add pbtk

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 |

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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | <ul><li>1.0.2</li><li>[1.0.3](pasty/1.0.3/)</li></ul> | https://github.com/rpetit3/pasty |
 | [Pavian](https://hub.docker.com/r/staphb/pavian) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | <ul><li>[1.2.1](pavian/1.2.1/)</li></ul> | https://github.com/fbreitwieser/pavian |
 | [pbptyper](https://hub.docker.com/r/staphb/pbptyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | <ul><li>1.0.0</li><li>1.0.1</li><li>1.0.4</li></ul> | https://github.com/rpetit3/pbptyper |
+| [pbtk](https://hub.docker.com/r/staphb/pbtk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbtk)](https://hub.docker.com/r/staphb/pbtk) | <ul><li>[3.1.1](./pbtk/3.1.1/)</li></ul> | https://github.com/PacificBiosciences/pbtk |
 | [Phyml](https://hub.docker.com/r/staphb/phyml) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/phyml)](https://hub.docker.com/r/staphb/phyml) | <ul><li>3.3.20220408</li></ul> | https://github.com/stephaneguindon/phyml |
 | [phyTreeViz](https://hub.docker.com/r/staphb/phytreeviz) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/phytreeviz)](https://hub.docker.com/r/staphb/phytreeviz) | <ul><li>[0.1.0](./phytreeviz/0.1.0/)</li><li>[0.2.0](./phytreeviz/0.2.0/)</li></ul> | https://github.com/moshi4/phyTreeViz/ |
 | [Piggy](https://hub.docker.com/r/staphb/piggy) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/piggy)](https://hub.docker.com/r/staphb/piggy) | <ul><li>1.5</li></ul> | https://github.com/harry-thorpe/piggy |

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="${PBTK_VER}"
+LABEL description="PacBio BAM toolkit"
+LABEL website="https://github.com/PacificBiosciences/pbtk"
+LABEL license="https://github.com/PacificBiosciences/pbtk/blob/main/LICENSE.txt"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends  -y \
+    wget &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate https://github.com/PacificBiosciences/pbtk/releases/download/v${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)

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
+```