adding seqkit version 2.8.0 (#917)

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/) <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 |
 | [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></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></ul> | https://github.com/shenwei356/seqkit |
+| [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></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 |
 | [SeqSero2](https://hub.docker.com/r/staphb/seqsero2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero2)](https://hub.docker.com/r/staphb/seqsero2) | <ul><li>0.1.0</li><li>1.0.0</li><li>1.0.2</li><li>1.1.0</li><li>1.1.1</li><li>1.2.1</li></ul> | https://github.com/denglab/SeqSero2/ |
 | [seqtk](https://hub.docker.com/r/staphb/seqtk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqtk)](https://hub.docker.com/r/staphb/seqtk) | <ul><li>[1.3](seqtk/1.3/)</li><li>[1.4](seqtk/1.4/)</li></ul> | https://github.com/lh3/seqtk |

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=${SEQKIT_VER}
+LABEL description="SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation"
+LABEL website="https://github.com/shenwei356/seqkit"
+LABEL license="https://github.com/shenwei356/seqkit/blob/master/LICENSE"
+LABEL maintainer="Henry Kunerth"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Erin Young"
+LABEL maintainer2.email="[email protected]"
+
+# Install dependences (update as needed)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+	wget \
+	ca-certificates \
+	procps \
+	unzip && \
+	apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# download SEQKIT and organize directories
+RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${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 *

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 <file name(s)>
+
+# or with flags
+
+seqkit stats --all --tabular <file name(s)>
+
+# conversion from FASTA to FASTQ
+
+seqkit fa2fq <file name(s)>
+
+
+
+```