Commit 004a93ec authored by Hervé  MENAGER's avatar Hervé MENAGER

lots of different things, tests and Dind

* material to launch docker execution tests
* docker in docker setup
parent ee9a4d56
FROM ubuntu:18.04
#FROM ubuntu:18.04
FROM billyteves/ubuntu-dind:16.04
WORKDIR /app
RUN apt-get update && apt-get install -y \
git \
......@@ -8,7 +9,8 @@ RUN apt-get update && apt-get install -y \
make \
docker.io \
wget \
curl
curl \
libpq-dev
#RUN git clone --depth 1 --progress https://github.com/hmenager/galaxy.git /app/galaxy
RUN git clone --depth 1 --progress https://github.com/common-workflow-language/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
......@@ -16,6 +18,8 @@ RUN git clone --depth 1 --single-branch --branch assembly --progress https://git
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
#quickfix due to record not being in the right folder following rebase (04/03/2019)
RUN mv /app/galaxy/lib/galaxy/dataset_collections/types/record.py /app/galaxy/lib/galaxy/model/dataset_collections/types/record.py
RUN cd /app/galaxy && ./scripts/common_startup.sh
RUN cd /app/galaxy && ls database/*
RUN cd /app/galaxy && ./create_db.sh
......@@ -23,7 +27,11 @@ RUN cd /app/galaxy && ./manage_db.sh upgrade
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_test.xml /app/galaxy/config/tool_conf.xml
#COPY concatenate.cwl /app/galaxy/tools/
#COPY concatenate-docker.cwl /app/galaxy/tools/
COPY tool_conf.xml /app/galaxy/config/tool_conf.xml
COPY welcome.html /app/galaxy/static/welcome.html
CMD ["sh", "/app/galaxy/run.sh"]
COPY start.sh /app/start.sh
CMD ["sh", "/app/start.sh"]
EXPOSE 8080
class: CommandLineTool
cwlVersion: v1.0
baseCommand:
- cat
inputs:
- id: files
type: 'File'
inputBinding:
position: 1
streamable: true
outputs:
- id: result
type: File
outputBinding:
glob: result
outputEval: |
${ self[0].format = inputs.files.format;
return self; }
requirements:
- class: ResourceRequirement
ramMin: 100
coresMax: 1
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: 'alpine:3.7'
stdout: result
class: CommandLineTool
cwlVersion: v1.0
baseCommand:
- cat
inputs:
- id: files
type: 'File'
inputBinding:
position: 1
streamable: true
outputs:
- id: result
type: File
outputBinding:
glob: result
outputEval: |
${ self[0].format = inputs.files.format;
return self; }
requirements:
- class: ResourceRequirement
ramMin: 100
coresMax: 1
- class: InlineJavascriptRequirement
stdout: result
<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4" shell="none"/>
</plugins>
<destinations default="docker_local">
<destination id="local" runner="local"/>
......
service docker start
sh /app/galaxy/run.sh
......@@ -24,4 +24,8 @@
<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>
<section id="textutil" name="Text Manipulation">
<tool file="filters/catWrapper.xml" />
<tool file="filters/wc_gnu.xml" />
</section>
</toolbox>
<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="false">
<tool file="data_source/upload.xml" />
<section id="cwl_utils" name="Tests">
<tool file="concatenate.cwl" />
<tool file="concatenate-docker.cwl" />
</section>
</toolbox>
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