diff --git a/Program_Licenses.md b/Program_Licenses.md index af3b7694b..050518981 100644 --- a/Program_Licenses.md +++ b/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 | diff --git a/README.md b/README.md index 7e1fe9b94..228d72344 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ | | [Roary](https://hub.docker.com/r/staphb/roary/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | | https://github.com/sanger-pathogens/Roary | | [SalmID](https://hub.docker.com/r/staphb/salmid)
[![docker pulls](https://badgen.net/docker/pulls/staphb/salmid)](https://hub.docker.com/r/staphb/salmid) | | https://github.com/hcdenbakker/SalmID | +| [samclip](https://hub.docker.com/r/staphb/samclip)
[![docker pulls](https://badgen.net/docker/pulls/staphb/samclip)](https://hub.docker.com/r/staphb/samclip) | | https://github.com/tseemann/samclip | | [Samtools](https://hub.docker.com/r/staphb/samtools)
[![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) | | https://github.com/samtools/samtools | | [SeqKit](https://hub.docker.com/r/staphb/SeqKit)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqkit)](https://hub.docker.com/r/staphb/seqkit) | | https://github.com/shenwei356/seqkit | | [SeqSero](https://hub.docker.com/r/staphb/seqsero/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero)](https://hub.docker.com/r/staphb/seqsero) | | https://github.com/denglab/SeqSero | diff --git a/samclip/0.4.0/Dockerfile b/samclip/0.4.0/Dockerfile new file mode 100644 index 000000000..dd1fe7bb3 --- /dev/null +++ b/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="${SAMCLIP_VER}" +LABEL description="Samclip: filter SAM file for soft and hard clipped alignments" +LABEL website="https://github.com/tseemann/samclip" +LABEL license="https://github.com/tseemann/samclip/blob/master/LICENSE" +LABEL maintainer="Dhatri Badri" +LABEL maintainer.email="dhatrib@umich.edu" + +# install dependencies +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + wget \ + software-properties-common \ + perl && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install samclip +RUN wget https://github.com/tseemann/samclip/archive/refs/tags/v${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 diff --git a/samclip/0.4.0/README.md b/samclip/0.4.0/README.md new file mode 100644 index 000000000..ef19ee2f7 --- /dev/null +++ b/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 +``` +