Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Greg Von Kuster
Hi Michael, The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that. However, the communication layer between Galaxy and the tool shed is backward compatible

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous post you mention is outdated. The main Galaxy tool

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Greg Von Kuster
Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, The previous

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Greg Von Kuster
...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
, January 29, 2013 10:07 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Have you made some changes to your local Galaxy code base that require merging? On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote: To be honest

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Greg Von Kuster
-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Have you made some changes to your local Galaxy code base that require merging? On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote: To be honest, I barely understand this enough to just follow

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread James Taylor
Computing Center University of North Carolina at Chapel Hill From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following: File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Dannon Baker
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 11:15 AM To: Waldron, Michael H Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository You might try an 'hg merge --preview' to see what it actually wants

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Dannon Baker
Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 11:15 AM To: Waldron, Michael H Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository You might try an 'hg merge --preview' to see what it actually

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
at Chapel Hill From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 11:27 AM To: Waldron, Michael H Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Oh

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread James Taylor
: Re: [galaxy-dev] Error trying to add tools from tool shed respository Hi Michael, Your paster log still is showing the older code. Any idea how this happens in your environment? On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote: I had stopped the Galaxy server before running

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Paul Boddie
On 29/01/13 17:33, James Taylor wrote: Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. If upgrading Mercurial will involve introducing another detour, you could potentially check which

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
to add tools from tool shed respository As it turns out, it was fairly simple to install a newer hg version (2.4.2). So now running hg merger --preview and hg heads returns: $ hg merge --preview abort: branch 'default' has one head - please merge with an explicit rev (run 'hg heads' to see all heads

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Dannon Baker
, January 29, 2013 1:28 PM To: Paul Boddie; James Taylor Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository As it turns out, it was fairly simple to install a newer hg version (2.4.2). So now running hg merger --preview

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository So that's interesting. My best

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Dannon Baker
...@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository So that's interesting. My best guess was that this was caused

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository I don't know why I thought we'd already checked this, but -- 'hg st' will tell you which files have been modified in your local repository

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Dannon Baker
From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 1:37 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository So

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread Waldron, Michael H
From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, January 29, 2013 2:04 PM To: Waldron, Michael H Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Ok