Commit 91c6de2d authored by Hervé  MENAGER's avatar Hervé MENAGER

add first draft

parent c12b1213
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>
<tool_shed_packages />
<galaxy_packages />
<conda />
<galaxy_packages versionless="true" />
<conda versionless="true" />
</dependency_resolvers>
This diff is collapsed.
#!/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
<?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>
<?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>
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