installing the tool
dependency package worked.
Thanks for the advice.
-Sheldon
-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Tuesday, March 25, 2014 10:34 AM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu Dev
Subject: Re: [galaxy-dev] tophat2 install
If
eldon
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 3:11 PM
To: 'Greg Von Kuster'
Cc: galaxy-dev@lists.bx.psu.edu Dev
Subject: Re: [galaxy-dev] tophat2 install
No difference. Same error
-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:56 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu Dev
Subject: Re: [galaxy-dev] tophat2 install
Sorry, should have advised this:
> hg pull ht
pulling from https://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:36 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] tophat2 install
There
$ hg summary
parent: 12441:dc067a95261d
>From the tool_dependencies.xml:
http://toolshed.g2.bx.psu.edu"; />
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:23 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re:
Hi,
dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
contains only:
env.sh
If that isn't the right place to look let me know.
-Sheldon
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.
.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] tophat2 install
Hi,
Yes the error is:
Error installing tool dependency pack
Hi,
Yes the error is:
Error installing tool dependency package tophat2 version 2.0.9: coercing to
Unicode: need string or buffer, NoneType found
-Sheldon
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.ps
ion is required:
The following assumes you're using postgres:
update tool_shed_repository set deleted=True, uninstalled=True,
status='Uninstalled', error_message=Null where name = 'bcftools_view';
From: Briand, Sheldon
Sent: Wednesday, March 12, 2014 11:44 AM
To: gala
Hi,
I ran into a problem installing tophat2 here:
tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType
found
I have only used the interface to do the installation (no manual deletes). The
rest of the dependencies for tophat2 installed just fine.
Repairing the repository
per), I only have the package option and so I can't get the tool
to appear in my menu.
Thanks!
-Sheldon
-Original Message-
From: Briand, Sheldon
Sent: Monday, March 03, 2014 2:16 PM
To: 'Greg Von Kuster'
Subject: RE: [galaxy-dev] tool trouble
Hi,
Not sure if you were s
_
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
On Behalf Of Briand, Sheldon [sheldon.bri...@ssc-spc.gc.ca]
Sent: Friday, February 28, 2014 6:02 PM
To: 'Greg Von Kuster'
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool trouble
Hi,
So tho
uster [mailto:g...@bx.psu.edu]
Sent: Friday, February 28, 2014 4:59 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool trouble
Hello Sheldon,
What is the configuration setting you are using for the location to install
repositories? This is defined by the tool_path attrib
be missing the .py and .xml files in the shed_tools directory.
-Sheldon
From: Briand, Sheldon
Sent: Friday, February 28, 2014 2:11 PM
To: 'Greg Von Kuster'
Subject: RE: [galaxy-dev] tool trouble
Hi,
Thanks for getting back to me.
I didn't get your first reply (email trouble her
] "POST
/admin_toolshed/manage_repositories HTTP/1.1" 302 -
"http://localhost:8080/admin_toolshed/reinstall_repository?id=827fffb0dffdf
266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
127.0.0.1 - - [28/Feb/2014:09:59:03 -0300] "GET
/admi
Hi,
I'm having trouble with some of my tools not appearing in the Analyze Data
menu. I've successfully installed the tools via the manage installed tool shed
repositories(so they are installed to disk). I have tried uninstalling and
installing again. The tool installs but does not appear in
Hi,
I'm trying to debug file uploads using the file browser. I have nginx setup to
proxy but not to a sub directory.
/usr/sbin/nginx -V
nginx version: nginx/1.4.3
--add-module=/usr/local/src/nginx_upload_module-2.2.0
Here are the settings in my universe_wsgi.ini:
nginx_upload_store = database/t
Hi,
Thanks for your help. It turns out an extra carriage return snuck into the end
of the .loc file. Once I removed that everything worked.
-Sheldon
From: bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 2:05 PM
To: Briand, Sheldon
Cc: galaxy
s. We
didn't see the reference genome hg19 until the loc file for the repo was
populated.
Thanks!
-Sheldon
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 1:33 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: R
_working_direc
tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/software/packages/galaxy/galaxy-dist/database/j
ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY;
sh -c "exit $return_code"
echo $? > /software/packages/gala
Hi,
I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here.
I've run into the following error:
# ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does
not exist.
I see via much googling that this error is due to a user input problem. I've
tried po
board and my chair. I'll get it figured
out. Thanks for the responses and sorry to waste your time.
Cheers,
-Sheldon
-Original Message-
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Wednesday, January 15, 2014 4:32 PM
To: Briand, Sheldon;
ocess directly, removing the middle
man, and it looks like the problem still exists.
-Sheldon
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Wednesday, January 15, 2014 4:21 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] after update unable to login
7;ve missed?
Thanks,
-Sheldon
From: Briand, Sheldon
Sent: Thursday, January 09, 2014 2:26 PM
To: 'galaxy-dev@lists.bx.psu.edu'
Subject: after update unable to login
Hi,
I had a working local install of galaxy. I wanted to install gatk2 and wasn't
able to install it. I upgrade
Hi,
I had a working local install of galaxy. I wanted to install gatk2 and wasn't
able to install it. I upgraded and I am now unable to log in to galaxy.
I should note that I am relatively new to galaxy. I had a previously logged in
admin session (before the update). So I am able to see tha
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