Re: [galaxy-dev] Installing Tool Dependencies

2018-07-18 Thread Gudrun Mareike Amedick
Hi, I found the source of the tools. I think. tool_conf.xml.sample from release_18.05 contains this:   There are the four tools. If I delete the section entirely, they disappear from the dependencies list.  Since those tools weren't

Re: [galaxy-dev] Installing Tool Dependencies

2018-07-18 Thread Björn Grüning
Hi Gudrun, it seems this PASS tool is not yet available as Conda package. Do you know which ToolShed repo this is, you might want to contact the developer and ask for an upgrade to conda. > I don't know where they come from, I didn't install them explicitly. This is scary. Can you

Re: [galaxy-dev] Installing Tool Dependencies

2018-07-18 Thread Gudrun Mareike Amedick
Hi, I have those four tools, too. And they won't install properly.  I don't know where they come from, I didn't install them explicitly. They just popped up in my dependencies list. I've chosen to ignore them, since they don't seem to cause any trouble. But if anyone had this problem too and

Re: [galaxy-dev] Installing Tool Dependencies

2018-07-17 Thread Tom Misilo
To: Tom Misilo Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Installing Tool Dependencies Hello Tom, that page is very very outdated and I wouldn't trust it. Do you have any specific tools from that list that are giving you trouble? If not then I would ignore it completely. Majority

Re: [galaxy-dev] Installing Tool Dependencies

2018-07-16 Thread Martin Čech
kages. > > > > Thank you! > > Tom > > > > *From:* Martin Čech > *Sent:* Monday, July 16, 2018 12:42 PM > *To:* Tom Misilo > *Cc:* galaxy-...@bx.psu.edu > *Subject:* Re: [galaxy-dev] Installing Tool Dependencies > > > > Hello Tom, > > > > that

Re: [galaxy-dev] Installing Tool Dependencies

2018-07-16 Thread Martin Čech
Hello Tom, that page is very very outdated and I wouldn't trust it. Do you have any specific tools from that list that are giving you trouble? If not then I would ignore it completely. Majority of the tools are now installed through the Toolshed and dependencies are auto-managed by Galaxy's own

[galaxy-dev] Installing Tool Dependencies

2018-07-16 Thread Tom Misilo
Hello, I am trying to help a research here at Florida Tech setup Galaxy locally to process their data. However, I am running into a problem installing some tool dependencies was on this page (https://moin.galaxyproject.org/Admin/Tools/ToolDependencies). For example, I am trying to install

Re: [galaxy-dev] installing tool dependencies

2017-01-12 Thread Jochen Bick
Hej Marius, > what version of galaxy are you running? we are running 15.10 but it will be updated next Monday. > When you are doing this you should have a traceback in your logs, > this would be helpful to understand what is going on. ok I will check the logs for the error. > > When you say

Re: [galaxy-dev] installing tool dependencies

2017-01-12 Thread Marius van den Beek
Hello Jochen, what version of galaxy are you running? When you are doing this you should have a traceback in your logs, this would be helpful to understand what is going on. When you say "I installed a bunch of tools at the same time", did you really trigger multiple installations at the same

[galaxy-dev] installing tool dependencies

2017-01-12 Thread Jochen Bick
Hi, I installed a bunch of tools at the same time and ran into some errors. After repairing those tools some of the dependencies installations did not work. If I try to repair the tools again I also get this error message: Internal Server Error Galaxy was unable to successfully complete your