Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

unarchive -> get_url; unarchive #24

Open
wants to merge 9 commits into
base: master
Choose a base branch
from
Open

unarchive -> get_url; unarchive #24

Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
94fb2a5
Merge pull request #1 from dnanexus-rnd/master
tomkinsc Jul 31, 2018
4e3070f
cast n_streaming_threads to int
tomkinsc Jul 31, 2018
f411afc
Merge pull request #2 from tomkinsc/ct-cast-n_streaming_threads
tomkinsc Jul 31, 2018
be86229
Merge pull request #3 from dnanexus-rnd/master
tomkinsc Aug 28, 2018
8d385cf
migrate from unarchive -> get_url
tomkinsc Aug 28, 2018
0b7b6b8
etc -> opt
tomkinsc Sep 14, 2018
246fe00
remote_src=yes
tomkinsc Sep 14, 2018
177dc37
unquote ints stored in config file
tomkinsc Nov 9, 2018
64a52e4
Merge pull request #4 from tomkinsc/unquote-ints
tomkinsc Nov 9, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
48 changes: 33 additions & 15 deletions tasks/main.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,19 @@
---
# Install Dx-toolkit
- name: Get DX tarball
unarchive:
src: https://wiki.dnanexus.com/images/files/dx-toolkit-current-ubuntu-14.04-amd64.tar.gz
remote_src: yes
dest: /opt/
get_url:
url: https://wiki.dnanexus.com/images/files/dx-toolkit-current-ubuntu-16.04-amd64.tar.gz
dest: /opt/dx-toolkit-current-ubuntu-16.04-amd64.tar.gz
mode: 0740
timeout: 600

- name: unpack DX tarball
unarchive: src=/opt/dx-toolkit-current-ubuntu-16.04-amd64.tar.gz dest=/opt/ remote_src=yes

- name: Remove DX tarball
file:
state: absent
path: /opt/dx-toolkit-current-ubuntu-16.04-amd64.tar.gz

# http://stackoverflow.com/questions/22256884/not-possible-to-source-bashrc-with-ansible
- name: check dx version
Expand All @@ -21,11 +30,20 @@
- name: Create folder to house upload agent
file: path=/opt/dnanexus-upload-agent state=directory mode=0755

- name: Download and unzip UA tarball
unarchive:
src: https://wiki.dnanexus.com/images/files/dnanexus-upload-agent-1.5.10-linux.tar.gz
dest: /opt/dnanexus-upload-agent
copy: no
- name: Get UA tarball
get_url:
url: https://wiki.dnanexus.com/images/files/dnanexus-upload-agent-current-linux.tar.gz
dest: /opt/dnanexus-upload-agent-current-linux.tar.gz
mode: 0740
timeout: 600

- name: unpack UA tarball
unarchive: src=/opt/dnanexus-upload-agent-current-linux.tar.gz dest=/opt/dnanexus-upload-agent remote_src=yes

- name: Remove UA tarball
file:
state: absent
path: /opt/dnanexus-upload-agent-current-linux.tar.gz

- name: Move ua executable to un-versioned folder location for ease of reference
shell: mv /opt/dnanexus-upload-agent/*/* /opt/dnanexus-upload-agent/
Expand Down Expand Up @@ -104,21 +122,21 @@
when: item.run_length is defined

- name: Change multiplier of run_times to wait
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_seq_intervals:.*' line='n_seq_intervals: \"{{ item.n_seq_intervals }}\"'"
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_seq_intervals:.*' line='n_seq_intervals: {{ item.n_seq_intervals }}'"
with_items: "{{ monitored_users }}"
become: yes
become_user: "{{ item.username }}"
when: item.n_seq_intervals is defined

- name: Change number of retries for incremental_upload
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_retries:.*' line='n_retries: \"{{ item.n_retries }}\"'"
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_retries:.*' line='n_retries: {{ item.n_retries }}'"
with_items: "{{ monitored_users }}"
become: yes
become_user: "{{ item.username }}"
when: item.n_retries is defined

- name: Change number of upload threads for UA
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_upload_threads:.*' line='n_upload_threads: \"{{ item.n_upload_threads }}\"'"
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_upload_threads:.*' line='n_upload_threads: {{ item.n_upload_threads }}'"
with_items: "{{ monitored_users }}"
become: yes
become_user: "{{ item.username }}"
Expand All @@ -135,21 +153,21 @@
when: item.downstream_input is defined

- name: Change specification for minimum upload size
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^min_size:.*' line='min_size: \"{{ item.min_size }}\"'"
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^min_size:.*' line='min_size: {{ item.min_size }}'"
with_items: "{{ monitored_users }}"
become: yes
become_user: "{{ item.username }}"
when: item.min_size is defined

- name: Change specification for minimum sync interval
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^min_interval:.*' line='min_interval: \"{{ item.min_interval }}\"'"
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^min_interval:.*' line='min_interval: {{ item.min_interval }}'"
with_items: "{{ monitored_users }}"
become: yes
become_user: "{{ item.username }}"
when: item.min_interval is defined

- name: Change specification for number of concurrent uploads
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_streaming_threads:.*' line='n_streaming_threads: \"{{ item.n_streaming_threads }}\"'"
lineinfile: "dest=~/dnanexus/config/monitor_runs.config regexp='^n_streaming_threads:.*' line='n_streaming_threads: {{ item.n_streaming_threads }}'"
with_items: "{{ monitored_users }}"
become: yes
become_user: "{{ item.username }}"
Expand Down