From 7d834ec35a5b719c1d90dc67cba29b8fa9aa4ed2 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 11 Dec 2018 13:42:27 +0100
Subject: [PATCH 01/38] update galaxyextras 18.09

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index e6612923a..67081dc46 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -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

From 9998785680cfde5f8b2c60f19e5ff5e3cae1e180 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 11 Dec 2018 14:24:39 +0100
Subject: [PATCH 02/38] need munge

---
 compose/galaxy-slurm/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/compose/galaxy-slurm/Dockerfile b/compose/galaxy-slurm/Dockerfile
index fb780ef11..ebbe73e75 100644
--- a/compose/galaxy-slurm/Dockerfile
+++ b/compose/galaxy-slurm/Dockerfile
@@ -14,7 +14,7 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
     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 && \
+        libslurm32 libslurmdb32 munge && \
     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 && \

From beb8440b0c898a3e4ed1f5d2cd3c86802ae9940a Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 11 Dec 2018 14:40:30 +0100
Subject: [PATCH 03/38] fix slurm install

---
 compose/galaxy-slurm/Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/compose/galaxy-slurm/Dockerfile b/compose/galaxy-slurm/Dockerfile
index ebbe73e75..0f660395f 100644
--- a/compose/galaxy-slurm/Dockerfile
+++ b/compose/galaxy-slurm/Dockerfile
@@ -13,13 +13,14 @@ 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" $GALAXY_USER && \
     apt-get update -qq && apt-get install -y --no-install-recommends apt-transport-https \
-        unattended-upgrades python-pip python-psutil supervisor wget build-essential \
-        libslurm32 libslurmdb32 munge && \
+        unattended-upgrades python-pip python-psutil python-setuptools supervisor wget \
+        build-essential libslurm32 libslurmdb32 munge locales && \
     wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
     wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa-dev_1.2.0-dev.deca826_amd64.deb && \
     dpkg -i slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
     dpkg -i slurm-drmaa-dev_1.2.0-dev.deca826_amd64.deb && \
     /usr/sbin/create-munge-key && \
+    mkdir /var/log/slurm-llnl && \
     touch /var/log/slurm-llnl/slurmctld.log /var/log/slurm-llnl/slurmd.log && \
     mkdir /tmp/slurm && pip install --upgrade supervisor virtualenv && \
     wget https://github.com/singularityware/singularity/releases/download/$SINGULARITY_VERSION/singularity-$SINGULARITY_VERSION.tar.gz && \

From 1be3274c25c9c9be248180c96110f96ab0bba193 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 11 Dec 2018 14:50:25 +0100
Subject: [PATCH 04/38] fix requirements install

---
 compose/galaxy-slurm/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/compose/galaxy-slurm/Dockerfile b/compose/galaxy-slurm/Dockerfile
index 0f660395f..7b182ab54 100644
--- a/compose/galaxy-slurm/Dockerfile
+++ b/compose/galaxy-slurm/Dockerfile
@@ -70,7 +70,7 @@ 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/
 
 

From 2efd5251921b18e9ea39e0c5ab240abb389cc419 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 11 Dec 2018 16:39:36 +0100
Subject: [PATCH 05/38] try hack for ansible rule

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 20b3dbb39..a0fc5b388 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -110,6 +110,7 @@ before_install:
 
   # start building this repo
   - git submodule update --init --recursive
+  - sed -i 's|/galaxy.ini|/galaxy.yml|g' galaxy/roles/galaxyprojectdotorg.galaxyextras/defaults/main.yml
   - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
   - |
     if [ "${COMPOSE_SLURM}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${KUBE}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]

From c194c51f89eff91abc6d6d8e2a7ebf70112ccbcb Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 11 Dec 2018 17:03:13 +0100
Subject: [PATCH 06/38] fix for the hack

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a0fc5b388..9baa311dc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -110,7 +110,7 @@ before_install:
 
   # start building this repo
   - git submodule update --init --recursive
-  - sed -i 's|/galaxy.ini|/galaxy.yml|g' galaxy/roles/galaxyprojectdotorg.galaxyextras/defaults/main.yml
+  - sed -i 's|/galaxy.ini|/galaxy.yml|g' ../galaxy/roles/galaxyprojectdotorg.galaxyextras/defaults/main.yml
   - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
   - |
     if [ "${COMPOSE_SLURM}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${KUBE}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]

From 14814930b46b43a99d8e978c306ebb5016e443d2 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 11 Dec 2018 17:08:29 +0100
Subject: [PATCH 07/38] hack for the hack

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 9baa311dc..0e2b1fed2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -110,7 +110,7 @@ before_install:
 
   # start building this repo
   - git submodule update --init --recursive
-  - sed -i 's|/galaxy.ini|/galaxy.yml|g' ../galaxy/roles/galaxyprojectdotorg.galaxyextras/defaults/main.yml
+  - sed -i 's|/galaxy.ini|/galaxy.yml|g' /home/travis/build/abretaud/docker-galaxy-stable/galaxy/roles/galaxyprojectdotorg.galaxyextras/defaults/main.yml
   - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
   - |
     if [ "${COMPOSE_SLURM}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${KUBE}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]

From 5bd1ba5c1e408765f8376de0f3e00dc675829071 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 09:34:26 +0100
Subject: [PATCH 08/38] supervisor stuff

---
 compose/galaxy-slurm/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/compose/galaxy-slurm/Dockerfile b/compose/galaxy-slurm/Dockerfile
index 7b182ab54..2f505af80 100644
--- a/compose/galaxy-slurm/Dockerfile
+++ b/compose/galaxy-slurm/Dockerfile
@@ -22,7 +22,7 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
     /usr/sbin/create-munge-key && \
     mkdir /var/log/slurm-llnl && \
     touch /var/log/slurm-llnl/slurmctld.log /var/log/slurm-llnl/slurmd.log && \
-    mkdir /tmp/slurm && pip install --upgrade supervisor virtualenv && \
+    mkdir /tmp/slurm && 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 && \
@@ -30,7 +30,7 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
     make && \
     make install && \
     rm -rf singularity-$SINGULARITY_VERSION singularity-$SINGULARITY_VERSION.tar.gz && \
-    apt-get remove -y supervisor build-essential && \
+    apt-get remove -y build-essential && \
     mkdir /var/log/supervisor && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
     mkdir -p /tmp/download && \

From 9efc04cda4829eaccaf4f715940ac102411d2ede Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 09:52:23 +0100
Subject: [PATCH 09/38] no need to mkdir

---
 compose/galaxy-slurm/Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/compose/galaxy-slurm/Dockerfile b/compose/galaxy-slurm/Dockerfile
index 2f505af80..178a6084f 100644
--- a/compose/galaxy-slurm/Dockerfile
+++ b/compose/galaxy-slurm/Dockerfile
@@ -31,7 +31,6 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
     make install && \
     rm -rf singularity-$SINGULARITY_VERSION singularity-$SINGULARITY_VERSION.tar.gz && \
     apt-get remove -y build-essential && \
-    mkdir /var/log/supervisor && \
     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 && \

From 2312f4f6d26c2fa7b56495ed1026e09e15a87f52 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 10:30:16 +0100
Subject: [PATCH 10/38] slurm startup fix

---
 compose/galaxy-slurm/startup.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/compose/galaxy-slurm/startup.sh b/compose/galaxy-slurm/startup.sh
index e6ebf8994..799796c6c 100644
--- a/compose/galaxy-slurm/startup.sh
+++ b/compose/galaxy-slurm/startup.sh
@@ -16,6 +16,7 @@ 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
@@ -23,4 +24,4 @@ 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

From b533b207d733d70a9082e7581dcd76f4c9539b14 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 11:57:51 +0100
Subject: [PATCH 11/38] For 18.09 uses migration 142, not 144

---
 compose/galaxy-postgres/init-galaxy-db.sql.in | 190 +-----------------
 1 file changed, 1 insertion(+), 189 deletions(-)

diff --git a/compose/galaxy-postgres/init-galaxy-db.sql.in b/compose/galaxy-postgres/init-galaxy-db.sql.in
index b23916dec..5fa025111 100644
--- a/compose/galaxy-postgres/init-galaxy-db.sql.in
+++ b/compose/galaxy-postgres/init-galaxy-db.sql.in
@@ -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: -
 --
@@ -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: -
 --
@@ -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: -
 --
@@ -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
+Galaxy	lib/galaxy/model/migrate	142
 \.
 
 
@@ -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: -
 --
@@ -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: -
 --
@@ -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: -
 --
@@ -16651,4 +16464,3 @@ ALTER TABLE ONLY workflow_tag_association
 --
 -- PostgreSQL database dump complete
 --
-

From d456e53d3d41683abccdf05ae1cee48ece736467 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 15:23:22 +0100
Subject: [PATCH 12/38] condor fixes

---
 compose/galaxy-htcondor-executor/Dockerfile | 4 ++++
 compose/galaxy-htcondor-executor/startup.sh | 2 --
 compose/galaxy-htcondor/Dockerfile          | 4 ++++
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/compose/galaxy-htcondor-executor/Dockerfile b/compose/galaxy-htcondor-executor/Dockerfile
index 46f4a6e27..d4daf3e78 100644
--- a/compose/galaxy-htcondor-executor/Dockerfile
+++ b/compose/galaxy-htcondor-executor/Dockerfile
@@ -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
 
diff --git a/compose/galaxy-htcondor-executor/startup.sh b/compose/galaxy-htcondor-executor/startup.sh
index cf7f728ab..147a1d417 100644
--- a/compose/galaxy-htcondor-executor/startup.sh
+++ b/compose/galaxy-htcondor-executor/startup.sh
@@ -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
diff --git a/compose/galaxy-htcondor/Dockerfile b/compose/galaxy-htcondor/Dockerfile
index 4c26d3265..59e79cbc7 100644
--- a/compose/galaxy-htcondor/Dockerfile
+++ b/compose/galaxy-htcondor/Dockerfile
@@ -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"]

From 716b859066ebd8ea8d036dd37bfbb5fac39cab02 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 15:23:48 +0100
Subject: [PATCH 13/38] avoid harmless error message

---
 compose/galaxy-init/startup.sh | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/compose/galaxy-init/startup.sh b/compose/galaxy-init/startup.sh
index ef5fd69b1..88e7537d8 100644
--- a/compose/galaxy-init/startup.sh
+++ b/compose/galaxy-init/startup.sh
@@ -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"

From 8f42276150398a41d6ceaf77cbc5b3db33126e72 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 15:24:02 +0100
Subject: [PATCH 14/38] slurm install

---
 compose/galaxy-slurm/Dockerfile | 6 ++----
 compose/galaxy-web/Dockerfile   | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/compose/galaxy-slurm/Dockerfile b/compose/galaxy-slurm/Dockerfile
index 178a6084f..e640f6951 100644
--- a/compose/galaxy-slurm/Dockerfile
+++ b/compose/galaxy-slurm/Dockerfile
@@ -14,15 +14,13 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
     useradd -u $GALAXY_UID -m -r -g $GALAXY_USER -c "Galaxy user" $GALAXY_USER && \
     apt-get update -qq && apt-get install -y --no-install-recommends apt-transport-https \
         unattended-upgrades python-pip python-psutil python-setuptools supervisor wget \
-        build-essential libslurm32 libslurmdb32 munge locales && \
+        build-essential munge locales slurm-wlm slurm-wlm-torque && \
     wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
     wget https://depot.galaxyproject.org/deb/ubuntu/18.04/slurm-drmaa-dev_1.2.0-dev.deca826_amd64.deb && \
     dpkg -i slurm-drmaa1_1.2.0-dev.deca826_amd64.deb && \
     dpkg -i slurm-drmaa-dev_1.2.0-dev.deca826_amd64.deb && \
     /usr/sbin/create-munge-key && \
-    mkdir /var/log/slurm-llnl && \
-    touch /var/log/slurm-llnl/slurmctld.log /var/log/slurm-llnl/slurmd.log && \
-    mkdir /tmp/slurm && pip install --upgrade virtualenv && \
+    pip install --upgrade virtualenv && \
     wget https://github.com/singularityware/singularity/releases/download/$SINGULARITY_VERSION/singularity-$SINGULARITY_VERSION.tar.gz && \
     tar xvf singularity-$SINGULARITY_VERSION.tar.gz && \
     cd singularity-$SINGULARITY_VERSION && \
diff --git a/compose/galaxy-web/Dockerfile b/compose/galaxy-web/Dockerfile
index 8a207fec0..33748be1a 100644
--- a/compose/galaxy-web/Dockerfile
+++ b/compose/galaxy-web/Dockerfile
@@ -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 && \
+    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 && \

From 57dcde9678961efc433b2896f4f389d481a9d5ff Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 16:01:36 +0100
Subject: [PATCH 15/38] fix missing ansible tag

---
 compose/build-orchestration-images.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/compose/build-orchestration-images.sh b/compose/build-orchestration-images.sh
index a56c501d5..95c2db152 100755
--- a/compose/build-orchestration-images.sh
+++ b/compose/build-orchestration-images.sh
@@ -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

From 933b13a1d0a1ea9fc9f83579e5551779e94526cf Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 16:03:46 +0100
Subject: [PATCH 16/38] kube fix?

---
 .travis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 0e2b1fed2..65ea591af 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -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

From 05be0b7e93f5ae9128fc05aa59c7caba039ab2a4 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 12 Dec 2018 17:12:52 +0100
Subject: [PATCH 17/38] not needed

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 65ea591af..71e24511f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -114,7 +114,6 @@ before_install:
 
   # start building this repo
   - git submodule update --init --recursive
-  - sed -i 's|/galaxy.ini|/galaxy.yml|g' /home/travis/build/abretaud/docker-galaxy-stable/galaxy/roles/galaxyprojectdotorg.galaxyextras/defaults/main.yml
   - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
   - |
     if [ "${COMPOSE_SLURM}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${KUBE}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]

From 209b057d878747d97cd5e3a4af98adf2fb658471 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Thu, 13 Dec 2018 09:40:34 +0100
Subject: [PATCH 18/38] move to htcondor-base

---
 compose/galaxy-htcondor-base/Dockerfile     | 5 +++++
 compose/galaxy-htcondor-executor/Dockerfile | 4 ----
 compose/galaxy-htcondor/Dockerfile          | 4 ----
 3 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/compose/galaxy-htcondor-base/Dockerfile b/compose/galaxy-htcondor-base/Dockerfile
index 3087fa2d2..afe67f87e 100644
--- a/compose/galaxy-htcondor-base/Dockerfile
+++ b/compose/galaxy-htcondor-base/Dockerfile
@@ -18,3 +18,8 @@ RUN wget https://dl.influxdata.com/telegraf/releases/telegraf-1.5.0_linux_amd64.
     rm telegraf-1.5.0_linux_amd64.tar.gz
 
 ADD telegraf.conf /etc/telegraf/telegraf.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/
diff --git a/compose/galaxy-htcondor-executor/Dockerfile b/compose/galaxy-htcondor-executor/Dockerfile
index d4daf3e78..46f4a6e27 100644
--- a/compose/galaxy-htcondor-executor/Dockerfile
+++ b/compose/galaxy-htcondor-executor/Dockerfile
@@ -27,10 +27,6 @@ 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
 
diff --git a/compose/galaxy-htcondor/Dockerfile b/compose/galaxy-htcondor/Dockerfile
index 59e79cbc7..4c26d3265 100644
--- a/compose/galaxy-htcondor/Dockerfile
+++ b/compose/galaxy-htcondor/Dockerfile
@@ -3,8 +3,4 @@ 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"]

From edbef97c5fa8f4d9d0f8e54db72b85bccba6d51e Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Thu, 13 Dec 2018 09:50:11 +0100
Subject: [PATCH 19/38] need 18.09 branch of ansible-galaxy-extras

---
 compose/build-orchestration-images.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/compose/build-orchestration-images.sh b/compose/build-orchestration-images.sh
index 95c2db152..1002f4fab 100755
--- a/compose/build-orchestration-images.sh
+++ b/compose/build-orchestration-images.sh
@@ -121,7 +121,7 @@ DOCKER_REPO=${CONTAINER_REGISTRY:-}
 DOCKER_USER=${CONTAINER_USER:-pcm32}
 
 ANSIBLE_REPO=${ANSIBLE_REPO:-galaxyproject/ansible-galaxy-extras}
-ANSIBLE_RELEASE=${ANSIBLE_RELEASE:-master}
+ANSIBLE_RELEASE=${ANSIBLE_RELEASE:-18.09}
 
 GALAXY_VERSION=${GALAXY_VERSION:-18.09}
 

From b50f1d1c122f5b1f35905e0e1ed7a53ff05158e5 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Thu, 13 Dec 2018 15:55:11 +0100
Subject: [PATCH 20/38] need nodejs installed (but can't use the ansible task
 as the galaxy code is not available yet at build time)

---
 compose/galaxy-web/Dockerfile | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/compose/galaxy-web/Dockerfile b/compose/galaxy-web/Dockerfile
index 33748be1a..5394f628b 100644
--- a/compose/galaxy-web/Dockerfile
+++ b/compose/galaxy-web/Dockerfile
@@ -22,11 +22,10 @@ GALAXY_HANDLER_NUMPROCS=2
 
 RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
     apt-get -qq update && apt-get install --no-install-recommends -y apt-transport-https wget && \
-    # echo "deb [arch=amd64] http://ppa.launchpad.net/galaxyproject/nginx/ubuntu trusty main" > /etc/apt/sources.list.d/nginx.list && \
-    # apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 9735427B && \
-    # apt-get update -qq && apt-get upgrade -y && \
-    # apt-get update -qq && \
-    apt-get install --no-install-recommends -y \
+    echo "deb https://deb.nodesource.com/node_9.x $(lsb_release -sc) main" > /etc/apt/sources.list.d/nodejs.list && \
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 68576280 && \
+    apt-get update -qq && \
+    apt-get install --no-install-recommends -y nodejs \
     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 && \

From 95a5d7cb71de1c8adae51bd5684ef027ad70afa6 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Fri, 14 Dec 2018 11:05:38 +0100
Subject: [PATCH 21/38] trigger rebuild


From 33d03bca6d341911ba6bf33c24dc3701ea6782d5 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Fri, 14 Dec 2018 15:01:49 +0100
Subject: [PATCH 22/38] fix error at startup: this line mounted a not-yet
 existing file (created later by galaxy-init). It was mounted as an empty dir,
 so galaxy refused to run. The /usr/bin/startup script will copy the good file
 from $GALAXY_ROOT a bit later during galaxy-web startup, after galaxy-init
 has created it
 (https://github.com/galaxyproject/ansible-galaxy-extras/blob/18.09/templates/startup.sh.j2#L42).

---
 compose/docker-compose.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/compose/docker-compose.yml b/compose/docker-compose.yml
index fa458df04..8517a3dd4 100644
--- a/compose/docker-compose.yml
+++ b/compose/docker-compose.yml
@@ -324,7 +324,6 @@ services:
     volumes:
         # This is the directory where all your files from Galaxy will be stored
         # on your host system
-        - ${EXPORT_DIR:-/export}/galaxy-central/config/galaxy.yml.sample:/etc/galaxy/galaxy.yml
         - ${EXPORT_DIR:-/export}/:/export/
         - /var/run/docker.sock:/var/run/docker.sock
     depends_on:

From 52f92d42d2c67489ffd8cab77ed512620b703ed9 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Fri, 14 Dec 2018 15:33:53 +0100
Subject: [PATCH 23/38] update bioblend testing

---
 test/bioblend/Dockerfile | 2 +-
 test/bioblend/test.sh    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/bioblend/Dockerfile b/test/bioblend/Dockerfile
index 0750accfd..6e44daf75 100644
--- a/test/bioblend/Dockerfile
+++ b/test/bioblend/Dockerfile
@@ -14,7 +14,7 @@ ENV TOX_ENV=py27 \
     BIOBLEND_GALAXY_API_KEY=admin \
     BIOBLEND_GALAXY_URL=http://galaxy
 
-CMD /bin/bash -c "export PATH=/tool_deps/_conda/bin/:$PATH && cd /home/galaxy/bioblend-master && tox -e $TOX_ENV -- -e 'test_download_dataset|test_upload_from_galaxy_filesystem|test_get_datasets|test_datasets_from_fs|test_tool_dependency_install|test_download_history|test_export_and_download'"
+CMD /bin/bash -c "export PATH=/tool_deps/_conda/bin/:$PATH && cd /home/galaxy/bioblend-master && tox -e $TOX_ENV -- -k 'not test_download_dataset and not test_upload_from_galaxy_filesystem and not test_get_datasets and not test_datasets_from_fs and not test_tool_dependency_install and not test_download_history and not test_export_and_download'"
 
 # library tests, needs share /tmp filesystem
 # * test_upload_from_galaxy_filesystem
diff --git a/test/bioblend/test.sh b/test/bioblend/test.sh
index 5eac22fd2..a031967f3 100644
--- a/test/bioblend/test.sh
+++ b/test/bioblend/test.sh
@@ -12,7 +12,7 @@ then
     export BIOBLEND_GALAXY_API_KEY=admin ;
     export BIOBLEND_GALAXY_URL=http://galaxy ;
     cd /home/galaxy/bioblend-master ;
-    tox -e $TOX_ENV -- -e "test_download_dataset|test_upload_from_galaxy_filesystem|test_get_datasets|test_datasets_from_fs|test_existing_history|test_new_history|test_params|test_tool_dependency_install|test_download_history|test_export_and_download"'
+    tox -e $TOX_ENV -- -k "not test_download_dataset and not test_upload_from_galaxy_filesystem and not test_get_datasets and not test_datasets_from_fs and not test_existing_history and not test_new_history and not test_params and not test_tool_dependency_install and not test_download_history and not test_export_and_download"'
 
 else
     docker build -t bioblend_test .

From e938b860f2d0ea2edbc90fe05c8bcc1235283124 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Fri, 14 Dec 2018 17:08:46 +0100
Subject: [PATCH 24/38] fix bioblend test env

---
 test/bioblend/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/bioblend/test.sh b/test/bioblend/test.sh
index a031967f3..381590641 100644
--- a/test/bioblend/test.sh
+++ b/test/bioblend/test.sh
@@ -2,7 +2,7 @@
 if [ "${COMPOSE_SLURM}" ] || [ "${KUBE}" ] || [ "${COMPOSE_CONDOR_DOCKER}" ] || [ "${COMPOSE_SLURM_SINGULARITY}" ]
 then
     docker_exec bash -c 'cd /home/galaxy ;
-    export PATH=/tool_deps/_conda/bin/:$PATH; . activate galaxy_env;
+    . /galaxy_venv/bin/activate ;
     wget https://github.com/galaxyproject/bioblend/archive/master.tar.gz && tar xfz master.tar.gz ;
     cd bioblend-master ;
     pip install --upgrade "tox>=1.8.0" "pep8<=1.6.2" ;

From 7e53dc0edc72b2529593b6ba889e8d63b94d879b Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 11:48:08 +0100
Subject: [PATCH 25/38] fix image tag

---
 compose/dumpsql.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/compose/dumpsql.sh b/compose/dumpsql.sh
index efe6c488d..e18fba5f1 100755
--- a/compose/dumpsql.sh
+++ b/compose/dumpsql.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-TAG=18.09
+TAG=v18.09
 
 # Sets the image of postgres to use
 POSTGRES=postgres:9.6.5

From 5516786d8d7afe7d5cdafcb94ef2cadbd44c503f Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 12:26:02 +0100
Subject: [PATCH 26/38] dump fix

---
 compose/galaxy-postgres/init-galaxy-db.sql.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/compose/galaxy-postgres/init-galaxy-db.sql.in b/compose/galaxy-postgres/init-galaxy-db.sql.in
index 5fa025111..eb19cbb2b 100644
--- a/compose/galaxy-postgres/init-galaxy-db.sql.in
+++ b/compose/galaxy-postgres/init-galaxy-db.sql.in
@@ -16464,3 +16464,4 @@ ALTER TABLE ONLY workflow_tag_association
 --
 -- PostgreSQL database dump complete
 --
+

From 72866eddaa6ccdd8ca08c9fcf4ae1c87b5f08211 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 14:49:51 +0100
Subject: [PATCH 27/38] reenable client building

---
 compose/galaxy-init/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/compose/galaxy-init/Dockerfile b/compose/galaxy-init/Dockerfile
index 7ccd3d1d3..b1b2eab7c 100644
--- a/compose/galaxy-init/Dockerfile
+++ b/compose/galaxy-init/Dockerfile
@@ -98,7 +98,7 @@ RUN export PATH=/tool_deps/_conda/bin/:$PATH && \
     # Install all required Node dependencies. This is required to get proxy support to work for Interactive Environments
     cd $GALAXY_ROOT/lib/galaxy/web/proxy/js && \
     npm install && \
-    ##cd $GALAXY_ROOT/client && yarn install --network-timeout 120000 --check-files && yarn run build-production-maps && \
+    cd $GALAXY_ROOT/client && yarn install --network-timeout 120000 --check-files && yarn run build-production-maps && \
     rm -rf /home/galaxy/.cache/
 
 # Switch back to User root

From c21cfccff70dae64d834953f61d995857ddc5b6e Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 14:50:12 +0100
Subject: [PATCH 28/38] fix slurm_singularity test

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 71e24511f..e86646da4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -179,7 +179,7 @@ before_install:
             sleep 15
             # we are lucky that the out test image has a small bug and always prints a warning. We use this to grep if the tool was running with SINGULARITY
             # WARNING Bind file destination does not exist in container /usr/local/var/singularity/mnt/overlay/final/etc/...
-            parsec datasets show_dataset $OUTPUT_ID | jq .misc_info | grep singularity
+            parsec jobs show_job --full_details $OUTPUT_ID | jq .stderr | grep singularity
 
         fi
 

From 7ec499efa27a36312000b8f708a9edc6612f3100 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 15:32:36 +0100
Subject: [PATCH 29/38] Need to delay setting of GALAXY_CONFIG_TOOL_CONFIG_FILE

---
 .travis.yml                     |  3 +++
 compose/.env_slurm_singularity  |  2 +-
 compose/.env_slurm_singularity2 | 23 +++++++++++++++++++++++
 3 files changed, 27 insertions(+), 1 deletion(-)
 create mode 100644 compose/.env_slurm_singularity2

diff --git a/.travis.yml b/.travis.yml
index e86646da4..3aced9433 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -169,6 +169,9 @@ before_install:
             sudo curl -L -o /export/cat_tool_conf.xml https://github.com/bgruening/singularity-galaxy-tests/raw/master/cat_tool_conf.xml
             sudo curl -L -o /export/cat.xml https://github.com/bgruening/singularity-galaxy-tests/raw/master/cat.xml
 
+            rm .env
+            ln -sf .env_slurm_singularity2 .env
+
             docker-compose up -d
             sleep 60
 
diff --git a/compose/.env_slurm_singularity b/compose/.env_slurm_singularity
index 0dcd70a00..b3481110e 100644
--- a/compose/.env_slurm_singularity
+++ b/compose/.env_slurm_singularity
@@ -15,7 +15,7 @@ GALAXY_RUNNERS_ENABLE_SLURM=True
 # With this Galaxy will search for mulled based images (in /export/database/container_images/singularity/mulled/)
 GALAXY_CONFIG_ENABLE_BETA_MULLED_CONTAINERS=True
 
-GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/shed_tool_conf.xml,/export/cat_tool_conf.xml
+GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/shed_tool_conf.xml
 
 GALAXY_SINGULARITY_VOLUMES=$tool_directory:rw,$working_directory:rw,$default_file_path:rw
 
diff --git a/compose/.env_slurm_singularity2 b/compose/.env_slurm_singularity2
new file mode 100644
index 000000000..0dcd70a00
--- /dev/null
+++ b/compose/.env_slurm_singularity2
@@ -0,0 +1,23 @@
+# This file is setting up a composed Galaxy instance with support
+# for submitting SLURM.
+# Docker compose will use parameters specified in an `.env` file
+# next to the docker-compose.yml file.
+# We recommend to symlink this file and play around with different
+# Galaxy deployments.
+# ln -sf .env_slurm .env
+
+TAG=18.01
+
+# default destination is our SLURM cluster with Singularity enabled
+GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_singularity
+GALAXY_RUNNERS_ENABLE_SLURM=True
+
+# With this Galaxy will search for mulled based images (in /export/database/container_images/singularity/mulled/)
+GALAXY_CONFIG_ENABLE_BETA_MULLED_CONTAINERS=True
+
+GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/shed_tool_conf.xml,/export/cat_tool_conf.xml
+
+GALAXY_SINGULARITY_VOLUMES=$tool_directory:rw,$working_directory:rw,$default_file_path:rw
+
+GALAXY_CONFIG_CLEANUP_JOB=onsuccess
+GALAXY_PORT=8080

From 27ee4ab0fce3bc4c66366ef075b5816b6e36ceea Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 17:07:45 +0100
Subject: [PATCH 30/38] create needed dirs/files for condor

---
 compose/galaxy-base/Dockerfile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/compose/galaxy-base/Dockerfile b/compose/galaxy-base/Dockerfile
index 8c1e1beb3..51ade8aa6 100644
--- a/compose/galaxy-base/Dockerfile
+++ b/compose/galaxy-base/Dockerfile
@@ -81,6 +81,10 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup && \
     rm -rf /tmp/download && \
     rm -rf ~/.cache/
 
+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/
+
 RUN groupadd -r $GALAXY_USER -g $GALAXY_GID && \
     useradd -u $GALAXY_UID -r -g $GALAXY_USER -d $GALAXY_HOME -c "Galaxy user" $GALAXY_USER && \
     mkdir $EXPORT_DIR $GALAXY_LOGS_DIR && chown -R $GALAXY_USER:$GALAXY_USER $GALAXY_HOME $GALAXY_LOGS_DIR $EXPORT_DIR

From 2c0be5203b4559586c6476eafe75feaea817866c Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 17:42:26 +0100
Subject: [PATCH 31/38] update tag

---
 compose/.env_htcondor_docker    | 2 +-
 compose/.env_k8_native          | 2 +-
 compose/.env_slurm              | 2 +-
 compose/.env_slurm_singularity  | 2 +-
 compose/.env_slurm_singularity2 | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/compose/.env_htcondor_docker b/compose/.env_htcondor_docker
index 12182a726..e082eb769 100644
--- a/compose/.env_htcondor_docker
+++ b/compose/.env_htcondor_docker
@@ -6,7 +6,7 @@
 # Galaxy deployments.
 # ln -sf .env_htcondor_docker .env
 
-TAG=18.01
+TAG=18.09
 
 GALAXY_DESTINATIONS_DEFAULT=condor_cluster
 
diff --git a/compose/.env_k8_native b/compose/.env_k8_native
index dccbab79a..f1c4f7c63 100644
--- a/compose/.env_k8_native
+++ b/compose/.env_k8_native
@@ -4,4 +4,4 @@ GALAXY_DESTINATIONS_DOCKER_DEFAULT=k8s_default
 GALAXY_DESTINATIONS_NO_DOCKER_DEFAULT=local_no_container
 GALAXY_CONFIG_CONTAINERS_RESOLVERS_CONFIG_FILE=/export/config/container_resolvers_conf.xml
 
-TAG=18.01
+TAG=18.09
diff --git a/compose/.env_slurm b/compose/.env_slurm
index 7cd741493..11d8abf70 100644
--- a/compose/.env_slurm
+++ b/compose/.env_slurm
@@ -6,7 +6,7 @@
 # Galaxy deployments.
 # ln -sf .env_slurm .env
 
-TAG=18.01
+TAG=18.09
 
 # default destination is our SLURM cluster
 GALAXY_DESTINATIONS_DEFAULT=slurm_cluster
diff --git a/compose/.env_slurm_singularity b/compose/.env_slurm_singularity
index b3481110e..926b6c534 100644
--- a/compose/.env_slurm_singularity
+++ b/compose/.env_slurm_singularity
@@ -6,7 +6,7 @@
 # Galaxy deployments.
 # ln -sf .env_slurm .env
 
-TAG=18.01
+TAG=18.09
 
 # default destination is our SLURM cluster with Singularity enabled
 GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_singularity
diff --git a/compose/.env_slurm_singularity2 b/compose/.env_slurm_singularity2
index 0dcd70a00..83c6d3134 100644
--- a/compose/.env_slurm_singularity2
+++ b/compose/.env_slurm_singularity2
@@ -6,7 +6,7 @@
 # Galaxy deployments.
 # ln -sf .env_slurm .env
 
-TAG=18.01
+TAG=18.09
 
 # default destination is our SLURM cluster with Singularity enabled
 GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_singularity

From 40b74acd413bcaae64f527bb980310b9dcac91e6 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 17:43:50 +0100
Subject: [PATCH 32/38] latest kubernetes needs go >=1.11.1

---
 .travis.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3aced9433..a86a92182 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -45,10 +45,10 @@ before_install:
     if [ "${KUBE}" ]
     then
       # setup k8s, we will do this before building Galaxy because it takes some time and hopefully we can do both in prallel
-      gimme 1.8
-      source ~/.gimme/envs/go1.8.env
-      sudo ln -s /home/travis/.gimme/versions/go1.7.linux.amd64/bin/gofmt /usr/bin/gofmt
-      sudo ln -s /home/travis/.gimme/versions/go1.7.linux.amd64/bin/go /usr/bin/go
+      gimme 1.11.1
+      source ~/.gimme/envs/go1.11.1.env
+      sudo ln -s /home/travis/.gimme/versions/go1.11.1.linux.amd64/bin/gofmt /usr/bin/gofmt
+      sudo ln -s /home/travis/.gimme/versions/go1.11.1.linux.amd64/bin/go /usr/bin/go
       go version
       mkdir ../kubernetes
       wget -q -O - https://github.com/kubernetes/kubernetes/archive/master.tar.gz | tar xzf - --strip-components=1 -C ../kubernetes

From 7beba07a3f3dbccdd80af95eed372a95d793971e Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 18 Dec 2018 17:44:55 +0100
Subject: [PATCH 33/38] fix path problem (not sure if sudo is really needed)

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a86a92182..22f1923b5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -59,7 +59,7 @@ before_install:
       sudo ln -s `pwd`/third_party/etcd/etcd /usr/bin/etcd
       sudo ln -s `pwd`/third_party/etcd/etcdctl /usr/bin/etcdctl
       # this needs to run in backgroud later, for now try to see the output
-      sudo ./hack/local-up-cluster.sh &
+      ./hack/local-up-cluster.sh &
       cd ../docker-galaxy-stable
     fi
 

From bb3083d95c27f6975d7ae02ae899bfaf418f2202 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <abretaud@irisa.fr>
Date: Tue, 18 Dec 2018 18:53:41 +0100
Subject: [PATCH 34/38] longer timeout

---
 test/bioblend/test.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/bioblend/test.sh b/test/bioblend/test.sh
index 381590641..aeefa876d 100644
--- a/test/bioblend/test.sh
+++ b/test/bioblend/test.sh
@@ -11,6 +11,7 @@ then
     export TOX_ENV=py27 ;
     export BIOBLEND_GALAXY_API_KEY=admin ;
     export BIOBLEND_GALAXY_URL=http://galaxy ;
+    export BIOBLEND_TEST_JOB_TIMEOUT="120";
     cd /home/galaxy/bioblend-master ;
     tox -e $TOX_ENV -- -k "not test_download_dataset and not test_upload_from_galaxy_filesystem and not test_get_datasets and not test_datasets_from_fs and not test_existing_history and not test_new_history and not test_params and not test_tool_dependency_install and not test_download_history and not test_export_and_download"'
 

From 83e2f2458b2ded8dab50bc5e7d272c56085f086d Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <abretaud@irisa.fr>
Date: Tue, 18 Dec 2018 18:54:04 +0100
Subject: [PATCH 35/38] Longer timeout

---
 test/bioblend/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/bioblend/Dockerfile b/test/bioblend/Dockerfile
index 6e44daf75..2374df727 100644
--- a/test/bioblend/Dockerfile
+++ b/test/bioblend/Dockerfile
@@ -12,7 +12,8 @@ RUN wget https://github.com/galaxyproject/bioblend/archive/master.tar.gz && tar
 
 ENV TOX_ENV=py27 \
     BIOBLEND_GALAXY_API_KEY=admin \
-    BIOBLEND_GALAXY_URL=http://galaxy
+    BIOBLEND_GALAXY_URL=http://galaxy \
+    BIOBLEND_TEST_JOB_TIMEOUT="120"
 
 CMD /bin/bash -c "export PATH=/tool_deps/_conda/bin/:$PATH && cd /home/galaxy/bioblend-master && tox -e $TOX_ENV -- -k 'not test_download_dataset and not test_upload_from_galaxy_filesystem and not test_get_datasets and not test_datasets_from_fs and not test_tool_dependency_install and not test_download_history and not test_export_and_download'"
 

From 1cf32151926fa670f8b6e9f8e61e01b68f22c810 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 19 Dec 2018 10:01:47 +0100
Subject: [PATCH 36/38] fix ignored BIOBLEND_TEST_JOB_TIMEOUT

---
 test/bioblend/Dockerfile | 3 ++-
 test/bioblend/test.sh    | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/test/bioblend/Dockerfile b/test/bioblend/Dockerfile
index 2374df727..fb353d660 100644
--- a/test/bioblend/Dockerfile
+++ b/test/bioblend/Dockerfile
@@ -8,7 +8,8 @@ RUN wget https://github.com/galaxyproject/bioblend/archive/master.tar.gz && tar
     export PATH=/tool_deps/_conda/bin/:$PATH && . activate galaxy_env && \
     pip install --upgrade "tox>=1.8.0" "pep8<=1.6.2" && \
     python setup.py install && \
-    sed -i.bak "s/commands.*$/commands =/" tox.ini
+    sed -i.bak "s/commands.*$/commands =/" tox.ini && \
+    sed -i.bak2 "s/GALAXY_VERSION/GALAXY_VERSION BIOBLEND_TEST_JOB_TIMEOUT/" tox.ini
 
 ENV TOX_ENV=py27 \
     BIOBLEND_GALAXY_API_KEY=admin \
diff --git a/test/bioblend/test.sh b/test/bioblend/test.sh
index aeefa876d..fa683b8b3 100644
--- a/test/bioblend/test.sh
+++ b/test/bioblend/test.sh
@@ -8,6 +8,7 @@ then
     pip install --upgrade "tox>=1.8.0" "pep8<=1.6.2" ;
     python setup.py install ;
     sed -i.bak "s/commands.*$/commands =/" tox.ini ;
+    sed -i.bak2 "s/GALAXY_VERSION/GALAXY_VERSION BIOBLEND_TEST_JOB_TIMEOUT/" tox.ini ;
     export TOX_ENV=py27 ;
     export BIOBLEND_GALAXY_API_KEY=admin ;
     export BIOBLEND_GALAXY_URL=http://galaxy ;

From 76185aa6f96b0cc29399c981bbb693b31e5e9402 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 19 Dec 2018 11:06:53 +0100
Subject: [PATCH 37/38] wait more!?

---
 test/bioblend/Dockerfile | 2 +-
 test/bioblend/test.sh    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/bioblend/Dockerfile b/test/bioblend/Dockerfile
index fb353d660..2dccfcd76 100644
--- a/test/bioblend/Dockerfile
+++ b/test/bioblend/Dockerfile
@@ -14,7 +14,7 @@ RUN wget https://github.com/galaxyproject/bioblend/archive/master.tar.gz && tar
 ENV TOX_ENV=py27 \
     BIOBLEND_GALAXY_API_KEY=admin \
     BIOBLEND_GALAXY_URL=http://galaxy \
-    BIOBLEND_TEST_JOB_TIMEOUT="120"
+    BIOBLEND_TEST_JOB_TIMEOUT="240"
 
 CMD /bin/bash -c "export PATH=/tool_deps/_conda/bin/:$PATH && cd /home/galaxy/bioblend-master && tox -e $TOX_ENV -- -k 'not test_download_dataset and not test_upload_from_galaxy_filesystem and not test_get_datasets and not test_datasets_from_fs and not test_tool_dependency_install and not test_download_history and not test_export_and_download'"
 
diff --git a/test/bioblend/test.sh b/test/bioblend/test.sh
index fa683b8b3..1f84d7add 100644
--- a/test/bioblend/test.sh
+++ b/test/bioblend/test.sh
@@ -12,7 +12,7 @@ then
     export TOX_ENV=py27 ;
     export BIOBLEND_GALAXY_API_KEY=admin ;
     export BIOBLEND_GALAXY_URL=http://galaxy ;
-    export BIOBLEND_TEST_JOB_TIMEOUT="120";
+    export BIOBLEND_TEST_JOB_TIMEOUT="240";
     cd /home/galaxy/bioblend-master ;
     tox -e $TOX_ENV -- -k "not test_download_dataset and not test_upload_from_galaxy_filesystem and not test_get_datasets and not test_datasets_from_fs and not test_existing_history and not test_new_history and not test_params and not test_tool_dependency_install and not test_download_history and not test_export_and_download"'
 

From e5b586febeb1b1f878053b1243d89ddd82670981 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Wed, 19 Dec 2018 14:00:44 +0100
Subject: [PATCH 38/38] update kompose

---
 .travis.yml                    | 2 +-
 compose/galaxy-init/Dockerfile | 5 -----
 2 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 22f1923b5..27f98763c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -107,7 +107,7 @@ before_install:
         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
+        curl -L https://github.com/kubernetes-incubator/kompose/releases/download/v1.17.1/kompose-linux-amd64 -o kompose
         chmod +x kompose
         sudo mv ./kompose /usr/bin/kompose
     fi
diff --git a/compose/galaxy-init/Dockerfile b/compose/galaxy-init/Dockerfile
index b1b2eab7c..975212a12 100644
--- a/compose/galaxy-init/Dockerfile
+++ b/compose/galaxy-init/Dockerfile
@@ -65,11 +65,6 @@ RUN ansible-playbook /ansible/provision.yml \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
     chown -R $GALAXY_USER:$GALAXY_USER $GALAXY_HOME $EXPORT_DIR $GALAXY_LOGS_DIR
 
-#--extra-vars galaxy_extras_config_container_resolution=True \
-#--extra-vars container_resolution_explicit=True \
-#--extra-vars container_resolution_cached_mulled=False \
-#--extra-vars container_resolution_build_mulled=False \
-
 
 # The following commands will be executed as User galaxy
 USER galaxy