Re: [galaxy-dev] Problem upgrading

And as for "sudo git checkout v16.04" not working, it appears to me that the release commits have not been given tags since v15.07. -Will On Fri, May 20, 2016 at 11:52 AM, Scott Szakonyi wrote: > Will, thank you so much! That absolutely did the trick. > > -Scott > >

Re: [galaxy-dev] Problem upgrading

There is a 'git' missing in there. Try: sudo git checkout master && git pull --ff-only origin master -Will On Fri, May 20, 2016 at 11:42 AM, Scott Szakonyi wrote: > Hello, > > I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04. > However, when I

[galaxy-dev] Problem upgrading

Hello, I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04. However, when I attempt to do so, I get an error, and git log shows I'm still on 16.01. $ sudo git checkout master && pull --ff-only origin master M tool-data/all_fasta.loc.sample Already on 'master' -bash: pull:

Re: [galaxy-dev] STACKS error

Hi Yvan, We had this issue as well, and fixed it for now by adding the checkers.py from an old galaxy server. I've added it in attachment if you don't have it anymore. put it in "galaxy-dist/lib/galaxy/datatypes/checkers.py" If relevant, I also made a few changes to the stacks script

Re: [galaxy-dev] Error when executing cleanup scripts

Hi Dannon, That absolutely did the trick. Thanks so much for your assistance. Best, Scott On Fri, May 20, 2016 at 9:11 AM, Dannon Baker wrote: > Hi Scott, > > The quick fix is to source your virtualenv first and you should be good to > go. > > -Dannon > > On Fri, May

Re: [galaxy-dev] STACKS error

Hi Amos, Thanks to use Stacks on Galaxy! I already seen this error. This is due, I think, to newest Galaxy versions who don't have the checkers.py anymore on the datatypes folder Thios can be fixed using an older Galaxy version... Otherwise, we are working on a new version of the Stacks

[galaxy-dev] STACKS error

Anyone encountered this error? Fatal error: Exit code 1 (Error in Stacks Process radtag execution) Traceback (most recent call last): File "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/STACKS_procrad.py", line 16, in from stacks

Re: [galaxy-dev] Error when executing cleanup scripts

Hi Scott, The quick fix is to source your virtualenv first and you should be good to go. -Dannon On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi wrote: > Hi all, > > I'm getting an error when executing the cleanup scripts in Galaxy 16.01. > It appears the script is

[galaxy-dev] Error when executing cleanup scripts

Hi all, I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It appears the script is unable to import sqlalchemy, but my understanding is that Galaxy can't function without it, so I'm at a loss to explain. Here's the error I'm getting: $ sh

Re: [galaxy-dev] not sure what I can do about this...

Hi Edgar, it’s a good idea to use python2.7 for galaxy, since 16.01 is the last release supporting python 2.6. In general you can create a new virrtualenv with a a specific python interpreter like this: virtualenv -p If you create a new new virtualenv .venv in your galaxy source folder,