diff --git a/README.md b/README.md index ac56aa0d6..dcabe9739 100644 --- a/README.md +++ b/README.md @@ -244,7 +244,7 @@ To learn more about the docker pull rate limits and the open source software pro | [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 | | [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 | +| [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 | | [SeqSero2](https://hub.docker.com/r/staphb/seqsero2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero2)](https://hub.docker.com/r/staphb/seqsero2) | | https://github.com/denglab/SeqSero2/ | | [seqtk](https://hub.docker.com/r/staphb/seqtk)
[![docker pulls](https://badgen.net/docker/pulls/staphb/seqtk)](https://hub.docker.com/r/staphb/seqtk) | | https://github.com/lh3/seqtk | diff --git a/seqkit/2.8.0/Dockerfile b/seqkit/2.8.0/Dockerfile new file mode 100644 index 000000000..03a040109 --- /dev/null +++ b/seqkit/2.8.0/Dockerfile @@ -0,0 +1,55 @@ +# FROM defines the base docker image. This command has to come first in the file +# The 'as' keyword lets you name the folowing stage. We use `app` for the production image +FROM ubuntu:jammy as app + +# ARG sets environment variables during the build stage +ARG SEQKIT_VER="2.8.0" + +# LABEL instructions tag the image with metadata that might be important to the user +# Optional, but highly recommended +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="SeqKit" +LABEL software.version=${SEQKIT_VER} +LABEL description="SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation" +LABEL website="https://github.com/shenwei356/seqkit" +LABEL license="https://github.com/shenwei356/seqkit/blob/master/LICENSE" +LABEL maintainer="Henry Kunerth" +LABEL maintainer.email="henrykunerth@gmail.com" +LABEL maintainer2="Erin Young" +LABEL maintainer2.email="eriny@utah.gov" + +# Install dependences (update as needed) +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + procps \ + unzip && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# download SEQKIT and organize directories +RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${SEQKIT_VER}/seqkit_linux_amd64.tar.gz && \ + tar -xzf seqkit_linux_amd64.tar.gz && \ + mv seqkit /usr/local/bin/. && \ + rm seqkit_linux_amd64.tar.gz && \ + mkdir /data + +# singularity compatibility +ENV LC_ALL=C + +CMD seqkit --help + +# WORKDIR sets working directory +WORKDIR /data + +# A second FROM insruction creates a new stage +# We use `test` for the test image +FROM app as test + +WORKDIR /test + +RUN seqkit --help + +#download test .fasta and check that SEQKIT can run to generate stats +RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \ + seqkit stat * diff --git a/seqkit/2.8.0/README.md b/seqkit/2.8.0/README.md new file mode 100644 index 000000000..de048f057 --- /dev/null +++ b/seqkit/2.8.0/README.md @@ -0,0 +1,36 @@ +# SeqKit container + +Main tool : [SeqKit](https://github.com/shenwei356/seqkit) + +SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. + +Citation: + +W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962. + + +- **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit) +([**Usage**](http://bioinf.shenwei.me/seqkit/usage/), +[**FAQ**](http://bioinf.shenwei.me/seqkit/faq/), +[**Tutorial**](http://bioinf.shenwei.me/seqkit/tutorial/), +and +[**Benchmark**](http://bioinf.shenwei.me/seqkit/benchmark/)) + +## Example Usage + +```bash +# get simple statistics from FASTA/Q files + +seqkit stats + +# or with flags + +seqkit stats --all --tabular + +# conversion from FASTA to FASTQ + +seqkit fa2fq + + + +```