and then 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
-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
-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
Hi,
Just wondering if I can still use the following to fix up my messed up tophat2
install (the install had hung up on me, for 2 hours, and I tried to
remove/repair it via the interface). I haven't had problems installing any
other tools or packages. I am using postgres but this advice was
Hi Sheldon,
I recommend not manually changing any database entries. You should be able to
install the repository and all of its dependencies using the Repair Repository
feature. See https://wiki.galaxyproject.org/RepairingInstalledRepositories
Greg Von Kuster
On Mar 20, 2014, at 8:59 AM,
'
Subject: Re: [galaxy-dev] tophat2 install
Hi Sheldon,
I recommend not manually changing any database entries. You should be able
to install the repository and all of its dependencies using the Repair
Repository feature. See
https://wiki.galaxyproject.org/RepairingInstalledRepositories
'
Subject: Re: [galaxy-dev] tophat2 install
You should be able to click on the missing tool dependency and see its
installation log. It should show you whatever error is occuring that is not
allowing successful installation.
Greg Von Kuster
On Mar 20, 2014, at 9:46 AM, Briand, Sheldon
, 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 package tophat2 version 2.0.9: coercing to
Unicode: need string or buffer, NoneType found
...@lists.bx.psu.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 package
'
Subject: Re: [galaxy-dev] tophat2 install
It looks like your database and file system are out of sync. Your database
seems to think you have an installed repository but your file system does not
seem to have the repository's installation directory. Can you confirm that
this is the case
, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] tophat2 install
It looks like your database and file system are out of sync. Your database
seems to think you have an installed repository but your file system does not
seem to have the repository's installation directory
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: [galaxy-dev] tophat2 install
What version of Galaxy are you running? You want to look in the tophat2
repository directory, not its package dependency
://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: [galaxy-dev] tophat2 install
What version of Galaxy are you running? You want to look in the tophat2
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 have been
Briand, Sheldon:
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
@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] tophat2 install
There have been several fixes released to the stable branch that you do not
have in 12441. I would recommend doing the following:
hg pull
hg update stable
Then uninstall the tophat2 repository and reinstall it. See if that makes
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 https
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
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