add first draft

Dockerfile

+FROM ubuntu:18.04
+WORKDIR /app
+RUN apt-get update && apt-get install -y \
+  git \
+  python-dev \
+  python-pip \
+  gcc \
+  make \
+  docker.io \
+  wget \
+  curl
+RUN git clone --depth 1 --progress https://github.com/hmenager/galaxy.git /app/galaxy
+RUN git clone --depth 1 --single-branch --branch master --progress https://github.com/hmenager/workflow-is-cwl /app/workflow-is-cwl
+RUN git clone --depth 1 --single-branch --branch assembly --progress https://github.com/hmenager/workflow-is-cwl /app/workflow-is-cwl_assembly
+RUN curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | apt-key add -
+RUN echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list
+RUN apt-get update && apt-get install -y yarn
+COPY job_conf.xml /app/galaxy/config/job_conf.xml
+COPY dependency_resolvers_conf.xml /app/galaxy/config/dependency_resolvers_conf.xml
+COPY galaxy.yml /app/galaxy/config/galaxy.yml
+COPY tool_conf.xml /app/galaxy/config/tool_conf.xml
+#COPY init_galaxy.sh /app/galaxy/init_galaxy.sh
+RUN cd /app/galaxy && ./scripts/common_startup.sh 
+RUN cd /app/galaxy && . .venv/bin/activate && pip install cwltool==1.0.20181012180214
+RUN cd /app/galaxy && ls database/*
+RUN cd /app/galaxy && ./create_db.sh
+RUN cd /app/galaxy && ./manage_db.sh upgrade
+CMD ["sh", "/app/galaxy/run.sh"]

dependency_resolvers_conf.xml

+<dependency_resolvers>
+  <tool_shed_packages />
+  <galaxy_packages />
+  <conda />
+  <galaxy_packages versionless="true" />
+  <conda versionless="true" />
+</dependency_resolvers>

init_galaxy.sh

+#!/bin/sh
+
+
+# Usage: ./run.sh <start|stop|restart>
+#
+#
+# Description: This script can be used to start or stop the galaxy
+# web application.
+
+cd "$(dirname "$0")"
+
+. ./scripts/common_startup_functions.sh
+
+# If there is a file that defines a shell environment specific to this
+# instance of Galaxy, source the file.
+if [ -z "$GALAXY_LOCAL_ENV_FILE" ];
+then
+    GALAXY_LOCAL_ENV_FILE='./config/local_env.sh'
+fi
+
+if [ -f "$GALAXY_LOCAL_ENV_FILE" ];
+then
+    . "$GALAXY_LOCAL_ENV_FILE"
+fi
+
+GALAXY_PID=${GALAXY_PID:-galaxy.pid}
+GALAXY_LOG=${GALAXY_LOG:-galaxy.log}
+PID_FILE=$GALAXY_PID
+LOG_FILE=$GALAXY_LOG
+
+parse_common_args $@
+
+run_common_start_up
+
+setup_python
+
+
+if [ ! -z "$GALAXY_RUN_WITH_TEST_TOOLS" ];
+then
+    export GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="test/functional/tools/samples_tool_conf.xml"
+    export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES="true"
+    export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_FORMAT="true"
+    export GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_TOOL_FORMATS="true"
+    export GALAXY_CONFIG_OVERRIDE_WEBHOOKS_DIR="test/functional/webhooks"
+fi
+
+if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
+    python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
+fi
+
+set_galaxy_config_file_var
+
+if [ "$INITIALIZE_TOOL_DEPENDENCIES" -eq 1 ]; then
+    # Install Conda environment if needed.
+    python ./scripts/manage_tool_dependencies.py init_if_needed
+fi

job_conf.xml

+<?xml version="1.0"?>
+<job_conf>
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+    </plugins>
+    <destinations default="docker_local">
+        <destination id="local" runner="local"/>
+        <destination id="docker_local" runner="local">
+            <param id="docker_enabled">true</param>
+            <param id="docker_sudo">false</param>
+        </destination>
+    </destinations>
+</job_conf>

tool_conf.xml

+<?xml version='1.0' encoding='utf-8'?>
+<toolbox monitor="false">
+  <tool file="data_source/upload.xml" />
+  <section id="cwl_tools" name="Annotation">
+    <tool file="../../workflow-is-cwl/tools/Diamond/Diamon.makedb-v0.9.21.cwl" />
+    <tool file="../../workflow-is-cwl/tools/Diamond/Diamon.blastx-v0.9.21.cwl" />
+    <tool file="../../workflow-is-cwl/tools/TransDecoder/TransDecoder.LongOrfs-v5.cwl" />
+    <tool file="../../workflow-is-cwl/tools/TransDecoder/TransDecoder.Predict-v5.cwl" />
+    <tool file="../../workflow-is-cwl/tools/Infernal/cmsearch/infernal-cmsearch-v1.1.2.cwl" />
+    <tool file="../../workflow-is-cwl/tools/InterProScan/InterProScan-v5.cwl" />
+    <tool file="../../workflow-is-cwl/tools/HMMER/phmmer-v3.2.cwl" />
+    <tool file="../../workflow-is-cwl/tools/BUSCO/BUSCO-v3.cwl" />
+    <tool file="../../workflow-is-cwl/tools/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.cwl" />
+  </section>
+  <section id="cwl_utils" name="Utilities">
+    <tool file="../../workflow-is-cwl/utils/clean_fasta_headers.cwl" />
+    <tool file="../../workflow-is-cwl/utils/concatenate.cwl" />
+    <tool file="../../workflow-is-cwl/utils/esl-reformat.cwl" />
+    <tool file="../../workflow-is-cwl/utils/fasta_chunker.cwl" />
+  </section>
+  <section id="cwl_tools_assemb" name="Assembly">
+    <tool file="../../workflow-is-cwl_assembly/tools/FastQC/FastQC-v0.11.7.cwl" />
+    <tool file="../../workflow-is-cwl_assembly/tools/Transrate/Transrate-V1.0.3.cwl" />
+    <tool file="../../workflow-is-cwl_assembly/tools/Trimmomatic/Trimmomatic-v0.36.cwl" />
+    <tool file="../../workflow-is-cwl_assembly/tools/Trinity/Trinity-V2.6.5.cwl" />
+  </section>
+</toolbox>