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Hervé MENAGER
galaxy-cwl-is-docker
Commits
2523e2fb
Commit
2523e2fb
authored
Jun 14, 2019
by
Hervé MENAGER
Browse files
modify the Dockerfile to include all new material
parent
17d9987e
Pipeline
#12584
passed with stages
in 12 minutes and 16 seconds
Changes
1
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2523e2fb
...
...
@@ -10,15 +10,13 @@ RUN apt-get update && apt-get install -y \
docker.io
\
wget
\
curl
\
libpq-dev
libpq-dev \
vim
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
RUN
git clone
--depth
1
--single-branch
--branch
assembly
--progress
https://github.com/hmenager/workflow-is-cwl /app/workflow-is-cwl_assembly
RUN
git clone
--depth
1
--single-branch
--branch
master
--progress
https://github.com/EBI-metagenomics/workflow-is-cwl /app/workflow-is-cwl
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
# init Galaxy (download deps and init DB...)
RUN
cd
/app/galaxy
&&
./scripts/common_startup.sh
#RUN cd /app/galaxy && . .venv/bin/activate && cwltool --pack /app/workflow-is-cwl/tools/Diamond/Diamon.blastx-v0.9.21.cwl > /app/workflow-is-cwl/tools/Diamond/Diamon.blastx-v0.9.21.packed.cwl
...
...
@@ -38,5 +36,19 @@ COPY tool_conf.xml /app/galaxy/config/tool_conf.xml
COPY
welcome.html /app/galaxy/static/welcome.html
# create entry point
COPY
start.sh /app/start.sh
# test modified gx annotation for type
COPY
Diamon.makedb-v0.9.21.cwl /app/workflow-is-cwl/tools/Diamond/Diamon.makedb-v0.9.21.cwl
COPY
create_user.py /app/galaxy/create_user.py
# copy a fixed version of workflows.py to allow Workflow API uploads until
# https://github.com/common-workflow-language/galaxy/pull/105 is merged
COPY
workflows.py /app/galaxy/lib/galaxy/managers/workflows.py
# create the admin user
RUN
bash
-c
"cd /app/galaxy && . .venv/bin/activate && python create_user.py"
# upload workflows and data
RUN
git clone https://github.com/vishnubob/wait-for-it.git
RUN
cd
/app/galaxy
&&
.
.venv/bin/activate
&&
pip
install
bioblend
COPY
upload_material.py /app
COPY
start_galaxy_and_upload_material.sh /app
RUN
bash /app/start_galaxy_and_upload_material.sh
CMD
["sh", "/app/start.sh"]
EXPOSE
8080
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