From fa9f5325dd3262af5fc49264537647a45edb0abb Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 24 May 2018 23:39:05 -0400 Subject: [PATCH 1/4] More testing... --- .../templates/check-planemo-machine.sh.j2 | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 b/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 index 2b81cf9..2b817fc 100644 --- a/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 +++ b/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 @@ -40,10 +40,17 @@ supervisorctl status nginx | grep -q RUNNING echo "Checking GIE proxy is running." supervisorctl status galaxy:galaxy_nodejs_proxy | grep -q RUNNING -## TODO: Move linuxbrew & miniconda stuff from .bashrc to .profile I guess? +## TODO: Move miniconda stuff from .bashrc to .profile I guess? ## su -l {{ dev_user_name }} /bin/bash -c 'planemo --help' su -l {{ dev_user_name }} /bin/bash -c '{{ dev_planemo_virtualenv }}/bin/planemo --help' +DOC_TEST_RUNNER="https://raw.githubusercontent.com/galaxyproject/planemo/master/scripts/run_doc_test.sh" +curl -s "$DOC_TEST_RUNNER" /tmp/run_doc_test.sh +su -l {{ dev_user_name }} /bin/bash -c "PLANEMO_VIRTUAL_ENV={{ dev_planemo_virtualenv }} DOCS=building bash /tmp/run_doc_test.sh" +su -l {{ dev_user_name }} /bin/bash -c "PLANEMO_VIRTUAL_ENV={{ dev_planemo_virtualenv }} DOCS=building_cwl bash /tmp/run_doc_test.sh" +su -l {{ dev_user_name }} /bin/bash -c "PLANEMO_VIRTUAL_ENV={{ dev_planemo_virtualenv }} DOCS=conda bash /tmp/run_doc_test.sh" +su -l {{ dev_user_name }} /bin/bash -c "PLANEMO_VIRTUAL_ENV={{ dev_planemo_virtualenv }} DOCS=conda_cwl bash /tmp/run_doc_test.sh" + ## TODO: Check Conda in the future. # echo "Checking if Docker is running." # docker ps From 560f47bf933b1b823a491019ee64c2b2ad3fd3ed Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 25 May 2018 08:34:41 -0400 Subject: [PATCH 2/4] Fix. --- .../templates/check-planemo-machine.sh.j2 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 b/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 index 2b817fc..883f69d 100644 --- a/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 +++ b/roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2 @@ -1,4 +1,4 @@ -#/bin/sh +#/bin/bash set -e @@ -45,7 +45,7 @@ supervisorctl status galaxy:galaxy_nodejs_proxy | grep -q RUNNING su -l {{ dev_user_name }} /bin/bash -c '{{ dev_planemo_virtualenv }}/bin/planemo --help' DOC_TEST_RUNNER="https://raw.githubusercontent.com/galaxyproject/planemo/master/scripts/run_doc_test.sh" -curl -s "$DOC_TEST_RUNNER" /tmp/run_doc_test.sh +curl -s "$DOC_TEST_RUNNER" > /tmp/run_doc_test.sh su -l {{ dev_user_name }} /bin/bash -c "PLANEMO_VIRTUAL_ENV={{ dev_planemo_virtualenv }} DOCS=building bash /tmp/run_doc_test.sh" su -l {{ dev_user_name }} /bin/bash -c "PLANEMO_VIRTUAL_ENV={{ dev_planemo_virtualenv }} DOCS=building_cwl bash /tmp/run_doc_test.sh" su -l {{ dev_user_name }} /bin/bash -c "PLANEMO_VIRTUAL_ENV={{ dev_planemo_virtualenv }} DOCS=conda bash /tmp/run_doc_test.sh" From 598fa15214bfe480a34eb597997bbb1a34946ec6 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 29 May 2018 10:30:04 -0400 Subject: [PATCH 3/4] Updates for building latest Ubuntu container. --- Makefile | 4 ++-- packer.json | 10 +++++----- packer.yaml | 4 ++-- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/Makefile b/Makefile index 2a730c1..4cc1507 100644 --- a/Makefile +++ b/Makefile @@ -14,8 +14,8 @@ init: git submodule init && git submodule update setup-venv: - if [ -f $(VENV) ]; then virtualenv $(VENV); fi; - $(IN_VENV) pip install -r requirements.txt && pip install -r dev-requirements.txt + if [ ! -f $(VENV) ]; then virtualenv $(VENV); fi; + $(IN_VENV) pip install -r requirements.txt packer: $(IN_VENV) python yaml-to-json.py --force packer.yaml diff --git a/packer.json b/packer.json index 03dee8a..c07588b 100644 --- a/packer.json +++ b/packer.json @@ -30,7 +30,7 @@ "builders": [ { "guest_additions_path": "VBoxGuestAdditions_{{.Version}}.iso", - "iso_url": "http://releases.ubuntu.com/16.04/ubuntu-16.04.3-server-amd64.iso", + "iso_url": "http://releases.ubuntu.com/16.04/ubuntu-16.04.4-server-amd64.iso", "ssh_port": 22, "ssh_username": "{{ user `username` }}", "iso_checksum_type": "sha256", @@ -83,7 +83,7 @@ ], "guest_os_type": "Ubuntu_64", "name": "virtualbox-iso", - "iso_checksum": "a06cd926f5855d4f21fb4bc9978a35312f815fbda0d0ef7fdc846861f4fc4600", + "iso_checksum": "0a03608988cfd2e50567990dc8be96fb3c501e198e2e6efcb846d89efc7b89f2", "boot_wait": "10s", "http_directory": "http", "headless": true, @@ -93,7 +93,7 @@ }, { "guest_additions_path": "VBoxGuestAdditions_{{.Version}}.iso", - "iso_url": "http://releases.ubuntu.com/16.04/ubuntu-16.04.3-server-amd64.iso", + "iso_url": "http://releases.ubuntu.com/16.04/ubuntu-16.04.4-server-amd64.iso", "ssh_port": 22, "ssh_username": "{{ user `username` }}", "iso_checksum_type": "sha256", @@ -146,7 +146,7 @@ ], "guest_os_type": "Ubuntu_64", "name": "virtualbox-iso-vagrant", - "iso_checksum": "a06cd926f5855d4f21fb4bc9978a35312f815fbda0d0ef7fdc846861f4fc4600", + "iso_checksum": "0a03608988cfd2e50567990dc8be96fb3c501e198e2e6efcb846d89efc7b89f2", "boot_wait": "10s", "http_directory": "http", "headless": true, @@ -286,4 +286,4 @@ ] } ] -} +} \ No newline at end of file diff --git a/packer.yaml b/packer.yaml index 97cc718..b08ee92 100644 --- a/packer.yaml +++ b/packer.yaml @@ -54,9 +54,9 @@ builders: guest_os_type: Ubuntu_64 headless: true http_directory: http - iso_checksum: a06cd926f5855d4f21fb4bc9978a35312f815fbda0d0ef7fdc846861f4fc4600 + iso_checksum: 0a03608988cfd2e50567990dc8be96fb3c501e198e2e6efcb846d89efc7b89f2 iso_checksum_type: sha256 - iso_url: http://releases.ubuntu.com/16.04/ubuntu-16.04.3-server-amd64.iso + iso_url: http://releases.ubuntu.com/16.04/ubuntu-16.04.4-server-amd64.iso shutdown_command: echo 'shutdown -P now' > shutdown.sh; echo '{{ user `username` }}'|sudo -S sh 'shutdown.sh' ssh_password: '{{ user `password` }}' ssh_port: 22 From 0d7b33bbdb9284ca6a86d7effbb9562d42d43b66 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 29 May 2018 10:30:21 -0400 Subject: [PATCH 4/4] Add optional planemo dependency for doctests. --- roles/galaxyprojectdotorg.devbox/tasks/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/roles/galaxyprojectdotorg.devbox/tasks/main.yml b/roles/galaxyprojectdotorg.devbox/tasks/main.yml index 484443a..320003e 100644 --- a/roles/galaxyprojectdotorg.devbox/tasks/main.yml +++ b/roles/galaxyprojectdotorg.devbox/tasks/main.yml @@ -125,10 +125,10 @@ become_user: "{{ dev_user_name }}" shell: "virtualenv {{ dev_planemo_virtualenv }}" -- name: Install planemo +- name: Install planemo and optional dependencies become: True become_user: "{{ dev_user_name }}" - shell: ". {{ dev_planemo_virtualenv }}/bin/activate && pip install planemo" + shell: ". {{ dev_planemo_virtualenv }}/bin/activate && pip install toil && pip install planemo" - name: Setup planemo virtualenv on PATH lineinfile: "dest={{ dev_user_shellrc }} line='export PATH=$PATH:{{ dev_planemo_virtualenv }}/bin'"