diff --git a/Program_Licenses.md b/Program_Licenses.md index 7c1593784..955523efe 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -114,6 +114,7 @@ The licenses of the open-source software that is contained in these Docker image | pasty | Apache 2.0 | https://github.com/rpetit3/pasty/blob/main/LICENSE | | Pavian | GNU GPLv3 | https://github.com/fbreitwieser/pavian/blob/master/DESCRIPTION | | pbptyper | MIT | https://github.com/rpetit3/pbptyper/blob/main/LICENSE | +| pbtk | BSD-3 | https://github.com/PacificBiosciences/pbtk/blob/main/LICENSE.txt | | Phyml | GNU GPLv3 | https://github.com/stephaneguindon/phyml/blob/master/COPYING | | phyTreeViz | MIT | https://github.com/moshi4/phyTreeViz/blob/main/LICENSE | | Piggy | GNU GPLv3 | https://github.com/harry-thorpe/piggy/blob/master/LICENSE | diff --git a/README.md b/README.md index c56cc30a7..cf38b5dd5 100644 --- a/README.md +++ b/README.md @@ -218,6 +218,7 @@ To learn more about the docker pull rate limits and the open source software pro | [pasty](https://hub.docker.com/r/staphb/pasty)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | | https://github.com/rpetit3/pasty | | [Pavian](https://hub.docker.com/r/staphb/pavian)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | | https://github.com/fbreitwieser/pavian | | [pbptyper](https://hub.docker.com/r/staphb/pbptyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | | https://github.com/rpetit3/pbptyper | +| [pbtk](https://hub.docker.com/r/staphb/pbtk)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbtk)](https://hub.docker.com/r/staphb/pbtk) | | https://github.com/PacificBiosciences/pbtk | | [Phyml](https://hub.docker.com/r/staphb/phyml)
[![docker pulls](https://badgen.net/docker/pulls/staphb/phyml)](https://hub.docker.com/r/staphb/phyml) | | https://github.com/stephaneguindon/phyml | | [phyTreeViz](https://hub.docker.com/r/staphb/phytreeviz)
[![docker pulls](https://badgen.net/docker/pulls/staphb/phytreeviz)](https://hub.docker.com/r/staphb/phytreeviz) | | https://github.com/moshi4/phyTreeViz/ | | [Piggy](https://hub.docker.com/r/staphb/piggy)
[![docker pulls](https://badgen.net/docker/pulls/staphb/piggy)](https://hub.docker.com/r/staphb/piggy) | | https://github.com/harry-thorpe/piggy | diff --git a/pbtk/3.1.1/Dockerfile b/pbtk/3.1.1/Dockerfile new file mode 100644 index 000000000..d3b8071d6 --- /dev/null +++ b/pbtk/3.1.1/Dockerfile @@ -0,0 +1,51 @@ +FROM ubuntu:jammy as app + +ARG PBTK_VER="3.1.1" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="pbtk" +LABEL software.version="${PBTK_VER}" +LABEL description="PacBio BAM toolkit" +LABEL website="https://github.com/PacificBiosciences/pbtk" +LABEL license="https://github.com/PacificBiosciences/pbtk/blob/main/LICENSE.txt" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget --no-check-certificate https://github.com/PacificBiosciences/pbtk/releases/download/v${PBTK_VER}/pbtk.tar.gz &&\ + tar -C /usr/local/bin/ -xvf pbtk.tar.gz &&\ + rm pbtk.tar.gz + +ENV LC_ALL=C + +CMD bam2fasta -h;\ + bam2fastq -h;\ + ccs-kinetics-bystrandify -h;\ + extracthifi -h;\ + pbindex -h;\ + pbindexdump -h;\ + pbmerge -h;\ + zmwfilter -h + +WORKDIR /data + +## Test ## +FROM app as test + +RUN wget -q --no-check-certificate https://downloads.pacbcloud.com/public/dataset/HiFiViral/Nov_2021/m64012_210821_095651.hifi_reads.bam + +RUN pbindex m64012_210821_095651.hifi_reads.bam &&\ + zmwfilter --include 1,2,4,8,16 m64012_210821_095651.hifi_reads.bam test.bam &&\ + zmwfilter --include 18,19,22,24,33 m64012_210821_095651.hifi_reads.bam test2.bam &&\ + pbindex test.bam &&\ + pbindexdump test.bam.pbi > test.json &&\ + bam2fasta -o test test.bam &&\ + bam2fastq -o test test.bam &&\ + extracthifi test.bam test.hifi.bam &&\ + ccs-kinetics-bystrandify test.bam test.bystrand.bam &&\ + pbmerge test.bam test2.bam > test.merged.bam &&\ + echo $(ls | grep test) \ No newline at end of file diff --git a/pbtk/3.1.1/README.md b/pbtk/3.1.1/README.md new file mode 100644 index 000000000..2a50bcc22 --- /dev/null +++ b/pbtk/3.1.1/README.md @@ -0,0 +1,42 @@ +# pbtk container + +Main tool: [pbtk](https://github.com/PacificBiosciences/pbtk) + +Code repository: https://github.com/PacificBiosciences/pbtk + +Basic information on how to use this tool: +- executables: + - bam2fasta + - bam2fastq + - ccs-kinetics-bystrandify + - extracthifi + - pbindex + - pbindexdump + - pbmerge + - zmwfilter +- help: -h, --help +- version: --version +- description: PacBio BAM toolkit + +Full documentation: https://github.com/PacificBiosciences/pbtk + +## Example Usage + +```bash +# bam2fasta +bam2fasta -o out in.bam +# bam2fastq +bam2fastq -o out in_1.bam in_2.bam in_3.xml in_4.bam +# ccs-kinetics-bystrandify +ccs-kinetics-bystrandify in.bam out.bam +# extracthifi +extracthifi in.bam out.bam +# pbindex +pbindex in.bam +# pbindexdump +pbindexdump in.bam.pbi > out.json +# pbmerge +pbmerge in1.bam in2.bam in3.bam > out.bam +# zmwfilter +zmwfilter --include 1,2,4,8,16 in.bam out.bam +```