[Request] Consider extracting web/js/jbrowse/plugins/CoGe into a separate repo

[vivekkrish]

Hello @LyonsLab CoGe JBrowse maintainers,

Just a thought, would you consider decoupling the jbrowse/plugins/CoGe directory from the main coge repo into its own standalone repository, so that, anyone who wishes to use your CoGe/View/Track/Wiggle/XYPlot track type (or other neat extensions) can easily clone the repo into their own JBrowse forks?

Thank you for your consideration.

[sdavey]

hi Vivek,

thanks for the great suggestion. We'll do this soon.

best, Sean

On May 4, 2017, at 10:56, Vivek Krishnakumar notifications@github.com<mailto:notifications@github.com> wrote:

Hello @LyonsLabhttps://github.com/LyonsLab CoGe JBrowse maintainers,

Just a thought, would you consider decoupling the jbrowse/plugins/CoGe directory from the main coge repo into its own standalone repository, so that, anyone who wishes to use your Wiggle/XYPlot glyph (or other neat extensions) can easily clone the repo into their own JBrowse forks?

Thank you for your consideration.

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/LyonsLab/coge/issues/75, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALOspsEOaDA00hkMf3Mxy4IjZJDa27Qyks5r2hE6gaJpZM4NRA03.

[vivekkrish]

Thank you for your consideration, @sdavey!

Just as an FYI, in the past, we've used this method to split out a particular subdirectory into its own repo. Following this, we removed it from the main repo and added it back as a git submodule.

[sdavey]

awesome. thanks for the tip!

On May 5, 2017, at 09:10, Vivek Krishnakumar notifications@github.com<mailto:notifications@github.com> wrote:

Thank you for your consideration, @sdaveyhttps://github.com/sdavey!

Just as an FYI, in the past, we've used this methodhttps://help.github.com/articles/splitting-a-subfolder-out-into-a-new-repository/ to split out a particular subdirectory into its own repo. Following this, we removed it from the main repo and added it back as a git submodule.

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/LyonsLab/coge/issues/75#issuecomment-299507397, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALOspixnKHNTrT2iQC7GF1FGDXcHXQNfks5r20oPgaJpZM4NRA03.

[sdavey]

Hi Vivek,

thanks again for the suggestion. I've completed the move of CoGe's JBrowse plugin to its own repository (https://github.com/LyonsLab/CoGe_plugin)

best, Sean Davey Dept. of Cellular and Molecular Medicine University of Arizona sdavey@email.arizona.edumailto:sdavey@email.arizona.edu

On May 5, 2017, at 9:10 AM, Vivek Krishnakumar notifications@github.com<mailto:notifications@github.com> wrote:

Thank you for your consideration, @sdaveyhttps://github.com/sdavey!

Just as an FYI, in the past, we've used this methodhttps://help.github.com/articles/splitting-a-subfolder-out-into-a-new-repository/ to split out a particular subdirectory into its own repo. Following this, we removed it from the main repo and added it back as a git submodule.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/LyonsLab/coge/issues/75#issuecomment-299507397, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALOspixnKHNTrT2iQC7GF1FGDXcHXQNfks5r20oPgaJpZM4NRA03.

[vivekkrish]

Thank you very much, @sdavey. This is perfect!

I would recommend adding a README.md to the new repo, with some instructions on how to install the plugin and use in JBrowse. You could also update the JBrowse registry entry for the CoGe plugin.

BTW, I've created a PR to your plugin repo (LyonsLab/CoGe_plugin#1) which addresses some issues with code minifying. Please review and accept changes at your convenience. Thanks!

[vivekkrish]

Just an FYI, might want to update your documentation here (https://genomevolution.org/wiki/index.php/Install_coge#Deploy_the_Web_Site) to run a git clone --recursive in order to pull down the CoGe JBrowse Plugin submodule.

[sdavey]

done. thanks for the suggestion!

Sean Davey Dept. of Cellular and Molecular Medicine University of Arizona sdavey@email.arizona.edumailto:sdavey@email.arizona.edu

On May 16, 2017, at 2:17 PM, Vivek Krishnakumar notifications@github.com<mailto:notifications@github.com> wrote:

Just an FYI, might want to update your documentation here (https://genomevolution.org/wiki/index.php/Install_coge#Deploy_the_Web_Site) to run a git clone --recursive in order to pull down the CoGe JBrowse Plugin submodule.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/LyonsLab/coge/issues/75#issuecomment-301918338, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALOspu1uqHWN-ZPkWO5i-ZytC0vkGCYhks5r6hJngaJpZM4NRA03.