Re: [galaxy-dev] Galaxy Interactive Environment devs
Hi, I attended the training session and loved the tool, Since then I was unable to get it running on my local machine. Are the slides and files from the training day available to try it again properly. Christian Manchester From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Björn Grüning [bjo...@gruenings.eu] Sent: Thursday, October 15, 2015 10:02 AM To: Sebastian Schaaf; Björn Grüning; Eric Rasche; N: Subject: Re: [galaxy-dev] Galaxy Interactive Environment devs >>> We are not yet on IEs, >> No, no, no. How can this happen? ;) > I interpret ";)" as "Indeed I remember all the issues you poor guys are > faced with" ;) >> >>> but we plan to upgrade our local production >>> instance soon (a recent version is already 'waiting' to take over), >>> apart from other goodies we intended to allow one pro user and ourselves >>> to use iPython's power this way. >>> So, do I read your message correctly as 'In terms of iPython it would be >>> best for us to wait for v15.10'? Or could we just start and do an >>> incremental upgrade as soon as v15.10 is released? >> 15.10 is not needed for IPython. It's running since 15.05 as I remember >> correctly. But we improved it a bit and you should take care that you >> use the correct Docker Image for IPython. But it should work out of the >> box. If not, let us know :) >> >> Cheers, >> Bjoern > We'll have an eye on this, thanks for the hint. And yes: We know how to > precisely annoy you and/or Eric ;). > > As it somehow picks up Eric's initial question: is your impression the > same as mine (because of no further replies to the post) that still very > few people use in fact the great opportunities of IEs in "non-main" > Galaxy instances? I have no clue how often this is used. We have 598 pulls on Docker Hub and I know a few building there own IPython Image. It's also integrated in Cloudman as far as I know. Would love to have some stats and impressions from users! Ciao, Bjoern > Cheers, > Sebastian > >> >>> Cheers to Texas, >>> >>> Sebastian >>> >>> >>> Eric Rasche schrieb: >>>> Howdy y'all, >>>> >>>> I'm building some changes to the IE infrastructure that will fix some >>>> initial hacks we did, however they will be backwards incompatible. >>>> Specifically these changes will fix some of the enterprise deployment >>>> pains (running with an external upstream proxy like apache) and allow >>>> for safely running IEs on a separate host. >>>> >>>> I'm emailing the dev list to see if anyone else has started building >>>> IEs, or if it just Björn and myself. Feel free to make yourselves known >>>> to us so we know who to contact when we're planning new features :) >>>> >>>> If you're just building on top of our existing containers, this >>>> won't be >>>> an issue for you, you'll just need to rebuild your containers once we >>>> release 15.10 versions. >>>> >>>> Cheers, >>>> Eric >>>> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Interactive Environment devs
Björn Grüning wrote: Am 13.10.2015 um 13:41 schrieb Sebastian Schaaf: Hey Eric, We are not yet on IEs, No, no, no. How can this happen? ;) I interpret ";)" as "Indeed I remember all the issues you poor guys are faced with" ;) but we plan to upgrade our local production instance soon (a recent version is already 'waiting' to take over), apart from other goodies we intended to allow one pro user and ourselves to use iPython's power this way. So, do I read your message correctly as 'In terms of iPython it would be best for us to wait for v15.10'? Or could we just start and do an incremental upgrade as soon as v15.10 is released? 15.10 is not needed for IPython. It's running since 15.05 as I remember correctly. But we improved it a bit and you should take care that you use the correct Docker Image for IPython. But it should work out of the box. If not, let us know :) Cheers, Bjoern We'll have an eye on this, thanks for the hint. And yes: We know how to precisely annoy you and/or Eric ;). As it somehow picks up Eric's initial question: is your impression the same as mine (because of no further replies to the post) that still very few people use in fact the great opportunities of IEs in "non-main" Galaxy instances? Cheers, Sebastian Cheers to Texas, Sebastian Eric Rasche schrieb: Howdy y'all, I'm building some changes to the IE infrastructure that will fix some initial hacks we did, however they will be backwards incompatible. Specifically these changes will fix some of the enterprise deployment pains (running with an external upstream proxy like apache) and allow for safely running IEs on a separate host. I'm emailing the dev list to see if anyone else has started building IEs, or if it just Björn and myself. Feel free to make yourselves known to us so we know who to contact when we're planning new features :) If you're just building on top of our existing containers, this won't be an issue for you, you'll just need to rebuild your containers once we release 15.10 versions. Cheers, Eric -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Interactive Environment devs
On 10/15/2015 04:02 AM, Björn Grüning wrote: > We are not yet on IEs, >>> No, no, no. How can this happen? ;) >> I interpret ";)" as "Indeed I remember all the issues you poor guys are >> faced with" ;) >>> but we plan to upgrade our local production instance soon (a recent version is already 'waiting' to take over), apart from other goodies we intended to allow one pro user and ourselves to use iPython's power this way. So, do I read your message correctly as 'In terms of iPython it would be best for us to wait for v15.10'? Or could we just start and do an incremental upgrade as soon as v15.10 is released? >>> 15.10 is not needed for IPython. It's running since 15.05 as I remember >>> correctly. But we improved it a bit and you should take care that you >>> use the correct Docker Image for IPython. But it should work out of the >>> box. If not, let us know :) >>> >>> Cheers, >>> Bjoern >> We'll have an eye on this, thanks for the hint. And yes: We know how to >> precisely annoy you and/or Eric ;). >> >> As it somehow picks up Eric's initial question: is your impression the >> same as mine (because of no further replies to the post) that still very >> few people use in fact the great opportunities of IEs in "non-main" >> Galaxy instances? > > I have no clue how often this is used. We have 598 pulls on Docker Hub > and I know a few building there own IPython Image. It's also integrated > in Cloudman as far as I know. > > Would love to have some stats and impressions from users! If people wouldn't be opposed to it, we could be something as simple as an admin-enabled, opt-in tracking pixel just to track/report notebook usage? Or maybe a "+1/-1" button at the top for "It was useful/it wasn't useful" but maybe that's getting way far ahead of the state of GIEs given how many issues I've seen people have deploy GIEs. > Ciao, > Bjoern > >> Cheers, >> Sebastian >> >>> Cheers to Texas, Sebastian Eric Rasche schrieb: > Howdy y'all, > > I'm building some changes to the IE infrastructure that will fix some > initial hacks we did, however they will be backwards incompatible. > Specifically these changes will fix some of the enterprise deployment > pains (running with an external upstream proxy like apache) and allow > for safely running IEs on a separate host. > > I'm emailing the dev list to see if anyone else has started building > IEs, or if it just Björn and myself. Feel free to make yourselves known > to us so we know who to contact when we're planning new features :) > > If you're just building on top of our existing containers, this > won't be > an issue for you, you'll just need to rebuild your containers once we > release 15.10 versions. > > Cheers, > Eric > >> -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A University College Station, TX 77843 404-692-2048 e...@tamu.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Interactive Environment devs
Hey Eric, We are not yet on IEs, but we plan to upgrade our local production instance soon (a recent version is already 'waiting' to take over), apart from other goodies we intended to allow one pro user and ourselves to use iPython's power this way. So, do I read your message correctly as 'In terms of iPython it would be best for us to wait for v15.10'? Or could we just start and do an incremental upgrade as soon as v15.10 is released? Cheers to Texas, Sebastian Eric Rasche schrieb: Howdy y'all, I'm building some changes to the IE infrastructure that will fix some initial hacks we did, however they will be backwards incompatible. Specifically these changes will fix some of the enterprise deployment pains (running with an external upstream proxy like apache) and allow for safely running IEs on a separate host. I'm emailing the dev list to see if anyone else has started building IEs, or if it just Björn and myself. Feel free to make yourselves known to us so we know who to contact when we're planning new features :) If you're just building on top of our existing containers, this won't be an issue for you, you'll just need to rebuild your containers once we release 15.10 versions. Cheers, Eric -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Interactive Environment devs
Hey Sebastian On 10/13/2015 06:41 AM, Sebastian Schaaf wrote: > Hey Eric, > > We are not yet on IEs, but we plan to upgrade our local production > instance soon (a recent version is already 'waiting' to take over), > apart from other goodies we intended to allow one pro user and ourselves > to use iPython's power this way. Great! Hope it works well for your power users. Feel free to ping me on IRC (erasche) if you have any deployment issues. > So, do I read your message correctly as 'In terms of iPython it would be > best for us to wait for v15.10'? Or could we just start and do an > incremental upgrade as soon as v15.10 is released? You should be fine to do an incremental upgrade. However, if GIEs are important to you, I'd personally consider going to 15.10 now (we're in freeze pending release) as there were some nice bugfixes/enhancements for GIEs. In 15.07 GIEs had issues accessing static resources rendering them unavailable without special apache/nginx routes or symlinks (https://github.com/galaxyproject/galaxy/pull/500), they also naively bound ports rather than using `docker -P` properly (https://github.com/galaxyproject/galaxy/pull/790) and it was unpleasant/complex to have your Galaxy user `sudo` or `sg` to run docker (https://github.com/galaxyproject/galaxy/pull/777) > > Cheers to Texas, > > Sebastian Grüße nach München, > > > Eric Rasche schrieb: >> Howdy y'all, >> >> I'm building some changes to the IE infrastructure that will fix some >> initial hacks we did, however they will be backwards incompatible. >> Specifically these changes will fix some of the enterprise deployment >> pains (running with an external upstream proxy like apache) and allow >> for safely running IEs on a separate host. >> >> I'm emailing the dev list to see if anyone else has started building >> IEs, or if it just Björn and myself. Feel free to make yourselves known >> to us so we know who to contact when we're planning new features :) >> >> If you're just building on top of our existing containers, this won't be >> an issue for you, you'll just need to rebuild your containers once we >> release 15.10 versions. >> >> Cheers, >> Eric >> > -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A University College Station, TX 77843 404-692-2048 e...@tamu.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy Interactive Environment devs
Howdy y'all, I'm building some changes to the IE infrastructure that will fix some initial hacks we did, however they will be backwards incompatible. Specifically these changes will fix some of the enterprise deployment pains (running with an external upstream proxy like apache) and allow for safely running IEs on a separate host. I'm emailing the dev list to see if anyone else has started building IEs, or if it just Björn and myself. Feel free to make yourselves known to us so we know who to contact when we're planning new features :) If you're just building on top of our existing containers, this won't be an issue for you, you'll just need to rebuild your containers once we release 15.10 versions. Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A University College Station, TX 77843 404-692-2048 e...@tamu.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
