that '-h' works for all tools
+RUN for tool in $(ls /bbmap/*sh | cut -f 3 -d "/") ; do $tool -h ; done
+
+# get test data and test one thing that uses samtools/sambamba
+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

bbtools/39.06/README.md

@@ -0,0 +1,43 @@
+## BBTools
+
+This image implements Brian Bushnell's [BBTools](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/).
+
+### Includes
+- [BBDuk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/): `bbduk.sh` (or `bbduk2.sh`)
+- [BBMap](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/): `bbmap.sh`
+- [BBMerge](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmerge-guide/): `bbmerge.sh`
+- [Reformat](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/reformat-guide/): `reformat.sh`
+
+In addition to the BBTools, this container also provides the following pieces of software to enhance the BBTools:
+- [Samtools](https://github.com/samtools/samtools) v1.16.1 (although without gnuplot)
+- [Sambamba](https://github.com/biod/sambamba) v0.8.2
+
+To see all of the executables in this image, run the following command inside a container:
+
+```text
+ls /usr/local/bin
+```
+
+Documentation is in the `/opt/bbmap/docs/` directory, and in each tool's shell script in `/opt/bbmap/`.
+
+### Example Usage
+(adapted from `/opt/bbmap/pipelines/covid/processCorona.sh`)
+
+Interleave a pair of FASTQ files for downstream processing:
+
+```text
+reformat.sh \
+    in1=${SAMPLE}_R1.fastq.gz \
+    in2=${SAMPLE}_R2.fastq.gz \
+    out=${SAMPLE}.fastq.gz
+```
+Split into SARS-CoV-2 and non-SARS-CoV-2 reads:
+
+```text
+bbduk.sh ow -Xmx1g \
+    in=${SAMPLE}.fq.gz \
+    ref=REFERENCE.fasta \
+    outm=${SAMPLE}_viral.fq.gz \
+    outu=${SAMPLE}_nonviral.fq.gz \
+    k=25
+```