From 6bfcf1a2cc6411f7abf7a139bebb65b97f0c3c6d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <balajtimate@gmail.com>
Date: Wed, 13 Nov 2024 11:32:51 +0100
Subject: [PATCH] remove docker image and build

---
 .dockerignore            |  8 -------
 .github/workflows/ci.yml | 35 -----------------------------
 Dockerfile               | 48 ----------------------------------------
 3 files changed, 91 deletions(-)
 delete mode 100644 .dockerignore
 delete mode 100644 Dockerfile

diff --git a/.dockerignore b/.dockerignore
deleted file mode 100644
index 2de06c86..00000000
--- a/.dockerignore
+++ /dev/null
@@ -1,8 +0,0 @@
-*
-!data/
-!htsinfer/
-!tests/
-!setup.py
-!environment.yml
-!LICENSE
-!README.md
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3993e32a..1fd8e310 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -126,38 +126,3 @@ jobs:
       - name: integration test - paired-ended library
         run: htsinfer --cleanup-regime=KEEP_NONE --verbosity=DEBUG tests/files/adapter_{1,2}.fastq
 
-  publish:
-    name: build and publish app image
-    runs-on: ubuntu-latest
-    if: |
-      github.event_name == 'push' && 
-      github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
-
-    steps:
-
-      - name: check out repository
-        uses: actions/checkout@v3
-
-      - name: generate tag
-        run: |
-          echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV
-
-      - name: build and publish image
-        id: docker
-        uses: philips-software/docker-ci-scripts@v5.1.0
-        with:
-          dockerfile: .
-          image-name: "htsinfer"
-          tags: "latest ${{ env.TAG }}"
-          push-branches: "${{ github.event.repository.default_branch }}"
-        env:
-          REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }}
-          REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}"
-          DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }}
-          GITHUB_ORGANIZATION: ${{ github.repository_owner }}
-
-      - name: Verify that image was pushed
-        run: |
-          echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}"
-          echo "# Set to 'true' if image was pushed, empty string otherwise"
-          test "${{ steps.docker.outputs.push-indicator }}" == "true"
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index a12a675a..00000000
--- a/Dockerfile
+++ /dev/null
@@ -1,48 +0,0 @@
-###### BASE IMAGE ######
-FROM continuumio/miniconda3:4.12.0
-
-####### METADATA #######
-LABEL base_image="continuumio/miniconda3:4.12.0"
-LABEL version="1.0"
-LABEL software="HTSinfer"
-LABEL software.version="v1.0.0"
-LABEL about.summary="HTSinfer infers metadata from Illumina high-throughput sequencing (HTS) data"
-LABEL about.home="https://github.com/zavolanlab/htsinfer"
-LABEL about.documentation="https://htsinfer.readthedocs.io/"
-LABEL about.license_file="https://spdx.org/licenses/Apache-2.0"
-LABEL about.license="Apache License 2.0"
-LABEL about.tags="Transcriptomics"
-
-###### MAINTAINER ######
-LABEL maintainer="Alexander Kanitz <alexander.kanitz@alumni.ethz.ch>"
-LABEL maintainer.organisation="Biozentrum, University of Basel"
-LABEL maintainer.location="Spitalstrasse 41, CH-4056 Basel, Switzerland"
-LABEL maintainer.lab="Zavolan Lab"
-
-##### INSTALLATION #####
-
-# COPY THE YAML & INSTALL SOFTWARE WITH CONDA
-WORKDIR /usr/src/app
-COPY ./ ./
-RUN conda env create --file environment.yml \
-    && conda clean --all
-
-# VARIABLES
-ARG WORKDIR="/home/USER"
-ARG USER="USER"
-ARG GROUP="GROUP"
-ENV PATH="${WORKDIR}:${PATH}"
-
-# CREATE USER
-RUN groupadd -r ${GROUP} && useradd --no-log-init -r -g ${GROUP} ${USER}
-
-# SET ENVIRONMENT
-WORKDIR ${WORKDIR}
-RUN chown -R ${USER}:${GROUP} ${WORKDIR} && chmod 700 ${WORKDIR}
-USER ${USER}
-RUN echo "source activate htsinfer" > ~/.bashrc
-ENV PATH /opt/conda/envs/htsinfer/bin:$PATH
-
-# SET ENTRYPOINT
-ENTRYPOINT ["htsinfer"]
-CMD ["-h"]