Give you seemingly have a custom deployment, a manual upgrade is probably best. Instructions are available here: https://wiki.galaxyproject.org/CloudMan/Services/Galaxy#Updating_Galaxy_sour...

We'll get the 16.07 release done too but juding by the way things look, it won't be until the next month.

On Wed, Sep 14, 2016 at 11:23 AM, Lapointe, David David.Lapointe@tufts.edu wrote:

Hi Enis,

Yes I figured what I was doing wrong. Using Cloudman to restart services overwrote my confs. Using the CLI to manage services keeps everything in place, though I would like to figure out what is the optimal way to move to 16.07. Wait for the AMI or update? -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: Enis Afgan enis.afgan@irb.hr Date: Wednesday, September 14, 2016 at 11:01 AM To: David Lapointe david.lapointe@tufts.edu Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists. galaxyproject.org> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance

Hi David, I totally missed this email from you - apologies! Are you still trying to do this or did you figure it out? Following the general guidelines on customizing the instance is a good place to start. There is an option in CloudMan to turn on non-signed SSL (from the Admin page) but the steps performed may be useful in trying to do the same manually. I believe it's necessary to just update and reload the Nginx configuration. A template can be found here https://github.com/galaxyproject/cloudman/blob/ 8db478a8d777bcc48ed8c838f1f9de8519a11e60/cm/conftemplates/ nginx_server_ssl.default

Hope this helps and, again, sorry for not getting back to you earlier.

On Thu, Aug 11, 2016 at 2:30 PM, Lapointe, David <David.Lapointe@tufts.edu

...

wrote:

...

This is on Amazon I should add.

David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: galaxy-dev galaxy-dev-bounces@lists.galaxyproject.org on behalf of David Lapointe david.lapointe@tufts.edu Date: Thursday, August 11, 2016 at 1:44 PM To: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyprojec t.org> Subject: [galaxy-dev] Modifying a Cloud Cluster Instance

I have a Cloudman instance up and running, but I would like to add SSL ( I have a signed cert and key ) and productionize it. I see several methods documented,but it's not clear which one is preferred: edit in place then persist changes and restart (wiki/Cloudman/CustomizeGalaxyCloud) seems best to me. Any advice?

Thanks

David

David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

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If you have a system that works, I don't see a need to change it. But yes, it's the Galaxy install is a clone of the repo so git pull will do the trick.

On Fri, Sep 16, 2016 at 9:24 AM, Lapointe, David David.Lapointe@tufts.edu wrote:

Yes that looks good. The git pull will work on top of the AMI (16.04)? I don't think that I need cloudman to stop/start, just supervisorctl, which I have been using to manage galaxy.

Thanks

David

-- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: Enis Afgan enis.afgan@irb.hr Date: Thursday, September 15, 2016 at 5:30 PM

To: David Lapointe david.lapointe@tufts.edu Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists. galaxyproject.org> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance

Give you seemingly have a custom deployment, a manual upgrade is probably best. Instructions are available here: https://wiki. galaxyproject.org/CloudMan/Services/Galaxy#Updating_Galaxy_source

We'll get the 16.07 release done too but juding by the way things look, it won't be until the next month.

On Wed, Sep 14, 2016 at 11:23 AM, Lapointe, David < David.Lapointe@tufts.edu> wrote:

...

Hi Enis,

Yes I figured what I was doing wrong. Using Cloudman to restart services overwrote my confs. Using the CLI to manage services keeps everything in place, though I would like to figure out what is the optimal way to move to 16.07. Wait for the AMI or update? -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: Enis Afgan enis.afgan@irb.hr Date: Wednesday, September 14, 2016 at 11:01 AM To: David Lapointe david.lapointe@tufts.edu Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyprojec t.org> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance

Hi David, I totally missed this email from you - apologies! Are you still trying to do this or did you figure it out? Following the general guidelines on customizing the instance is a good place to start. There is an option in CloudMan to turn on non-signed SSL (from the Admin page) but the steps performed may be useful in trying to do the same manually. I believe it's necessary to just update and reload the Nginx configuration. A template can be found here https://github.com/galaxyproject/cloudman/blob/8db478a8 d777bcc48ed8c838f1f9de8519a11e60/cm/conftemplates/nginx_ server_ssl.default

Hope this helps and, again, sorry for not getting back to you earlier.

On Thu, Aug 11, 2016 at 2:30 PM, Lapointe, David < David.Lapointe@tufts.edu> wrote:

...

This is on Amazon I should add.

David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: galaxy-dev galaxy-dev-bounces@lists.galaxyproject.org on behalf of David Lapointe david.lapointe@tufts.edu Date: Thursday, August 11, 2016 at 1:44 PM To: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyprojec t.org> Subject: [galaxy-dev] Modifying a Cloud Cluster Instance

I have a Cloudman instance up and running, but I would like to add SSL ( I have a signed cert and key ) and productionize it. I see several methods documented,but it's not clear which one is preferred: edit in place then persist changes and restart (wiki/Cloudman/CustomizeGalaxyCloud) seems best to me. Any advice?

Thanks

David

David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.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/

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Changes to the nginx config are probably best done within the CloudMan code at this point... You can edit this file to include the changes: https://github.com/galaxyproject/cloudman/blob/master/cm/conftemplates/nginx... If you look at the bottom of that file, with the includes, it might be possible to just create an additional *.conf file that will get included there. I’d start with that option.

If it becomes necessary to actually edit the original file, take a look at this section of the docs you pointed to on how to get a cluster to use it: https://wiki.galaxyproject.org/CloudMan/CustomizeGalaxyCloud#Using_custom_Cl...

The next major version of CloudMan will have better support for config changes but the way things are looking, we're still ways away from that version.

On Wed, Sep 28, 2016 at 2:20 PM, Lapointe, David David.Lapointe@tufts.edu wrote:

As it turns out I will need to use CloudMan. I am a bit confused about how to make changes that will persist. For example, making changes to the nginx configs to use my SSL certs, and/or changes to setup multiple galaxy processes. Do I make changes to the userData.yaml (CloudMan/UserData page) or follow the directions on CloudMan/CustomizeGalaxyCloud where I would edit the changes in and then persist using the Cloudman Admin.

David

-- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: galaxy-dev galaxy-dev-bounces@lists.galaxyproject.org on behalf of David Lapointe david.lapointe@tufts.edu Date: Friday, September 16, 2016 at 9:24 AM To: Enis Afgan enis.afgan@irb.hr

Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists. galaxyproject.org> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance

Yes that looks good. The git pull will work on top of the AMI (16.04)? I don't think that I need cloudman to stop/start, just supervisorctl, which I have been using to manage galaxy.

Thanks

David

-- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: Enis Afgan enis.afgan@irb.hr Date: Thursday, September 15, 2016 at 5:30 PM To: David Lapointe david.lapointe@tufts.edu Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists. galaxyproject.org> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance

Give you seemingly have a custom deployment, a manual upgrade is probably best. Instructions are available here: https://wiki. galaxyproject.org/CloudMan/Services/Galaxy#Updating_Galaxy_source

We'll get the 16.07 release done too but juding by the way things look, it won't be until the next month.

On Wed, Sep 14, 2016 at 11:23 AM, Lapointe, David < David.Lapointe@tufts.edu> wrote:

...

Hi Enis,

Yes I figured what I was doing wrong. Using Cloudman to restart services overwrote my confs. Using the CLI to manage services keeps everything in place, though I would like to figure out what is the optimal way to move to 16.07. Wait for the AMI or update? -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: Enis Afgan enis.afgan@irb.hr Date: Wednesday, September 14, 2016 at 11:01 AM To: David Lapointe david.lapointe@tufts.edu Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyprojec t.org> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance

Hi David, I totally missed this email from you - apologies! Are you still trying to do this or did you figure it out? Following the general guidelines on customizing the instance is a good place to start. There is an option in CloudMan to turn on non-signed SSL (from the Admin page) but the steps performed may be useful in trying to do the same manually. I believe it's necessary to just update and reload the Nginx configuration. A template can be found here https://github.com/galaxyproject/cloudman/blob/8db478a8 d777bcc48ed8c838f1f9de8519a11e60/cm/conftemplates/nginx_ server_ssl.default

Hope this helps and, again, sorry for not getting back to you earlier.

On Thu, Aug 11, 2016 at 2:30 PM, Lapointe, David < David.Lapointe@tufts.edu> wrote:

...

This is on Amazon I should add.

David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

From: galaxy-dev galaxy-dev-bounces@lists.galaxyproject.org on behalf of David Lapointe david.lapointe@tufts.edu Date: Thursday, August 11, 2016 at 1:44 PM To: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyprojec t.org> Subject: [galaxy-dev] Modifying a Cloud Cluster Instance

I have a Cloudman instance up and running, but I would like to add SSL ( I have a signed cert and key ) and productionize it. I see several methods documented,but it's not clear which one is preferred: edit in place then persist changes and restart (wiki/Cloudman/CustomizeGalaxyCloud) seems best to me. Any advice?

Thanks

David

David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144

Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.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/

----------------------------- Upozorenje -----------------------------

Automatskom detekcijom utvrdjeno je da tekst ove poruke podsjeca na tzv. phishing poruku.

AKO SE U PORUCI TRAZI DA POSALJETE VASU IRB LOZINKU ILI DA UNESETE IRB PODATKE NA NAVEDENOM LINKU, RADI SE O NAPADU S CILJEM KRADJE I ZLOUPOTREBE PODATAKA.

Centar za informatiku i racunarstvo, Institut Rudjer Boskovic

----------------------------- Upozorenje -----------------------------