Details

    • Type: Improvement
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      4
    • Sprint:
      Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov

      Description

      Set up test EC2 instance for galaxy project using ansible.

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            sameer Sameer Shanbhag (Inactive) added a comment -

            [~aloraine]

            The setup for Galaxy instance is complete (Currently uses Noor Zahara's Fork | Can be used for testing changes made by her):

            Instance can be found : https://18.204.227.154/

            I had a domain lying around so i used it to point to the same instance so it can be visited at : https://mapcoloring.me/

            Documentation on how to setup the instance : https://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible-galaxy/tutorial.html

            Info:
            Instance will show that the website is not secure as the website is using certbot which creates fake SSL Certificates with "well-known" Algorithm which is used by the Galaxy team to get you started with basic level of SSL configuration. We can add our own SSL certificate and remove the certbot when we deploy it on a production EC2 and a Production ready domain.

            Some Notes:
            The installation looks straightforward but due to limited control on the EC2 there are some "commands" that we have to run manually which are not available in the Documentation.

            Show
            sameer Sameer Shanbhag (Inactive) added a comment - [~aloraine] The setup for Galaxy instance is complete (Currently uses Noor Zahara 's Fork | Can be used for testing changes made by her): Instance can be found : https://18.204.227.154/ I had a domain lying around so i used it to point to the same instance so it can be visited at : https://mapcoloring.me/ Documentation on how to setup the instance : https://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible-galaxy/tutorial.html Info: Instance will show that the website is not secure as the website is using certbot which creates fake SSL Certificates with "well-known" Algorithm which is used by the Galaxy team to get you started with basic level of SSL configuration. We can add our own SSL certificate and remove the certbot when we deploy it on a production EC2 and a Production ready domain. Some Notes: The installation looks straightforward but due to limited control on the EC2 there are some "commands" that we have to run manually which are not available in the Documentation.
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            For the next step, please write a step-by-step "quick start" instructions explaining how another developer do the same.

            Make sure you document the additional steps and customizations you had to do.

            We need a set of instructions explaining to an IGB developer how to set up a Galaxy instance for testing new Galaxy code on EC2.

            The instructions also need to cover updating the instance when we push new code.

            Show
            ann.loraine Ann Loraine added a comment - - edited For the next step, please write a step-by-step "quick start" instructions explaining how another developer do the same. Make sure you document the additional steps and customizations you had to do. We need a set of instructions explaining to an IGB developer how to set up a Galaxy instance for testing new Galaxy code on EC2. The instructions also need to cover updating the instance when we push new code.
            Hide
            sameer Sameer Shanbhag (Inactive) added a comment -

            The Galaxy Instance is up and running:
            https://usegalaxy.bioviz.org/

            I will continue to create a Document on how to run the Playbook.

            Show
            sameer Sameer Shanbhag (Inactive) added a comment - The Galaxy Instance is up and running: https://usegalaxy.bioviz.org/ I will continue to create a Document on how to run the Playbook.
            Hide
            sameer Sameer Shanbhag (Inactive) added a comment -

            I have uploaded the support files for Galaxy Installation and steps on how to set up the instance in the following Github repository:
            https://bitbucket.org/sshanbh1/galaxy-ec2-setup/src/

            Show
            sameer Sameer Shanbhag (Inactive) added a comment - I have uploaded the support files for Galaxy Installation and steps on how to set up the instance in the following Github repository: https://bitbucket.org/sshanbh1/galaxy-ec2-setup/src/
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Nice work!
            I have a couple of change requests:

            • Could you figure out a graceful way to avoid hard-coding the following values in the YML file? Alternatively, include a note in the documentation telling the user that they will need to insert these values, and where they belong.

            galaxy_commit_id: IGBF-32-C
            galaxy_repo: https://github.com/nzahara1/galaxy.git

            • Also, can you change variable name "galaxy_commit_id" to "topic_branch_name" (assuming that's what it means)
            Show
            ann.loraine Ann Loraine added a comment - - edited Nice work! I have a couple of change requests: Could you figure out a graceful way to avoid hard-coding the following values in the YML file? Alternatively, include a note in the documentation telling the user that they will need to insert these values, and where they belong. galaxy_commit_id: IGBF-32 -C galaxy_repo: https://github.com/nzahara1/galaxy.git Also, can you change variable name "galaxy_commit_id" to "topic_branch_name" (assuming that's what it means)
            Hide
            sameer Sameer Shanbhag (Inactive) added a comment -

            The "galaxy_commit_id", "galaxy_repo", etc. are some of the variables required by the ansible scripts created by Developers at Galaxy project and that can't be changed.
            But I can try to find a way to not hardcode these values.

            Show
            sameer Sameer Shanbhag (Inactive) added a comment - The "galaxy_commit_id", "galaxy_repo", etc. are some of the variables required by the ansible scripts created by Developers at Galaxy project and that can't be changed. But I can try to find a way to not hardcode these values.
            Hide
            ann.loraine Ann Loraine added a comment -

            Another question:

            It looks like most of what appears in galaxy-ec2-setup repository has come originally from a Galaxy project repository.
            I'm worried that when they fix bugs or otherwise improve that repository, we will not be able to easily get their updates because our bitbucket repository does not appear to be a fork of theirs.
            If this indeed was originally a clone of a Galaxy project repository, can you give the address of that repository in the README?
            If yes, are you able to add their github repository as a remote and then let your new bitbucket repository track and merge their master branch?
            Let's talk!!

            Show
            ann.loraine Ann Loraine added a comment - Another question: It looks like most of what appears in galaxy-ec2-setup repository has come originally from a Galaxy project repository. I'm worried that when they fix bugs or otherwise improve that repository, we will not be able to easily get their updates because our bitbucket repository does not appear to be a fork of theirs. If this indeed was originally a clone of a Galaxy project repository, can you give the address of that repository in the README? If yes, are you able to add their github repository as a remote and then let your new bitbucket repository track and merge their master branch? Let's talk!!
            Hide
            sameer Sameer Shanbhag (Inactive) added a comment -

            The Files in the role folder get downloaded from the latest code at Ansible Galaxy. I forgot to add that part to the README.md file.
            You need to run "ansible-galaxy install -p roles -r requirements.yml" < this command to get that role folder which has all the automation scripts for the deployment.

            Look at "ansible-galaxy" is a command maintained by Ansible in collaboration with Galaxy and the role files it refers to can be viewed at: https://galaxy.ansible.com/ which is updated regularly.

            I'll make the required changes in the Git Repository and the Readme file regarding ansible-galaxy command.

            Show
            sameer Sameer Shanbhag (Inactive) added a comment - The Files in the role folder get downloaded from the latest code at Ansible Galaxy. I forgot to add that part to the README.md file. You need to run "ansible-galaxy install -p roles -r requirements.yml" < this command to get that role folder which has all the automation scripts for the deployment. Look at "ansible-galaxy" is a command maintained by Ansible in collaboration with Galaxy and the role files it refers to can be viewed at: https://galaxy.ansible.com/ which is updated regularly. I'll make the required changes in the Git Repository and the Readme file regarding ansible-galaxy command.
            Hide
            sameer Sameer Shanbhag (Inactive) added a comment -

            Updated the Git Repository:
            1. Removed Unwanted Files
            2. Updated the README.md file

            Git Repository: https://bitbucket.org/sshanbh1/galaxy-ec2-setup/src/master/

            Show
            sameer Sameer Shanbhag (Inactive) added a comment - Updated the Git Repository: 1. Removed Unwanted Files 2. Updated the README.md file Git Repository: https://bitbucket.org/sshanbh1/galaxy-ec2-setup/src/master/
            Hide
            ann.loraine Ann Loraine added a comment -

            See https://launch.usegalaxy.org/catalog (top one) for image already packaged.
            Should not need to modify anything for HTTP byte range requests. (using uwsgi)

            Show
            ann.loraine Ann Loraine added a comment - See https://launch.usegalaxy.org/catalog (top one) for image already packaged. Should not need to modify anything for HTTP byte range requests. (using uwsgi)
            Hide
            ann.loraine Ann Loraine added a comment -

            see read the docs for API instructions

            Show
            ann.loraine Ann Loraine added a comment - see read the docs for API instructions

              People

              • Assignee:
                sameer Sameer Shanbhag (Inactive)
                Reporter:
                noor91zahara Noor Zahara (Inactive)
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                Watchers:
                3 Start watching this issue

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                  Updated:
                  Resolved: