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HiCBrowser as Galaxy IE #3330

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merged 5 commits into from Sep 8, 2017

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@bgruening
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commented Dec 17, 2016

This is a new Galaxy IE for visualizing HiC data. It will be part of the upcoming HiC Galaxy flavor, based on HiCExplorer and HiCBrowser by @fidelram and friends.

hicbrowser_galaxy_ie

The underlying Docker Image is available here: https://github.com/maxplanck-ie/docker-hicbrowser

I labeled it as WIP as it depends on #3328 and to be really useful I need to find time to improve the HiCExplorer wrappers.

@bgruening bgruening added status/review and removed status/WIP labels Jan 8, 2017

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commented Jan 8, 2017

Ready for review!

@bgruening bgruening changed the title WIP: HiCBrowser as Galaxy IE HiCBrowser as Galaxy IE Jan 8, 2017

@galaxybot galaxybot added this to the 17.01 milestone Jan 8, 2017

@erasche erasche self-assigned this Jan 9, 2017

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commented Jan 9, 2017

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commented Jan 12, 2017

@bgruening the HiC browser doesn't respect PROXY_PREFIX. Would need something like

sed -i "s|PROXY_PREFIX|${PROXY_PREFIX}|" /etc/nginx/conf.d/nginx.conf;

in startup.sh and then some specialized NGINX config. I'm afraid I don't know enough to help with that. I've only ever done HTTP proxying in nginx (e.g. https://github.com/erasche/docker-rstudio-notebook/blob/master/proxy.conf#L12).

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commented Jan 12, 2017

@erasche the container is under our control. So I can change this here: https://github.com/maxplanck-ie/docker-hicbrowser/blob/master/nginx.conf

@erasche erasche modified the milestones: 17.05, 17.01 Jan 12, 2017

@martenson martenson modified the milestones: 17.09, 17.05 Apr 26, 2017

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commented Jun 8, 2017

@jxtx @msauria - can you comment on this?

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commented Jun 8, 2017

@nekrut I believe it still needs fixes per the previous two comments.

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Fix proxy prefix

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commented Aug 10, 2017

Marking as WIP until the proxy prefix issue is resolved.

@jmchilton jmchilton added status/WIP and removed status/review labels Aug 10, 2017

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commented Sep 5, 2017

I added PROXY_PREFIX support to the container and travis testing as well.

https://github.com/maxplanck-ie/docker-hicbrowser/blob/master/.travis.yml#L17

@bgruening bgruening added status/review and removed status/WIP labels Sep 5, 2017

@erasche erasche added this to the 18.01 milestone Sep 7, 2017

@erasche erasche removed this from the 17.09 milestone Sep 7, 2017

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commented Sep 7, 2017

bumped temporarily, hopefully I can get the necessary config changes in by end of tomorrow.

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commented Sep 7, 2017

@erasche the container does now support PROXY_PREFIX.

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erasche approved these changes Sep 8, 2017

@erasche erasche merged commit 508fdb9 into galaxyproject:dev Sep 8, 2017

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lgtm analysis: JavaScript No alert changes
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@erasche erasche modified the milestones: 17.09, 18.01 Sep 8, 2017

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commented Sep 8, 2017

Thanks @bgruening

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