adding flye 2.9.4 (#982)

* adding flye 2.9.4

* update to 2.9.4

README.md

@@ -159,7 +159,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Freebayes](https://hub.docker.com/r/staphb/freebayes) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/freebayes)](https://hub.docker.com/r/staphb/freebayes) | <ul><li>1.3.6</li><li>1.3.7</li><li>1.3.7</li><li>1.3.7</li></ul> | https://github.com/freebayes/freebayes |
 | [Filtlong](https://hub.docker.com/r/staphb/filtlong) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/filtlong)](https://hub.docker.com/r/staphb/filtlong) | <ul><li>0.2.0</li><li>0.2.1</li></ul> | https://github.com/rrwick/filtlong |
 | [FLASH](https://hub.docker.com/r/staphb/flash) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/flash)](https://hub.docker.com/r/staphb/flash) | <ul><li>1.2.11</li></ul> | http://ccb.jhu.edu/software/FLASH |
-| [Flye](https://hub.docker.com/r/staphb/flye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/flye)](https://hub.docker.com/r/staphb/flye) | <ul><li>[2.5](flye/2.5/)</li><li>[2.7](flye/2.7/)</li><li>[2.8](flye/2.8/)</li><li>[2.9](flye/2.9/)</li><li>[2.9.1](flye/2.9.1/)</li><li>[2.9.2](flye/2.9.2/)</li><li>[2.9.3](flye/2.9.3/)</li></ul> | https://github.com/fenderglass/Flye |
+| [Flye](https://hub.docker.com/r/staphb/flye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/flye)](https://hub.docker.com/r/staphb/flye) | <ul><li>[2.5](flye/2.5/)</li><li>[2.7](flye/2.7/)</li><li>[2.8](flye/2.8/)</li><li>[2.9](flye/2.9/)</li><li>[2.9.1](flye/2.9.1/)</li><li>[2.9.2](flye/2.9.2/)</li><li>[2.9.3](flye/2.9.3/)</li><li>[2.9.4](flye/2.9.4/)</li></ul> | https://github.com/fenderglass/Flye |
 | [Freyja](https://hub.docker.com/r/staphb/freyja) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/freyja)](https://hub.docker.com/r/staphb/freyja) | <ul><li>[1.2](./freyja/1.2/)</li><li>[1.2.1](./freyja/1.2.1/)</li><li>[1.3.1](./freyja/1.3.1/)</li><li>[1.3.2](./freyja/1.3.2/)</li><li>[1.3.4](./freyja/1.3.4/)</li><li>[1.3.7](./freyja/1.3.7/)</li><li>[1.3.8](./freyja/1.3.8/)</li><li>[1.3.9](./freyja/1.3.9/)</li><li>[1.3.10](./freyja/1.3.10/)</li><li>[1.3.11](./freyja/1.3.11/)</li><li>[1.3.12](./freyja/1.3.12/)</li><li>[1.4.2](./freyja/1.4.2/)</li><li>[1.4.3](freyja/1.4.3/)</li><li>[1.4.4](freyja/1.4.4/)</li><li>[1.4.5](freyja/1.4.5/)</li><li>[1.4.7](freyja/1.4.7/)</li><li>[1.4.8](freyja/1.4.8/)</li><li>[1.4.9](freyja/1.4.9/)</li><li>[1.5.0](freyja/1.5.0/)</li></ul> | https://github.com/andersen-lab/Freyja |
 | [GAMBIT](https://hub.docker.com/r/staphb/gambit) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gambit)](https://hub.docker.com/r/staphb/gambit) | <ul><li>0.3.0</li><li>0.4.0</li><li>0.5.0</li><li>1.0.0</li></ul> | https://github.com/jlumpe/gambit |
 | [GAMMA](https://hub.docker.com/r/staphb/gamma) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gamma)](https://hub.docker.com/r/staphb/gamma) | <ul><li>1.4</li><li>2.1</li><li>2.2</li></ul> | https://github.com/rastanton/GAMMA/ |

flye/2.9.4/Dockerfile

@@ -0,0 +1,69 @@
+# for easy upgrade later
+ARG FLYE_VER="2.9.4"
+
+FROM ubuntu:jammy as app
+
+# have to re-instantiate variable within app stage
+ARG FLYE_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="Flye"
+LABEL software.version="${FLYE_VER}"
+LABEL description="Fast and accurate de novo assembler for single molecule sequencing reads"
+LABEL website="https://github.com/fenderglass/Flye"
+LABEL license="https://github.com/fenderglass/Flye/blob/flye/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    make \
+    gcc \
+    g++ \
+    python3 \
+    python3-pip \
+    python3-setuptools \
+    zlib1g-dev \
+    wget \
+    ca-certificates \
+    procps && \
+    rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+# install flye
+RUN wget -q https://github.com/fenderglass/Flye/archive/${FLYE_VER}.tar.gz && \
+    tar -xf ${FLYE_VER}.tar.gz && \
+    rm -v ${FLYE_VER}.tar.gz && \
+    cd Flye-${FLYE_VER} && \
+    python3 setup.py build && \
+    python3 setup.py install && \
+    mkdir /data
+
+# set final working directory
+WORKDIR /data
+
+# for singularity compatibility
+ENV LC_ALL=C
+
+#### begin the test stage ####
+FROM app as test
+
+# have to re-instantiate variable within app stage
+ARG FLYE_VER
+
+# run flye toy dataset test
+RUN python3 /Flye-${FLYE_VER}/flye/tests/test_toy.py
+
+# download test data (ONT and ILMN FASTQs) and run through flye
+RUN echo "downloading ONT test data from bactopia/bactopia-tests on GitHub..." && \
+    wget -q https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data/species/portiera/nanopore/ERR3772599.fastq.gz && \
+    flye --nano-raw ERR3772599.fastq.gz -o flye-test-portiera -t 2 && \
+    flye --version
+
+# the following takes too long, but this would be the test I would recommend if testing this locally.
+# from https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md
+# RUN wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta && \
+#    flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --threads 4 && \
+#    wget https://zenodo.org/record/1172816/files/Loman_E.coli_MAP006-1_2D_50x.fasta && \
+#    flye --nano-raw Loman_E.coli_MAP006-1_2D_50x.fasta --out-dir out_nano --threads 4

flye/2.9.4/README.md

@@ -0,0 +1,14 @@
+# Flye container
+
+Main tool : [flye](https://github.com/fenderglass/Flye)
+
+Full documentation: [https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md](https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md)
+
+> Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
+
+## Example Usage
+
+```bash
+# sample.fastq.gz is compressed with bgzip
+flye --nano-raw sample.fastq.gz --threads 12 --out-dir flye/sample
+```