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Initial Documentation Testing #119

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Initial Documentation Testing #119

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fa9f532
More testing...
jmchilton May 25, 2018
560f47b
Fix.
jmchilton May 25, 2018
598fa15
Updates for building latest Ubuntu container.
jmchilton May 29, 2018
0d7b33b
Add optional planemo dependency for doctests.
jmchilton May 29, 2018
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4 changes: 2 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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10 changes: 5 additions & 5 deletions packer.json
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Expand Up @@ -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",
Expand Down Expand Up @@ -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,
Expand All @@ -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",
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -286,4 +286,4 @@
]
}
]
}
}
4 changes: 2 additions & 2 deletions packer.yaml
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions roles/galaxyprojectdotorg.devbox/tasks/main.yml
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Expand Up @@ -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'"
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11 changes: 9 additions & 2 deletions roles/galaxyprojectdotorg.devbox/templates/check-planemo-machine.sh.j2
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@@ -1,4 +1,4 @@
#/bin/sh
#/bin/bash

set -e

Expand Down Expand Up @@ -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