Merge pull request #1591 from cwoodside1278/seqkit-2.13.0

Update Seqkit to 2.13.0

Author: erinyoung

README.md

@@ -299,7 +299,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.4.0](./build-files/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) | <details><summary>Click to see all versions</summary> <ul><li>[1.9](./build-files/samtools/1.9/)</li><li>[1.10](./build-files/samtools/1.10/)</li><li>[1.11](./build-files/samtools/1.11/)</li><li>[1.12](./build-files/samtools/1.12/)</li><li>[1.13](./build-files/samtools/1.13/)</li><li>[1.14](./build-files/samtools/1.14/)</li><li>[1.15](./build-files/samtools/1.15/)</li><li>[1.16](./build-files/samtools/1.16/)</li><li>[1.16.1](./build-files/samtools/1.16.1/)</li><li>[1.17](./build-files/samtools/1.17/)</li><li>[1.17-2023-06](./build-files/samtools/1.17-2023-06/)</li><li>[1.18](./build-files/samtools/1.18/)</li><li>[1.19](./build-files/samtools/1.19/)</li><li>[1.20](./build-files/samtools/1.20/)</li><li>[1.20.c](./build-files/samtools/1.20.c/)</li><li>[1.21](./build-files/samtools/1.21/)</li><li>[1.22](./build-files/samtools/1.22/)</li><li>[1.22.1](./build-files/samtools/1.22.1/)</li><li>[1.23](./build-files/samtools/1.23/)</li></ul> </details> | https://github.com/samtools/samtools |
 | [SeqFu](https://hub.docker.com/r/staphb/SeqFu) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqfu)](https://hub.docker.com/r/staphb/seqfu) | <details><summary>Click to see all versions</summary> <ul><li>[1.20.3](./build-files/seqfu/1.20.3/)</li><li>[1.22.3](./build-files/seqfu/1.22.3/)</li><li>[1.23.0](./build-files/seqfu/1.23.0/)</li></ul> </details> |  https://github.com/telatin/seqfu2 |
-| [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) | <details><summary>Click to see all versions</summary> <ul><li>[2.3.1](./build-files/seqkit/2.3.1/)</li><li>[2.6.1](./build-files/seqkit/2.6.1/)</li><li>[2.7.0](./build-files/seqkit/2.7.0/)</li><li>[2.8.0](./build-files/seqkit/2.8.0/)</li><li>[2.8.1](./build-files/seqkit/2.8.1/)</li><li>[2.8.2](./build-files/seqkit/2.8.2/)</li><li>[2.9.0](./build-files/seqkit/2.9.0/)</li><li>[2.10.0](./build-files/seqkit/2.10.0/)</li><li>[2.10.1](./build-files/seqkit/2.10.1/)</li><li>[2.12.0](./build-files/seqkit/2.12.0/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[2.3.1](./build-files/seqkit/2.3.1/)</li><li>[2.6.1](./build-files/seqkit/2.6.1/)</li><li>[2.7.0](./build-files/seqkit/2.7.0/)</li><li>[2.8.0](./build-files/seqkit/2.8.0/)</li><li>[2.8.1](./build-files/seqkit/2.8.1/)</li><li>[2.8.2](./build-files/seqkit/2.8.2/)</li><li>[2.9.0](./build-files/seqkit/2.9.0/)</li><li>[2.10.0](./build-files/seqkit/2.10.0/)</li><li>[2.10.1](./build-files/seqkit/2.10.1/)</li><li>[2.12.0](./build-files/seqkit/2.12.0/)</li><li>[2.13.0](./build-files/seqkit/2.13.0/)</li></ul> </details> | https://github.com/shenwei356/seqkit |
 | [SeqSender](https://hub.docker.com/r/staphb/seqsender/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsender)](https://hub.docker.com/r/staphb/seqsender) | <details><summary>Click to see all versions</summary> <ul><li>[1.3.3](./build-files/seqsender/1.3.3/)</li><li>[1.3.4](./build-files/seqsender/1.3.4/)</li><li>[1.3.6](./build-files/seqsender/1.3.6/)</li><li>[1.3.9](./build-files/seqsender/1.3.9/)</li><li>[1.3.93](./build-files/seqsender/1.3.93/)</li></ul> </details> | https://github.com/CDCgov/seqsender |
 | [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) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.1](./build-files/seqsero/1.0.1/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.0](./build-files/seqsero2/0.1.0/)</li><li>[1.0.0](./build-files/seqsero2/1.0.0/)</li><li>[1.0.2](./build-files/seqsero2/1.0.2/)</li><li>[1.1.0](./build-files/seqsero2/1.1.0/)</li><li>[1.1.1](./build-files/seqsero2/1.1.1/)</li><li>[1.2.1](./build-files/seqsero2/1.2.1/)</li><li>[1.3.1](./build-files/seqsero2/1.3.1/)</li><li>[1.3.1-micromamba](./build-files/seqsero2/1.3.1-micromamba/)</li><li>[1.3.2](./build-files/seqsero2/1.3.2/)</li></ul> </details> | https://github.com/denglab/SeqSero2/ |

build-files/seqkit/2.13.0/Dockerfile

@@ -0,0 +1,54 @@
+FROM ubuntu:noble AS app
+
+# ARG sets environment variables during the build stage
+ARG SEQKIT_VER="2.13.0"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+# Optional, but highly recommended
+
+LABEL base.image="ubuntu:noble"
+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 *

build-files/seqkit/2.13.0/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)>
+
+
+
+```