Lskatz patch 1

.github/workflows/test-etoki.yml

@@ -0,0 +1,23 @@
+# This caller workflow builds an image to the "test" stage.
+# Instructions: replace all the <placeholder> stubs in this template with values for your image.
+# Some explanations come from: https://github.com/actions/starter-workflows/blob/main/automation/manual.yml
+
+name: Test etoki image
+
+# Controls when the action will run. Workflow runs when manually triggered using the UI or when you submit your pull request
+on:
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - "etoki/1.2/Dockerfile"  # Dockerfile path, e.g. 'htslib/1.14/Dockerfile' so that only your image is tested
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+
+  # This job calls a workflow to build the image to the 'test' stage
+  build-to-test:
+    uses: ./.github/workflows/build-to-test.yml
+    with:
+      path_to_context: "./etoki/1.2"  # Path to directory with Dockerfile and context, e.g. "./spades/3.12.0"
+      dockerfile_name: "Dockerfile"
+      cache: "etoki"  # Use the program name as a nickname for a GitHub cache of your image's layers, e.g. "spades". The cache will speed up re-running the workflow.

Program_Licenses.md

@@ -25,6 +25,7 @@ The licenses of the open-source software that is contained in these Docker image
 | colorid | MIT | https://github.com/hcdenbakker/colorid/blob/master/LICENSE |
 | DSK | GNU Affero GPLv3 | https://github.com/GATB/dsk/blob/master/LICENSE |
 | emm-typing-tool | GNU GPLv3 | https://github.com/phe-bioinformatics/emm-typing-tool/blob/master/LICENCE |
+| EToKi | GNU GPLv3 | https://github.com/zheminzhou/EToKi/blob/master/LICENSE |
 | FastANI | Apache v2.0 | https://github.com/ParBLiSS/FastANI/blob/master/LICENSE |
 | FastTree | GNU GPLv2 | http://www.microbesonline.org/fasttree/ |
 | FastQC | GNU GPLv3 | https://github.com/s-andrews/FastQC/blob/master/LICENSE.txt |

README.md

@@ -56,6 +56,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [datasets-sars-cov-2](https://github.com/CDCgov/datasets-sars-cov-2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) | <ul><li>0.6.2</li><li>0.6.3</li></ul> | https://github.com/CDCgov/datasets-sars-cov-2 |
 | [DSK](https://hub.docker.com/r/staphb/dsk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | <ul><li>0.0.100</li></ul> | https://gatb.inria.fr/software/dsk/ |
 | [emm-typing-tool](https://hub.docker.com/r/staphb/emm-typing-tool) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emm-typing-tool)](https://hub.docker.com/r/staphb/emm-typing-tool) | <ul><li>0.0.1 (no version)</li></ul> | https://github.com/phe-bioinformatics/emm-typing-tool |
+| [EToKi](https://hub.docker.com/r/staphb/etoki) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/etoki)](https://hub.docker.com/r/staphb/etoki) | <ul><li>1.2</li></ul> | https://github.com/zheminzhou/EToKi |
 | [FastANI](https://hub.docker.com/r/staphb/fastani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastani)](https://hub.docker.com/r/staphb/fastani) | <ul><li>1.1</li><li>1.32</li><li>1.33</li></ul> | https://github.com/ParBLiSS/FastANI |
 | [FastTree](https://hub.docker.com/r/staphb/fasttree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) | <ul><li>2.1.11</li></ul> | http://www.microbesonline.org/fasttree/ |
 | [FastQC](https://hub.docker.com/r/staphb/fastqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastqc)](https://hub.docker.com/r/staphb/fastqc) | <ul><li>0.11.8</li><li>0.11.9</li></ul> | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ <br/> https://github.com/s-andrews/FastQC |

etoki/1.2/Dockerfile

@@ -0,0 +1,109 @@
+# 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:focal as app
+# Copying the Freyja container a bit
+FROM mambaorg/micromamba:0.22.0 as app
+
+# ARG sets environment variables during the build stage
+ARG SOFTWARENAME_VER="1.2"
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building; set to /data at the end
+WORKDIR /
+
+# LABEL instructions tag the image with metadata that might be important to the user
+# Optional, but highly recommended
+LABEL base.image="ubuntu:focal"
+LABEL dockerfile.version="1"
+LABEL software="EToKi"
+LABEL software.version=$SOFTWARENAME_VER
+LABEL description="All methods related to Enterobase data analysis pipelines"
+LABEL website="https://github.com/zheminzhou/EToKi"
+LABEL license="https://github.com/zheminzhou/EToKi/blob/master/LICENSE"
+LABEL maintainer="Lee Katz"
+LABEL maintainer.email="[email protected]"
+
+# https://askubuntu.com/a/1013396
+# avoid asking about timezone during apt-get
+ARG DEBIAN_FRONTEND=noninteractive
+
+# RUN executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ python3-pip \
+ python3-dev \
+ libgconf-2-4 \
+ curl \
+ unzip \
+ libcurl4-openssl-dev \
+ build-essential \
+ git \
+ pigz \
+ libcurl4-openssl-dev \
+ libcurl4 \
+ ant \
+ libssl-dev \
+ python3-venv \
+ wget && \
+ apt-get autoclean
+
+ #openjdk-8-jdk \
+
+# Gimme python3 instead of python2
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
+
+# Double check the python version
+RUN python --version
+
+# set the environment, put new conda env in PATH by default
+ENV PATH="/opt/conda/envs/etoki/bin:/opt/conda/envs/env/bin:${PATH}" \
+ LC_ALL=C.UTF-8
+
+
+RUN micromamba create -n etoki python=3.8 -c conda-forge -c bioconda -c defaults ete3 numba numpy pandas scikit-learn psutil click scipy && \
+ micromamba clean -a -y
+# might also have to install sklearn??
+
+# Now get us into that yummy yummy EToKi env
+ENV ENV_NAME="etoki"
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+## EToKi itself ##
+
+# ENV instructions set environment variables that persist from the build into the resulting image
+# Use for e.g. $PATH and locale settings for compatibility with Singularity
+ENV PATH="/usr/local/bin/EToKi:$PATH" \
+ LC_ALL=C
+
+RUN cd /usr/local/bin && git clone https://github.com/zheminzhou/EToKi.git -b ${SOFTWARENAME_VER}
+
+# Installs all 3rd party software except the kraken database and usearch
+RUN cd /usr/local/bin/EToKi && python EToKi.py configure --install
+
+RUN find /usr/local/bin/EToKi -name '*.py' -exec sed -i.bak -e '1 i #!/usr/bin/env python\n# ^^^ inserted corrected shebang for this container' {} \;
+
+# 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
+
+# Demonstrate that the program is successfully installed
+
+# Option 1: run the program's internal tests, for example with SPAdes:
+RUN cd /usr/local/bin/EToKi && EToKi.py --help
+#RUN cd /usr/local/bin/EToKi && $(which python) $(which EToKi.py) --help
+RUN cd /usr/local/bin/EToKi && bash example.bash
+
+# Option 2: write your own tests in a bash script in the same directory as your Dockerfile:
+#COPY my_tests.sh .
+#RUN bash my_tests.sh
+
+# Option 3: write python unit tests in a tests/ directory in the same directory as your Dockerfile:
+#RUN apt-get install -y python3
+#RUN mkdir tests/
+#COPY tests/ tests/
+#RUN python3 -m unittest discover -s tests
+#