Merge pull request #969 from dhatribadri/dhatri-docker-builds

Adding samclip tool version 0.4.0

Program_Licenses.md

@@ -142,6 +142,7 @@ The licenses of the open-source software that is contained in these Docker image
 | ResFinder | Apache 2.0 | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
 | Roary | GNU GPLv3 | https://github.com/sanger-pathogens/Roary/blob/master/GPL-LICENSE |
 | SalmID| MIT | https://github.com/hcdenbakker/SalmID/blob/master/LICENSE |
+| samclip | GNU GPLv3 | https://github.com/tseemann/samclip/blob/master/LICENSE |
 | Samtools | GNU GPLv3 | https://github.com/samtools/samtools/blob/develop/LICENSE |
 | SeqKit | MIT | https://github.com/shenwei356/seqkit/blob/master/LICENSE
 | SeqSero | GNU GPLv2 | https://github.com/denglab/SeqSero/blob/master/LICENSE |

README.md

@@ -248,6 +248,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [ResFinder](https://hub.docker.com/r/staphb/resfinder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | <ul><li>[4.1.1](./resfinder/4.1.11/)</li><li>[4.5.0](./resfinder/4.5.0/)</li></ul> | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
 | [Roary](https://hub.docker.com/r/staphb/roary/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | <ul><li>3.12.0</li><li>3.13.0</li></ul> | https://github.com/sanger-pathogens/Roary |
 | [SalmID](https://hub.docker.com/r/staphb/salmid) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/salmid)](https://hub.docker.com/r/staphb/salmid) | <ul><li>0.1.23</li></ul> | https://github.com/hcdenbakker/SalmID |
+| [samclip](https://hub.docker.com/r/staphb/samclip) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/samclip)](https://hub.docker.com/r/staphb/samclip) | <ul><li>[0.4.0](./samclip/0.4.0/)</li></ul>| https://github.com/tseemann/samclip |
 | [Samtools](https://hub.docker.com/r/staphb/samtools) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) | <ul><li>[1.9](./samtools/1.9/)</li><li>[1.10](./samtools/1.10/)</li><li>[1.11](./samtools/1.11/)</li><li>[1.12](./samtools/1.12/)</li><li>[1.13](./samtools/1.13/)</li><li>[1.14](./samtools/1.14/)</li><li>[1.15](./samtools/1.15/)</li><li>[1.16](./samtools/1.16/)</li><li>[1.16.1](./samtools/1.16.1/)</li><li>[1.17](./samtools/1.17/)</li><li>[1.17-2023-06](./samtools/1.17-2023-06/)</li><li>[1.18](./samtools/1.18/)</li><li>[1.19](./samtools/1.19/)</li><li>[1.20](./samtools/1.20/)</li></ul> | https://github.com/samtools/samtools |
 | [SeqKit](https://hub.docker.com/r/staphb/SeqKit) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqkit)](https://hub.docker.com/r/staphb/seqkit) | <ul><li>[2.3.1](./seqkit/2.3.1/)</li><li>[2.6.1](./seqkit/2.6.1/)</li><li>[2.7.0](./seqkit/2.7.0/)</li><li>[2.8.0](./seqkit/2.8.0/)</li><li>[2.8.1](./seqkit/2.8.1/)</li></ul> | https://github.com/shenwei356/seqkit |
 | [SeqSero](https://hub.docker.com/r/staphb/seqsero/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero)](https://hub.docker.com/r/staphb/seqsero) | <ul><li>1.0.1</li></ul> | https://github.com/denglab/SeqSero |

samclip/0.4.0/Dockerfile

@@ -0,0 +1,50 @@
+ARG SAMCLIP_VER="0.4.0"
+
+FROM ubuntu:jammy as app
+
+ARG SAMCLIP_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="samclip"
+LABEL software.version="${SAMCLIP_VER}"
+LABEL description="Samclip: filter SAM file for soft and hard clipped alignments"
+LABEL website="https://github.com/tseemann/samclip"
+LABEL license="https://github.com/tseemann/samclip/blob/master/LICENSE"
+LABEL maintainer="Dhatri Badri"
+LABEL maintainer.email="[email protected]"
+
+# install dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    wget \
+    software-properties-common \
+    perl && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install samclip
+RUN wget https://github.com/tseemann/samclip/archive/refs/tags/v${SAMCLIP_VER}.tar.gz && \
+    tar -xvf v${SAMCLIP_VER}.tar.gz && \
+    rm v${SAMCLIP_VER}.tar.gz && \
+    chmod +x /samclip-${SAMCLIP_VER}/samclip && \
+    mkdir /data
+
+ENV PATH="${PATH}:/samclip-${SAMCLIP_VER}/" \
+    LC_ALL=C
+
+CMD [ "samclip", "--help" ]
+
+WORKDIR /data
+
+FROM app as test
+
+RUN samclip --help && \
+    samclip --version
+
+WORKDIR /test
+
+# Run test using samclip executable
+RUN wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna && \
+    wget https://raw.githubusercontent.com/tseemann/samclip/master/test.sam && \
+    wget https://raw.githubusercontent.com/tseemann/samclip/master/test.fna.fai && \
+    samclip --ref test.fna < test.sam > out.sam  

samclip/0.4.0/README.md

@@ -0,0 +1,22 @@
+# Samclip container
+
+Main tool: [samclip](https://github.com/tseemann/samclip)
+
+Basic information on how to use this tool:
+- executable: ./samclip
+- help: -h, --help
+- version: -V, --version
+- description: Filter SAM file for soft and hard clipped alignments
+
+## Example Usage
+
+Basic command to clip ends of reads
+```bash
+samclip --ref ref.fa < in.sam > out.sam
+```
+
+Integrate samclip with other tools like bwa and samtools
+```bash
+bwa mem ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam 
+```
+