Possible bug on "Create a collection of paired datasets"
Hi, I am a computer cluster admin and I am trying to install galaxy on our cluster. I used galaxy-release_15.05 and because we need to serve Galaxy at a sub directory, e.g. irida-galaxy I modified the options prefix and cookie_path in the galaxy configuration file as follow: prefix = /irida-galaxy filter-with = proxy-prefix cookie_path = /irida-galaxy We use apache as an interface with the Following configuration: <Proxy http://localhost:9010> Order deny,allow Allow from all </Proxy> RewriteRule ^/irida-galaxy$ /irida-galaxy/ [R] RewriteRule ^/irida-galaxy/static/style/(.*) /home/irida/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/irida-galaxy/static/scripts/(.*) /home/irida/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/irida-galaxy/static/(.*) /home/irida/galaxy-dist/static/$1 [L] #RewriteRule ^/irida-galaxy/favicon.ico /home/irida/galaxy-dist/static/favicon.ico [L] RewriteRule ^/irida-galaxy/robots.txt /home/irida/galaxy-dist/static/robots.txt [L] RewriteRule ^/irida-galaxy(.*) http://localhost:9010$1 [P] Everything works fairly good. Now I want to create a Dataset Pairs. first I uploads some fastaq files, e.g., a_1.fastaq a_2.fastaq b_1.fastaq b_2.fastaq c_1.fastaq c_2.fastaq then I choose: "Build List of Dataset Pairs" (See Fig-1 attached) There is a window appears on my screen with the title: Create a collection of paired datasets. Now I am able to choose a name and save the paired collection. However, once I click on "Create list" buttons I receive a error message on top of the windows: "An error occurred While creating this collection: Not found See Fig-2 attached. To be able to search the cause of error I turn on the "Browser Consul" on my web browser and notice that the error is related to the following web form post: https://newrobson.westgrid.ca:8444/api/histories/4936629215c25989/contents/d... Which makes sense because such address do not exist. The address should be https://newrobson.westgrid.ca:8444/irida-galaxy/api/histories/4936629215c259... So the prefix (irida-galaxy) is missing before /api/histories...../dataset_collection Is it a bug or am I missing something? Please note that such error does not appear when I do not use prefix in my galaxy configration. Thanks for your time, Cheers, Ata ---- Ata Roudgar Research Computing WestGrid Site IT Services Simon Fraser University Burnaby, British Columbia Canada V5A 1S6 phone: 778 782-8860 fax: 778 782-4242
Hi, Ata Roudgar It is indeed a bug. Thank you very much for the excellent and *helpful* report! We now have a fix for this on the release_15.05 branch of the github repository: https://github.com/galaxyproject/galaxy/commit/13a40b3ef206f8662a49dfd06fbbc... It should fix the issue but please let us know if it doesn't. Sorry for the trouble. On Fri, Jul 3, 2015 at 3:46 PM, Ata Roudgar <aroudgar@sfu.ca> wrote:
Hi,
I am a computer cluster admin and I am trying to install galaxy on our cluster. I used galaxy-release_15.05 and because we need to serve Galaxy at a sub directory, e.g. irida-galaxy I modified the options prefix and cookie_path in the galaxy configuration file as follow:
prefix = /irida-galaxy filter-with = proxy-prefix cookie_path = /irida-galaxy
We use apache as an interface with the Following configuration:
<Proxy http://localhost:9010> Order deny,allow Allow from all </Proxy>
RewriteRule ^/irida-galaxy$ /irida-galaxy/ [R] RewriteRule ^/irida-galaxy/static/style/(.*) /home/irida/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/irida-galaxy/static/scripts/(.*) /home/irida/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/irida-galaxy/static/(.*) /home/irida/galaxy-dist/static/$1 [L] #RewriteRule ^/irida-galaxy/favicon.ico /home/irida/galaxy-dist/static/favicon.ico [L] RewriteRule ^/irida-galaxy/robots.txt /home/irida/galaxy-dist/static/robots.txt [L] RewriteRule ^/irida-galaxy(.*) http://localhost:9010$1 [P]
Everything works fairly good. Now I want to create a Dataset Pairs. first I uploads some fastaq files, e.g.,
a_1.fastaq a_2.fastaq b_1.fastaq b_2.fastaq c_1.fastaq c_2.fastaq
then I choose: "Build List of Dataset Pairs" (See Fig-1 attached)
There is a window appears on my screen with the title: Create a collection of paired datasets. Now I am able to choose a name and save the paired collection. However, once I click on "Create list" buttons I receive a error message on top of the windows:
"An error occurred While creating this collection: Not found
See Fig-2 attached. To be able to search the cause of error I turn on the "Browser Consul" on my web browser and notice that the error is related to the following web form post:
https://newrobson.westgrid.ca:8444/api/histories/4936629215c25989/contents/d...
Which makes sense because such address do not exist. The address should be
https://newrobson.westgrid.ca:8444/irida-galaxy/api/histories/4936629215c259...
So the prefix (irida-galaxy) is missing before /api/histories...../dataset_collection
Is it a bug or am I missing something?
Please note that such error does not appear when I do not use prefix in my galaxy configration.
Thanks for your time, Cheers, Ata
---- Ata Roudgar Research Computing WestGrid Site IT Services Simon Fraser University Burnaby, British Columbia Canada V5A 1S6
phone: 778 782-8860 fax: 778 782-4242 ___________________________________________________________ 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/
Hi Carl, Yes, the problem is fixed. Thank you very much. Just in case, I see that galaxy-release-15.05 is now free of this bug but galaxy-release-15.07 has this bug again. Cheers, Ata On Wednesday 2015-07-15 07:54, Carl Eberhard wrote:
Date: Wed, 15 Jul 2015 07:54:05 From: Carl Eberhard <carlfeberhard@gmail.com> To: Ata Roudgar <aroudgar@sfu.ca> Cc: Galaxy Dev List <galaxy-dev@lists.galaxyproject.org>, Martin Siegert <siegert@sfu.ca>, Matthew Laird <lairdm@sfu.ca>, Franklin Bristow <franklin.bristow@phac-aspc.gc.ca> Subject: Re: [galaxy-dev] Possible bug on "Create a collection of paired datasets"
Hi, Ata Roudgar It is indeed a bug. Thank you very much for the excellent and *helpful* report!
We now have a fix for this on the release_15.05 branch of the github repository: https://github.com/galaxyproject/galaxy/commit/13a40b3ef206f8662a49dfd06fbbc...
It should fix the issue but please let us know if it doesn't. Sorry for the trouble.
On Fri, Jul 3, 2015 at 3:46 PM, Ata Roudgar <aroudgar@sfu.ca> wrote:
Hi,
I am a computer cluster admin and I am trying to install galaxy on our cluster. I used galaxy-release_15.05 and because we need to serve Galaxy at a sub directory, e.g. irida-galaxy I modified the options prefix and cookie_path in the galaxy configuration file as follow:
prefix = /irida-galaxy filter-with = proxy-prefix cookie_path = /irida-galaxy
We use apache as an interface with the Following configuration:
<Proxy http://localhost:9010> Order deny,allow Allow from all </Proxy>
RewriteRule ^/irida-galaxy$ /irida-galaxy/ [R] RewriteRule ^/irida-galaxy/static/style/(.*) /home/irida/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/irida-galaxy/static/scripts/(.*) /home/irida/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/irida-galaxy/static/(.*) /home/irida/galaxy-dist/static/$1 [L] #RewriteRule ^/irida-galaxy/favicon.ico /home/irida/galaxy-dist/static/favicon.ico [L] RewriteRule ^/irida-galaxy/robots.txt /home/irida/galaxy-dist/static/robots.txt [L] RewriteRule ^/irida-galaxy(.*) http://localhost:9010$1 [P]
Everything works fairly good. Now I want to create a Dataset Pairs. first I uploads some fastaq files, e.g.,
a_1.fastaq a_2.fastaq b_1.fastaq b_2.fastaq c_1.fastaq c_2.fastaq
then I choose: "Build List of Dataset Pairs" (See Fig-1 attached)
There is a window appears on my screen with the title: Create a collection of paired datasets. Now I am able to choose a name and save the paired collection. However, once I click on "Create list" buttons I receive a error message on top of the windows:
"An error occurred While creating this collection: Not found
See Fig-2 attached. To be able to search the cause of error I turn on the "Browser Consul" on my web browser and notice that the error is related to the following web form post:
https://newrobson.westgrid.ca:8444/api/histories/4936629215c25989/contents/d...
Which makes sense because such address do not exist. The address should be
https://newrobson.westgrid.ca:8444/irida-galaxy/api/histories/4936629215c259... tions
So the prefix (irida-galaxy) is missing before /api/histories...../dataset_collection
Is it a bug or am I missing something?
Please note that such error does not appear when I do not use prefix in my galaxy configration.
Thanks for your time, Cheers, Ata
---- Ata Roudgar Research Computing WestGrid Site IT Services Simon Fraser University Burnaby, British Columbia Canada V5A 1S6
phone: 778 782-8860 fax: 778 782-4242 ___________________________________________________________ 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/
---- Ata Roudgar Research Computing WestGrid Site IT Services Simon Fraser University Burnaby, British Columbia Canada V5A 1S6 phone: 778 782-8860 fax: 778 782-4242
participants (2)
-
Ata Roudgar -
Carl Eberhard