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| [[Category:Infrastructure]][[Category:Docs]][[Category:Revision Control]] | | [[Category:Software]][[Category:Revision Control]] |
| =Using UFRC Git Server=
| | {|<!--CONFIGURATION: REQUIRED--> |
| '''Note:''' Use git.ufhpc hostname from inside HiPerGator and git.rc.ufl.edu from the outside when cloning any repository from the UFRC Git Server.
| | |{{#vardefine:app|git}} |
| ==Request a group Git archive== | | |{{#vardefine:url|https://git-scm.com/}} |
| This is the first step. As a result the group will have a Git archive on the UFRC Git server that they can add any number of repositories to and have full control of access privileges and membership.
| | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> |
| | |{{#vardefine:conf|}} <!--CONFIGURATION--> |
| | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
| | |{{#vardefine:job|}} <!--JOB SCRIPTS--> |
| | |{{#vardefine:policy|}} <!--POLICY--> |
| | |{{#vardefine:testing|}} <!--PROFILING--> |
| | |{{#vardefine:faq|}} <!--FAQ--> |
| | |{{#vardefine:citation|}} <!--CITATION--> |
| | |{{#vardefine:installation|}} <!--INSTALLATION--> |
| | |} |
| | <!--BODY--> |
| | <!--Description--> |
| | {{#if: {{#var: url}}| |
| | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
|
| |
|
| As an example we'll use the ''awesome'' group, administrative user (set up by UFRC staff) ''admin'' and a regular user ''student''.
| | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. |
|
| |
|
| * Open a support ticket in the [http://support.rc.ufl.edu UFRC Support]] ticket system with a name like "Create an UFRC Git repository for the "Awesome" group.
| | Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows. |
| * List your projected git usage:
| |
|
| |
|
| #What group will be accessing it.
| | <!--Modules--> |
| #Who would be the group administrator (username).
| | ==Environment Modules== |
| #How soon you need it set up.
| | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| #How much space you need i.e. what type of content is going to be stored in the repository. | | ==System Variables== |
| #The uptime requirements i.e. whether the occasional downtime is acceptable.
| | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| #Where the repository administrator's public ssh key can be found (you can paste it into the support ticket). | |
|
| |
|
| * Assuming that your usage pattern falls within the limits of our resources we'll create a repository 'awesome' on git.rc.ufl.edu and configure it for the administrator. After that the administrator 'admin' can do the following:
| | <!--Configuration--> |
| | {{#if: {{#var: conf}}|==Configuration== |
| | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. |
| | |}} |
| | <!--Run--> |
| | {{#if: {{#var: exe}}|==Additional Information== |
|
| |
|
| ==Repository Administration==
| | UFRC git environment module also contains a 'git-lfs' instance, so you can run 'git lfs ...' after loading the git environment module. |
| Check out the admin repository
| |
| git clone awesome@git.rc.ufl.edu:gitolite-admin.git | |
| or change into the gitolite-admin directory if already cloned and run 'git pull' to refresh the local working tree from the server.
| |
|
| |
|
| ===Add users=== | | |}} |
| ;Single machine
| | <!--Job Scripts--> |
| : e.g. user 'jdoe' working on a single machine who provided the repository administrator with a public ssh key named ''jdoe.pub'' | | {{#if: {{#var: job}}|==Job Script Examples== |
| cd gitolite-admin
| | See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples. |
| cp ~/jdoe.pub keydir/
| | |}} |
| git add keydir/*
| | <!--Policy--> |
| git commit -m "added user jdoe"
| | {{#if: {{#var: policy}}|==Usage Policy== |
| git push
| |
|
| |
|
| ;Additional machines
| | WRITE USAGE POLICY HERE (Licensing, usage, access). |
| : if a user needs to access the repository from another machine named, for example, 'jdoe_laptop'
| |
| cd gitolite-admin/keydir
| |
| mkdir jdoe_laptop
| |
| cp ~/jdoe.pub jdoe_laptop
| |
| git add *
| |
| git commit -m "added a new key from jdoe_laptop for user jdoe"
| |
| git push
| |
|
| |
|
| ===Grant Access=== | | |}} |
| Once a new user (but not a new key for an existing user) is added they need to be granted access to appropriate repositories. This is done by editing the config/gitolite.conf file, then committing and pushing the commit to the server.
| | <!--Performance--> |
| | {{#if: {{#var: testing}}|==Performance== |
|
| |
|
| For example, to allow access from users 'janedoe' and 'johndoe' to a repository 'test1' either add their gitolite key names to the access list for that repository or create a gitolite group, add the users to the group and grant the group access to the repository.
| | WRITE_PERFORMANCE_TESTING_RESULTS_HERE |
|
| |
|
| repo test1
| | |}} |
| RW+ = janedoe johndoe
| | <!--Faq--> |
| R = @all
| | {{#if: {{#var: faq}}|==FAQ== |
| | *'''Q:''' **'''A:'''|}} |
| | <!--Citation--> |
| | {{#if: {{#var: citation}}|==Citation== |
| | If you publish research that uses {{#var:app}} you have to cite it as follows: |
|
| |
|
| or
| | WRITE_CITATION_HERE |
|
| |
|
| repo test1
| | |}} |
| RW+ = @mygroup
| | <!--Installation--> |
| R = @all
| | {{#if: {{#var: installation}}|==Installation== |
| | | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} |
| # Groups
| | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> |
| @test_group = janedoe johndoe
| | __NOTOC____NOEDITSECTION__ |
| | |
| Access types:
| |
| RW+ means 'Read and Write access'
| |
| R means 'Ready-only access'
| |
| | |
| ===Create a new repository===
| |
| ;For example, an admin wants to create a repository called ''denovo'' for ''de novo'' assembly scripts and set access to users ''admin'' and ''student''
| |
| cd gitolite-admin
| |
| vim conf/gitolite.conf
| |
| Add a group configuration:
| |
| @mygroup = admin student
| |
| Add a repository configuration
| |
| repo denovo
| |
| RW+ = @mygroup
| |
| R = @all
| |
| * Commit and push
| |
| git add *
| |
| git commit -m "Set up a new repository denovo for use by admin and student"
| |
| git push
| |
| * Create a local working tree for the ''denovo'' project:
| |
| cd
| |
| mkdir denovo
| |
| cd denovo
| |
| git init
| |
| git remote add origin awesome@git.rc.ufl.edu:denovo.git
| |
| * Add and edit some files
| |
| * Commit and push to the Git server
| |
| git add *
| |
| git commit -m "Initial import"
| |
| git push origin master
| |
| Output:
| |
| Initialized empty Git repository in /git/awesome/repositories/denovo.git/
| |
| Counting objects: 3, done.
| |
| Writing objects: 100% (3/3), 231 bytes, done.
| |
| Total 3 (delta 0), reused 0 (delta 0)
| |
| To awesome@git.rc.ufl.edu:denovo.git
| |
| * [new branch] master -> master
| |
| | |
| ===User Activities=== | |
| Regular cycle of git repository usage
| |
| * Clone the ''denovo'' repository
| |
| git clone awesome@git.rc.ufl.edu:denovo.git
| |
| Output:
| |
| Cloning into denovo...
| |
| remote: Counting objects: 3, done.
| |
| remote: Total 3 (delta 0), reused 0 (delta 0)
| |
| Receiving objects: 100% (3/3), done.
| |
| * Work in the git working tree
| |
| cd denovo
| |
| Edit and add files
| |
| * Commit and push the changes to the repository
| |
| git add *
| |
| git commit -m "The changes I made"
| |
| git push
| |
| | |
| ==Git email reports==
| |
| We can enable Git email reports for any repository. Please email the support or file a suport ticket. Once enabled, every "push" to the remote repository on git.rc.ufl.edu will produce a commit email report to a defined list of email addresses.
| |
| ==Multiple SSH keys==
| |
| To enable a user to have multiple ssh keys for accessing the UFRC Git server the repository administrator can simply put the user's keys under subdirectories in the 'keydir', add, commit, and push as usual. The user must make sure they're using the right key. It's often convenient to create a SSH configuration for each particular combination of repositories and keys. For example,
| |
| | |
| * Edit your <code>~/.ssh/config</code> file on a local machine that need to be configured. Let's assume that the main configuration is
| |
| Host hpcgit
| |
| HostName git.rc.ufl.edu
| |
| User awesomegroup
| |
| IdentityFile ~/.ssh/id_rsa
| |
|
| |
| To be able to use an alternate key add the following configuration
| |
| Host hpcgit2
| |
| HostName git.rc.ufl.edu
| |
| User awesomegroup
| |
| IdentityFile ~/.ssh/id_rsa_my_other_key
| |
| | |
| Once configuration is done you'll be able to check out the repository via
| |
| | |
| git clone hpcgit2:my_repository
| |
| | |
| '''Notes:''' Make sure that the '''User''' is set to your group's Git account and not your personal HPC account name.
| |
| | |
| ==Graphical User Interfaces to Git==
| |
| [[TortoiseGit_Clone_Repository|How to use TortoiseGit to clone a Git Repository]]
| |
Description
git website
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows.
Environment Modules
Run module spider git to find out what environment modules are available for this application.
System Variables
- HPC_GIT_DIR - installation directory
Additional Information
UFRC git environment module also contains a 'git-lfs' instance, so you can run 'git lfs ...' after loading the git environment module.