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
at helps.
>
> Thanks!
> -Sheldon
>
> -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
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
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 several fixes released to the stable branch that you do not
>> have in 12441. I would recommend do
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 inst
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
.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
su.edu>]
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto: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 hav
, March 20, 2014 2:04 PM
> To: Briand, 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 sy
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. Can you confirm that
th
in walk
> names = listdir(top)
> TypeError: coercing to Unicode: need string or buffer, NoneType found
>
> -Sheldon
>
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, March
.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
u.edu'
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, "
c: 'galaxy-dev@lists.bx.psu.edu'
> 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 f
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, "Br
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 gi
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
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