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git repositories (repos) and branches relevant to the standalone GMS

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malachig edited this page Sep 30, 2014 · 4 revisions

The following repositories are needed for the standalone GMS (sGMS) of The Genome Institute (TGI).

  • gms (https://github.com/genome/gms) - The sGMS installation code. This repo lives on github.com only. You can commit and push to this repo directly to github. There is currently only one branch (ubuntu-12.04).

  • gms-core (https://github.com/genome/gms-core) - This repo is known as 'genome' within TGI. This repo contains the bulk of pipeline and tool code. By far the largest repo needed for sGMS. There are two branches relevant to the sGMS (master and gms-pub). The gms-pub branch of this repo is used in the installation of the sGMS. This repo is maintained on a private git server within the firewall at TGI. There are hooks in place so that when something is pushed to the local git server it is automatically synced to github. Do not push changes directly to github. Within reason, the only things that should be specific to the gms-pub branch of this repo are things that are truly specific to the standalone environment. Forking should be minimized as much as possible and improvements from master should be merged into gms-pub as often as practical.

  • genome (https://github.com/genome/genome) - This is a new repo that is going to replace 'gms-core'. It is essentially the master branch of the old gms-core. For now we are keeping gms-core because the standalone GMS is using the gms-pub branch of that repo. Once we complete the next merge from master, we can remove gms-core and the standalone GMS can use either the master branch or another branch of the 'genome' repo.

  • tgi-workflow (https://github.com/genome/tgi-workflow) - This repo is known simply as 'workflow' within TGI. The setup is similar to gms-core. It is also maintained on a private git server that is automatically synced to github. Once again, do not push changes directly to github. There are two branches relevant to the sGMS (master and gms-pub). Changes committed to the 'gms-pub' branch are automatically synced to github.

  • ur (http://github.com/genome/UR.git) - This repo is maintained on a local server at TGI but in this case, changes must be committed to our internal code review server 'gerrit'. Once changes are approved commits are synced to github. There are two branches relevant to the sGMS (master and gms-pub). Since there is currently nothing that needs to be different in UR for the sGMS, we are using a tag instead of a branch in the installation of the sGMS. This tag is 'gms-pub-tag'.

  • gms-webviews (http://github.com/genome/gms-webviews.git) - I believe the setup of this repo is similar to that for gms-core. There are two branches relevant to the sGMS (master and gms-pub).

  • openlava (http://github.com/openlava/openlava.git) - This project is entirely external to TGI and we get it directly from github. We are currently cloning the branch '2.0-release'

All of these git repos are obtained during installation of the sGMS. See make target 'done-host/git-checkouts' in the gms Makefile for details (https://github.com/genome/gms/blob/ubuntu-12.04/Makefile).

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