Merge pull request #540 from bgruening/19.09

19.09 release

Author: bgruening

.travis.yml

@@ -1,14 +1,14 @@
 sudo: required
 
 language: python
-python: 2.7
+python: 3.6
 
 services:
   - docker
 
 env:
   matrix:
-    - TOX_ENV=py27
+    - TOX_ENV=py36
     - COMPOSE_SLURM=True
     - COMPOSE_SLURM_SINGULARITY=True
     # Compose version with Condor submitting Docker jobs
@@ -146,7 +146,7 @@ before_install:
         ./build-orchestration-images.sh --no-push --condor --grafana --slurm --k8s
         source ./tags-for-compose-to-source.sh
 
-        container_size_check   quay.io/bgruening/galaxy-base:$TAG               350 
+        container_size_check   quay.io/bgruening/galaxy-base:$TAG               350
         container_size_check   quay.io/bgruening/galaxy-web:$TAG                650
         container_size_check   quay.io/bgruening/galaxy-htcondor-base:$TAG      280
 

compose/galaxy-grafana/requirements.txt

@@ -2,7 +2,7 @@
 bx-python==0.7.3
 MarkupSafe==0.23
 pyyaml>=4.2b1
-SQLAlchemy==1.0.15
+SQLAlchemy==1.3.0
 mercurial==4.1.3
 numpy==1.9.2
 pycrypto==2.6.1
@@ -64,7 +64,7 @@ pyparsing==2.1.1
 # Fabric and dependencies
 Fabric==1.10.2
 paramiko>=2.0.9
-ecdsa==0.13
+ecdsa==0.13.3
 
 # Flexible BAM index naming
 pysam==0.8.4+gx5

compose/galaxy-slurm/requirements.txt

@@ -2,8 +2,8 @@
 bx-python==0.7.3
 MarkupSafe==0.23
 pyyaml>=4.2b1
-SQLAlchemy==1.0.15
-mercurial==3.7.3
+SQLAlchemy==1.3.0
+mercurial==4.1.3
 numpy==1.9.2
 pycrypto==2.6.1
 

galaxy/Dockerfile

@@ -16,7 +16,7 @@ MAINTAINER Björn A. Grüning, [email protected]
 ARG GALAXY_RELEASE
 ARG GALAXY_REPO
 
-ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_19.05} \
+ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_19.09} \
 GALAXY_REPO=${GALAXY_REPO:-https://github.com/galaxyproject/galaxy} \
 GALAXY_ROOT=/galaxy-central \
 GALAXY_CONFIG_DIR=/etc/galaxy \
@@ -286,8 +286,9 @@ ADD welcome.html $GALAXY_CONFIG_DIR/web/welcome.html
     #npm install && \
     #rm -rf ~/.cache/ $GALAXY_ROOT/client/node_modules/
 
-# change the default location of shed_tools to be ../shed_tools
-RUN sed -i 's|database|..|' $GALAXY_ROOT/config/shed_tool_conf.xml
+# This is a dead symlink in 19.09, triggering an error when creating /export at startup
+# See https://github.com/galaxyproject/galaxy/pull/9292
+RUN rm /galaxy-central/lib/galaxy/web/framework/static/toolshed/src
 
 # Switch back to User root
 USER root

galaxy/roles/galaxyprojectdotorg.galaxyextras

@@ -1,13 +1,16 @@
 FROM quay.io/bgruening/galaxy
 
+RUN apt-get -qq update && apt-get install --no-install-recommends -y python3-distutils \
+    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/
+
 USER galaxy
 WORKDIR /home/galaxy
 
-ENV TOX_ENV=py27 \
+ENV TOX_ENV=py36 \
     BIOBLEND_GALAXY_API_KEY=admin \
     BIOBLEND_GALAXY_URL=http://galaxy \
     BIOBLEND_TEST_JOB_TIMEOUT="240" \
-    GALAXY_VERSION=release_19.05
+    GALAXY_VERSION=release_19.09
 
 RUN mkdir bioblend-master \
     && curl -L -s https://github.com/galaxyproject/bioblend/archive/master.tar.gz | tar xzf - --strip-components=1 -C bioblend-master \

test/bioblend/Dockerfile

@@ -9,11 +9,11 @@ then
     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 TOX_ENV=py36 ;
     export BIOBLEND_GALAXY_API_KEY=admin ;
     export BIOBLEND_GALAXY_URL=http://galaxy ;
     export BIOBLEND_TEST_JOB_TIMEOUT="240";
-    export GALAXY_VERSION=release_19.05;
+    export GALAXY_VERSION=release_19.09;
     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"'