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18.09 update #464

Merged
merged 38 commits into from
Dec 21, 2018
Merged

18.09 update #464

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7d834ec
update galaxyextras 18.09
abretaud Dec 11, 2018
9998785
need munge
abretaud Dec 11, 2018
beb8440
fix slurm install
abretaud Dec 11, 2018
1be3274
fix requirements install
abretaud Dec 11, 2018
2efd525
try hack for ansible rule
abretaud Dec 11, 2018
c194c51
fix for the hack
abretaud Dec 11, 2018
1481493
hack for the hack
abretaud Dec 11, 2018
5bd1ba5
supervisor stuff
abretaud Dec 12, 2018
9efc04c
no need to mkdir
abretaud Dec 12, 2018
2312f4f
slurm startup fix
abretaud Dec 12, 2018
b533b20
For 18.09 uses migration 142, not 144
abretaud Dec 12, 2018
d456e53
condor fixes
abretaud Dec 12, 2018
716b859
avoid harmless error message
abretaud Dec 12, 2018
8f42276
slurm install
abretaud Dec 12, 2018
57dcde9
fix missing ansible tag
abretaud Dec 12, 2018
933b13a
kube fix?
abretaud Dec 12, 2018
05be0b7
not needed
abretaud Dec 12, 2018
209b057
move to htcondor-base
abretaud Dec 13, 2018
edbef97
need 18.09 branch of ansible-galaxy-extras
abretaud Dec 13, 2018
b50f1d1
need nodejs installed (but can't use the ansible task as the galaxy c…
abretaud Dec 13, 2018
95a5d7c
trigger rebuild
abretaud Dec 14, 2018
33d03bc
fix error at startup: this line mounted a not-yet existing file (crea…
abretaud Dec 14, 2018
52f92d4
update bioblend testing
abretaud Dec 14, 2018
e938b86
fix bioblend test env
abretaud Dec 14, 2018
7e53dc0
fix image tag
abretaud Dec 18, 2018
5516786
dump fix
abretaud Dec 18, 2018
72866ed
reenable client building
abretaud Dec 18, 2018
c21cfcc
fix slurm_singularity test
abretaud Dec 18, 2018
7ec499e
Need to delay setting of GALAXY_CONFIG_TOOL_CONFIG_FILE
abretaud Dec 18, 2018
27ee4ab
create needed dirs/files for condor
abretaud Dec 18, 2018
2c0be52
update tag
abretaud Dec 18, 2018
40b74ac
latest kubernetes needs go >=1.11.1
abretaud Dec 18, 2018
7beba07
fix path problem (not sure if sudo is really needed)
abretaud Dec 18, 2018
bb3083d
longer timeout
abretaud Dec 18, 2018
83e2f24
Longer timeout
abretaud Dec 18, 2018
1cf3215
fix ignored BIOBLEND_TEST_JOB_TIMEOUT
abretaud Dec 19, 2018
76185aa
wait more!?
abretaud Dec 19, 2018
e5b586f
update kompose
abretaud Dec 19, 2018
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2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
[submodule "galaxy/roles/galaxyproject.galaxyextras"]
path = galaxy/roles/galaxyprojectdotorg.galaxyextras
url = https://github.com/galaxyproject/ansible-galaxy-extras
branch = 18.01
branch = 18.09
[submodule "galaxy/roles/galaxy-postgresql"]
path = galaxy/roles/galaxy-postgresql
url = https://github.com/galaxyproject/ansible-postgresql
4 changes: 4 additions & 0 deletions .travis.yml
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Expand Up @@ -103,6 +103,10 @@ before_install:
- |
if [ "${KUBE}" ]
then
# The compose file recognises ENV vars to change the defaul behavior
cd ${COMPOSE_DIR}
ln -sf .env_k8_native .env

curl -L https://github.com/kubernetes-incubator/kompose/releases/download/v0.5.0/kompose-linux-amd64 -o kompose
chmod +x kompose
sudo mv ./kompose /usr/bin/kompose
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2 changes: 1 addition & 1 deletion compose/build-orchestration-images.sh
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Expand Up @@ -222,7 +222,7 @@ K8S_ANSIBLE_TAGS=""
if $BUILD_FOR_K8S; then
K8S_ANSIBLE_TAGS=,k8,k8s
fi
docker build $NO_CACHE --build-arg GALAXY_ANSIBLE_TAGS=supervisor,startup,scripts,nginx$K8S_ANSIBLE_TAGS -t $GALAXY_WEB_TAG -f galaxy-web/$DOCKERFILE_WEB galaxy-web/
docker build $NO_CACHE --build-arg GALAXY_ANSIBLE_TAGS=supervisor,startup,scripts,nginx,cvmfs$K8S_ANSIBLE_TAGS -t $GALAXY_WEB_TAG -f galaxy-web/$DOCKERFILE_WEB galaxy-web/
if $DOCKER_PUSH_ENABLED; then
docker push $GALAXY_WEB_TAG
fi
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4 changes: 4 additions & 0 deletions compose/galaxy-htcondor-executor/Dockerfile
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Expand Up @@ -27,6 +27,10 @@ RUN mkdir -p /tmp/download && \
#chmod +rx /root && \
chmod +x /usr/bin/startup.sh

RUN touch /var/log/condor/StartLog /var/log/condor/StarterLog /var/log/condor/CollectorLog /var/log/condor/NegotiatorLog && \
mkdir -p /var/run/condor/ /var/lock/condor/ && \
chown -R condor: /var/log/condor/StartLog /var/log/condor/StarterLog /var/log/condor/CollectorLog /var/log/condor/NegotiatorLog /var/run/condor/ /var/lock/condor/

ENV CONDOR_CPUS=1 \
CONDOR_MEMORY=1024

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2 changes: 0 additions & 2 deletions compose/galaxy-htcondor-executor/startup.sh
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Expand Up @@ -30,8 +30,6 @@ SCHED_NAME = $CONDOR_HOST
" > /etc/condor/condor_config.local

/usr/bin/telegraf --config /etc/telegraf/telegraf.conf &
sudo -u condor touch /var/log/condor/StartLog
sudo -u condor touch /var/log/condor/StarterLog
tail -f -n 1000 /var/log/condor/StartLog /var/log/condor/StarterLog &

# Mysterious bug? Docker doesn't output its version as condor user if this is not executed before
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4 changes: 4 additions & 0 deletions compose/galaxy-htcondor/Dockerfile
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Expand Up @@ -3,4 +3,8 @@ FROM quay.io/bgruening/galaxy-htcondor-base:18.09
ADD condor_config.local /etc/condor/condor_config.local
ADD supervisord.conf /etc/supervisord.conf

RUN touch /var/log/condor/StartLog /var/log/condor/StarterLog /var/log/condor/CollectorLog /var/log/condor/NegotiatorLog && \
mkdir -p /var/run/condor/ /var/lock/condor/ && \
chown -R condor: /var/log/condor/StartLog /var/log/condor/StarterLog /var/log/condor/CollectorLog /var/log/condor/NegotiatorLog /var/run/condor/ /var/lock/condor/

CMD ["/usr/bin/supervisord"]
15 changes: 9 additions & 6 deletions compose/galaxy-init/startup.sh
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Expand Up @@ -30,13 +30,16 @@ done

# Optional, might not work
{
if [ ! -d "/export/var/lib/docker" ]
if [ -d "/var/lib/docker" ]
then
echo "Moving to /export/var/lib/docker"
mkdir -p /export/var/lib/
mv /var/lib/docker /export/var/lib/docker
chown -R $GALAXY_UID:$GALAXY_GID /export/var/lib/docker
fi
if [ ! -d "/export/var/lib/docker" ]
then
echo "Moving to /export/var/lib/docker"
mkdir -p /export/var/lib/
mv /var/lib/docker /export/var/lib/docker
chown -R $GALAXY_UID:$GALAXY_GID /export/var/lib/docker
fi
fi
} || echo "Moving docker lib failed, this is not a fatal error"

echo "Initialization complete"
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190 changes: 1 addition & 189 deletions compose/galaxy-postgres/init-galaxy-db.sql.in
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Expand Up @@ -372,73 +372,6 @@ CREATE SEQUENCE cleanup_event_metadata_file_association_id_seq
ALTER SEQUENCE cleanup_event_metadata_file_association_id_seq OWNED BY cleanup_event_metadata_file_association.id;


--
-- Name: cleanup_event_user_association; Type: TABLE; Schema: public; Owner: -
--

CREATE TABLE cleanup_event_user_association (
id integer NOT NULL,
create_time timestamp without time zone,
cleanup_event_id integer,
user_id integer
);


--
-- Name: cleanup_event_user_association_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--

CREATE SEQUENCE cleanup_event_user_association_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
NO MAXVALUE
CACHE 1;


--
-- Name: cleanup_event_user_association_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--

ALTER SEQUENCE cleanup_event_user_association_id_seq OWNED BY cleanup_event_user_association.id;


--
-- Name: cloudauthz; Type: TABLE; Schema: public; Owner: -
--

CREATE TABLE cloudauthz (
id integer NOT NULL,
user_id integer,
provider character varying(255),
config bytea,
authn_id integer,
tokens bytea,
last_update timestamp without time zone,
last_activity timestamp without time zone,
description text
);


--
-- Name: cloudauthz_id_seq; Type: SEQUENCE; Schema: public; Owner: -
--

CREATE SEQUENCE cloudauthz_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
NO MAXVALUE
CACHE 1;


--
-- Name: cloudauthz_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
--

ALTER SEQUENCE cloudauthz_id_seq OWNED BY cloudauthz.id;


--
-- Name: data_manager_history_association; Type: TABLE; Schema: public; Owner: -
--
Expand Down Expand Up @@ -5759,20 +5692,6 @@ ALTER TABLE ONLY cleanup_event_library_folder_association ALTER COLUMN id SET DE
ALTER TABLE ONLY cleanup_event_metadata_file_association ALTER COLUMN id SET DEFAULT nextval('cleanup_event_metadata_file_association_id_seq'::regclass);


--
-- Name: cleanup_event_user_association id; Type: DEFAULT; Schema: public; Owner: -
--

ALTER TABLE ONLY cleanup_event_user_association ALTER COLUMN id SET DEFAULT nextval('cleanup_event_user_association_id_seq'::regclass);


--
-- Name: cloudauthz id; Type: DEFAULT; Schema: public; Owner: -
--

ALTER TABLE ONLY cloudauthz ALTER COLUMN id SET DEFAULT nextval('cloudauthz_id_seq'::regclass);


--
-- Name: data_manager_history_association id; Type: DEFAULT; Schema: public; Owner: -
--
Expand Down Expand Up @@ -7023,36 +6942,6 @@ COPY cleanup_event_metadata_file_association (id, create_time, cleanup_event_id,
SELECT pg_catalog.setval('cleanup_event_metadata_file_association_id_seq', 1, false);


--
-- Data for Name: cleanup_event_user_association; Type: TABLE DATA; Schema: public; Owner: -
--

COPY cleanup_event_user_association (id, create_time, cleanup_event_id, user_id) FROM stdin;
\.


--
-- Name: cleanup_event_user_association_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
--

SELECT pg_catalog.setval('cleanup_event_user_association_id_seq', 1, false);


--
-- Data for Name: cloudauthz; Type: TABLE DATA; Schema: public; Owner: -
--

COPY cloudauthz (id, user_id, provider, config, authn_id, tokens, last_update, last_activity, description) FROM stdin;
\.


--
-- Name: cloudauthz_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
--

SELECT pg_catalog.setval('cloudauthz_id_seq', 1, false);


--
-- Data for Name: data_manager_history_association; Type: TABLE DATA; Schema: public; Owner: -
--
Expand Down Expand Up @@ -8237,7 +8126,7 @@ GalaxyTools lib/tool_shed/galaxy_install/migrate 1
--

COPY migrate_version (repository_id, repository_path, version) FROM stdin;
Galaxy lib/galaxy/model/migrate 144
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My bad, I must have been testing a few things on 19.01 when I pushed this... sorry.

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I have been thinking for a while on incorporating

https://github.com/bgruening/docker-galaxy-stable/blob/dev/compose/dumpsql.sh#L9-L36

inside the build-orchestration-images script, right after the init container creation (using that init container created). Then this whole file would be generated on the fly when building the containers, based on the version that it was used of Galaxy for those containers (so fairly failure-proof). Would you consider adding that to your PR @abretaud ?

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Yep, that would be cool. I'm not sure how to do it properly though: do you mean that at the end of build-orchestration-images we should:

  1. run a docker-compose with an empty postgresql database
  2. run the install_db.sh in galaxy-web
  3. run the dumpsql.sh script
  4. (re)build the galaxy-postgres image

Not sure I'll have time to write this now, maybe it could be another PR?

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Yes, don't worry, I'll PR it soon.

Galaxy lib/galaxy/model/migrate 142
\.


Expand Down Expand Up @@ -9492,22 +9381,6 @@ ALTER TABLE ONLY cleanup_event
ADD CONSTRAINT cleanup_event_pkey PRIMARY KEY (id);


--
-- Name: cleanup_event_user_association cleanup_event_user_association_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--

ALTER TABLE ONLY cleanup_event_user_association
ADD CONSTRAINT cleanup_event_user_association_pkey PRIMARY KEY (id);


--
-- Name: cloudauthz cloudauthz_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--

ALTER TABLE ONLY cloudauthz
ADD CONSTRAINT cloudauthz_pkey PRIMARY KEY (id);


--
-- Name: data_manager_history_association data_manager_history_association_pkey; Type: CONSTRAINT; Schema: public; Owner: -
--
Expand Down Expand Up @@ -10919,34 +10792,6 @@ CREATE INDEX ix_cleanup_event_metadata_file_association_cleanup_event_id ON clea
CREATE INDEX ix_cleanup_event_metadata_file_association_metadata_file_id ON cleanup_event_metadata_file_association USING btree (metadata_file_id);


--
-- Name: ix_cleanup_event_user_association_cleanup_event_id; Type: INDEX; Schema: public; Owner: -
--

CREATE INDEX ix_cleanup_event_user_association_cleanup_event_id ON cleanup_event_user_association USING btree (cleanup_event_id);


--
-- Name: ix_cleanup_event_user_association_user_id; Type: INDEX; Schema: public; Owner: -
--

CREATE INDEX ix_cleanup_event_user_association_user_id ON cleanup_event_user_association USING btree (user_id);


--
-- Name: ix_cloudauthz_authn_id; Type: INDEX; Schema: public; Owner: -
--

CREATE INDEX ix_cloudauthz_authn_id ON cloudauthz USING btree (authn_id);


--
-- Name: ix_cloudauthz_user_id; Type: INDEX; Schema: public; Owner: -
--

CREATE INDEX ix_cloudauthz_user_id ON cloudauthz USING btree (user_id);


--
-- Name: ix_data_manager_history_association_history_id; Type: INDEX; Schema: public; Owner: -
--
Expand Down Expand Up @@ -14200,38 +14045,6 @@ ALTER TABLE ONLY cleanup_event_metadata_file_association
ADD CONSTRAINT cleanup_event_metadata_file_association_metadata_file_id_fkey FOREIGN KEY (metadata_file_id) REFERENCES metadata_file(id);


--
-- Name: cleanup_event_user_association cleanup_event_user_association_cleanup_event_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
--

ALTER TABLE ONLY cleanup_event_user_association
ADD CONSTRAINT cleanup_event_user_association_cleanup_event_id_fkey FOREIGN KEY (cleanup_event_id) REFERENCES cleanup_event(id);


--
-- Name: cleanup_event_user_association cleanup_event_user_association_user_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
--

ALTER TABLE ONLY cleanup_event_user_association
ADD CONSTRAINT cleanup_event_user_association_user_id_fkey FOREIGN KEY (user_id) REFERENCES galaxy_user(id);


--
-- Name: cloudauthz cloudauthz_authn_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
--

ALTER TABLE ONLY cloudauthz
ADD CONSTRAINT cloudauthz_authn_id_fkey FOREIGN KEY (authn_id) REFERENCES oidc_user_authnz_tokens(id);


--
-- Name: cloudauthz cloudauthz_user_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
--

ALTER TABLE ONLY cloudauthz
ADD CONSTRAINT cloudauthz_user_id_fkey FOREIGN KEY (user_id) REFERENCES galaxy_user(id);


--
-- Name: data_manager_history_association data_manager_history_association_history_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
--
Expand Down Expand Up @@ -16651,4 +16464,3 @@ ALTER TABLE ONLY workflow_tag_association
--
-- PostgreSQL database dump complete
--

12 changes: 5 additions & 7 deletions compose/galaxy-slurm/Dockerfile
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Expand Up @@ -13,24 +13,22 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
groupadd -r $GALAXY_USER -g $GALAXY_GID && \
useradd -u $GALAXY_UID -m -r -g $GALAXY_USER -c "Galaxy user" $GALAXY_USER && \
apt-get update -qq && apt-get install -y --no-install-recommends apt-transport-https \
unattended-upgrades python-pip python-psutil supervisor wget build-essential \
libslurm32 libslurmdb32 && \
unattended-upgrades python-pip python-psutil python-setuptools supervisor wget \
build-essential munge locales slurm-wlm slurm-wlm-torque && \
wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa-dev_1.2.0-dev.deca826_amd64.deb && \
dpkg -i slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
dpkg -i slurm-drmaa-dev_1.2.0-dev.deca826_amd64.deb && \
/usr/sbin/create-munge-key && \
touch /var/log/slurm-llnl/slurmctld.log /var/log/slurm-llnl/slurmd.log && \
mkdir /tmp/slurm && pip install --upgrade supervisor virtualenv && \
pip install --upgrade virtualenv && \
wget https://github.com/singularityware/singularity/releases/download/$SINGULARITY_VERSION/singularity-$SINGULARITY_VERSION.tar.gz && \
tar xvf singularity-$SINGULARITY_VERSION.tar.gz && \
cd singularity-$SINGULARITY_VERSION && \
./configure --prefix=/usr/local --sysconfdir=/etc && \
make && \
make install && \
rm -rf singularity-$SINGULARITY_VERSION singularity-$SINGULARITY_VERSION.tar.gz && \
apt-get remove -y supervisor build-essential && \
mkdir /var/log/supervisor && \
apt-get remove -y build-essential && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
mkdir -p /tmp/download && \
wget -qO - https://download.docker.com/linux/static/stable/x86_64/docker-17.06.2-ce.tgz | tar -xz -C /tmp/download && \
Expand Down Expand Up @@ -69,7 +67,7 @@ RUN chown -R $SLURM_UID:$SLURM_GID "$GALAXY_VENV" && \
. "$GALAXY_VENV"/bin/activate && \
pip install --upgrade pip && \
pip install galaxy-lib && \
pip install -r "$GALAXY_VENV"/requirements.txt --index-url https://wheels.galaxyproject.org/simple && \
pip install -r "$GALAXY_VENV"/requirements.txt --index-url https://wheels.galaxyproject.org/simple --extra-index-url https://pypi.python.org/simple && \
rm -rf ~/.cache/


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3 changes: 2 additions & 1 deletion compose/galaxy-slurm/startup.sh
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Expand Up @@ -16,11 +16,12 @@ fi

if [ ! -f "$SLURM_CONF_PATH" ]
then
mkdir -p /etc/slurm-llnl/
python /usr/local/bin/configure_slurm.py
cp /etc/slurm-llnl/slurm.conf "$SLURM_CONF_PATH"
fi
mkdir -p /tmp/slurm
chown $SLURM_USER_NAME /tmp/slurm
ln -sf "$GALAXY_DIR" "$SYMLINK_TARGET"
ln -sf "$SLURM_CONF_PATH" /etc/slurm-llnl/slurm.conf
exec /usr/local/bin/supervisord -n -c /etc/supervisor/supervisord.conf
exec /usr/bin/supervisord -n -c /etc/supervisor/supervisord.conf
2 changes: 1 addition & 1 deletion compose/galaxy-web/Dockerfile
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Expand Up @@ -27,7 +27,7 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
# apt-get update -qq && apt-get upgrade -y && \
# apt-get update -qq && \
apt-get install --no-install-recommends -y \
nginx-extras nginx-common supervisor autofs libslurm32 libslurmdb32 && \
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Although beyond this PR, it would be really great if things like slurm dependencies could be installable via ansible and then that could be enabled or disabled via injection of arguments on build time.

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@pcm32 are you using the pre-build images or are you building the images on your own again? Or what is your preferred use-case? We could also define those libs via an ENV and create different web containers during build-time - not sure this is a use-case.

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Maybe ourselves building different flavours might be too much trouble to maintain, but I would at least leave the flexibility for the advanced user who knows what is doing. I like the model of the labels that we have, where to add the support for certain things, you need to add that label (ie. k8s,cvmfs, etc). So I would extend that, as man power allows, to other sections (like telegraf, slumr, condor, etc) that are optional requirements depending on how you are using this.

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@bgruening I'm probably still building my own because I need to point to a version of ansible galaxy extras that includes this: galaxyproject/ansible-galaxy-extras#213
On my setup, it fails because uswgi process I think points to that galaxy.yml but that file doesn't exists at that point... the test not passed seems to be unrelated to the logic added on that PR.

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@bgruening in your compose setup works without my PR ansible-galaxy-extras due to https://github.com/bgruening/docker-galaxy-stable/blob/dev/compose/docker-compose.yml#L327 but the current PR (464) is actually removing that line, so the compose setup will need the solution proposed in https://github.com/bgruening/docker-galaxy-stable/blob/dev/compose/docker-compose.yml#L327 I think....

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I removed the mount of galaxy.yml because when you launch docker-compose up, the file doesn't exist yet, so Docker decides to create an empty directory named "galaxy.yml". This makes it impossible later to copy the good galaxy.yml file during startup. So galaxy fails to start because it can't read galaxy.yml.
Mounting a non existing file will never work as it will be considered a directory by docker

nginx-extras nginx-common supervisor autofs slurm-wlm slurm-wlm-torque && \
wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa-dev_1.2.0-dev.deca826_amd64.deb && \
dpkg -i slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
Expand Down