Re: [galaxy-dev] installing BWA from toolshed
Hi Quang, I didn't realize you were running on the cloud, which is not my area of expertise - my instructions were for a local Galaxy instance. I'll let others with more knowledge of the cloud environment answer your question. Please keep all replies on the mail list to enable optimal response to questions and issues. Greg Von Kuster On Dec 22, 2012, at 10:45 AM, Quang Trinh wrote:
Hi Greg, Quick question: I am running off Amazon EC2 and when I do the upgrade, I get the following error:
Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy abort: repository default not found!
How do I get around this?
THanks,
On 12/22/12, Quang Trinh <quang.trinh@gmail.com> wrote:
Thanks Greg, will follow the instructions from the news brief.
Q
On Sat, Dec 22, 2012 at 10:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Quang,
You'll need to upgrade your Galaxy instance to the distribution release that went out on December 20. Here is the link to the news brief for the December 20 release.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20
From this point forward, all communication between Galaxy and the tool shed will be backward compatible to this December 20 release, so new tool shed features introduced in the future will function for any Galaxy instance running the December 20 release or newer.
Greg Von Kuster
On Dec 22, 2012, at 9:53 AM, Quang Trinh wrote:
Hi, Trying to install BWA from toolshed just now and I get these error messages ( see below ). Installing BWA from toolshed works for me before.
Thanks
Q
Server Error
app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1199 in
URL: http://54.242.71.44/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=25bdd3c7f0d57b06&changeset_revisions=ffa8aaa14f7c Module paste.exceptions.errormiddleware:143 in __call__ prepare_for_install
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack
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My guess what's going on here is that you're still logged in as the ubuntu user. `sudo su galaxy` and give it another shot. -Dannon On Dec 22, 2012, at 1:51 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Quang,
I didn't realize you were running on the cloud, which is not my area of expertise - my instructions were for a local Galaxy instance. I'll let others with more knowledge of the cloud environment answer your question. Please keep all replies on the mail list to enable optimal response to questions and issues.
Greg Von Kuster
On Dec 22, 2012, at 10:45 AM, Quang Trinh wrote:
Hi Greg, Quick question: I am running off Amazon EC2 and when I do the upgrade, I get the following error:
Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy abort: repository default not found!
How do I get around this?
THanks,
On 12/22/12, Quang Trinh <quang.trinh@gmail.com> wrote:
Thanks Greg, will follow the instructions from the news brief.
Q
On Sat, Dec 22, 2012 at 10:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Quang,
You'll need to upgrade your Galaxy instance to the distribution release that went out on December 20. Here is the link to the news brief for the December 20 release.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20
From this point forward, all communication between Galaxy and the tool shed will be backward compatible to this December 20 release, so new tool shed features introduced in the future will function for any Galaxy instance running the December 20 release or newer.
Greg Von Kuster
On Dec 22, 2012, at 9:53 AM, Quang Trinh wrote:
Hi, Trying to install BWA from toolshed just now and I get these error messages ( see below ). Installing BWA from toolshed works for me before.
Thanks
Q
Server Error
> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ > environ, self.app) Module paste.wsgilib:539 in intercept_output > app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ > return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ > return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ > body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator > return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1199 in
URL: http://54.242.71.44/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=25bdd3c7f0d57b06&changeset_revisions=ffa8aaa14f7c Module paste.exceptions.errormiddleware:143 in __call__ prepare_for_install
> description, repository_clone_url, changeset_revision, ctx_rev, > repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack
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:
___________________________________________________________ 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:
Hi Dannon and Greg, upgrading as user 'galaxy' works. I also have to update the database from version 107 and 108. Thanks. Q On 12/22/12, Dannon Baker <dannonbaker@me.com> wrote:
My guess what's going on here is that you're still logged in as the ubuntu user. `sudo su galaxy` and give it another shot.
-Dannon
On Dec 22, 2012, at 1:51 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Quang,
I didn't realize you were running on the cloud, which is not my area of expertise - my instructions were for a local Galaxy instance. I'll let others with more knowledge of the cloud environment answer your question. Please keep all replies on the mail list to enable optimal response to questions and issues.
Greg Von Kuster
On Dec 22, 2012, at 10:45 AM, Quang Trinh wrote:
Hi Greg, Quick question: I am running off Amazon EC2 and when I do the upgrade, I get the following error:
Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy abort: repository default not found!
How do I get around this?
THanks,
On 12/22/12, Quang Trinh <quang.trinh@gmail.com> wrote:
Thanks Greg, will follow the instructions from the news brief.
Q
On Sat, Dec 22, 2012 at 10:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Quang,
You'll need to upgrade your Galaxy instance to the distribution release that went out on December 20. Here is the link to the news brief for the December 20 release.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20
From this point forward, all communication between Galaxy and the tool shed will be backward compatible to this December 20 release, so new tool shed features introduced in the future will function for any Galaxy instance running the December 20 release or newer.
Greg Von Kuster
On Dec 22, 2012, at 9:53 AM, Quang Trinh wrote:
Hi, Trying to install BWA from toolshed just now and I get these error messages ( see below ). Installing BWA from toolshed works for me before.
Thanks
Q
Server Error
URL: http://54.242.71.44/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=25bdd3c7f0d57b06&changeset_revisions=ffa8aaa14f7c Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1199 in prepare_for_install >> description, repository_clone_url, changeset_revision, ctx_rev, >> repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack ___________________________________________________________ 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:
___________________________________________________________ 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:
participants (3)
-
Dannon Baker -
Greg Von Kuster -
Quang Trinh