Hi Bjoern,
Changing the title to reflect the proper topic
I see now that the gem executables are installed under $INSTALLDIR/bin so I
added this to the environment for my protk install.
That got me to the point where my executable would run ... but now I'm seeing
that in my env.sh file I don
Hi Bjoern,
Ross just gave me some pointers and I realised that I could just set these
environment variables myself by doing
$INSTALL_DIR/bin
$INSTALL_DIR/
In my protk tool definition.
RUBYLIB isn't set ... hopefully this will not be a
Hi Ira,
that is strange, because PATH and GEM_HOME should be set automatically
for you.
Please have a look at
https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_ruby2_bioruby_1_4/tool_dependencies.xml
http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_ruby
Hi Ira,
> Hi Bjoern,
>
> I'll test,
thanks!
> but I wonder if the problem is that GEM_PATH is set instead of GEM_HOME. I
> think GEM_HOME needs to be set also. It's zoo of environment variables out
> there :)!!
Mh according to
http://stackoverflow.com/questions/11277227/whats-the-dif
Hi Bjoern,
I'll test, but I wonder if the problem is that GEM_PATH is set instead of
GEM_HOME. I think GEM_HOME needs to be set also. It's zoo of environment
variables out there :)!!
Also ... I think GEM_HOME should be set using "set_to" not "prepend_to" ...
I am using the latest galaxy
Hi Bjoern,
I've just done some more testing of my tool with a fresh install and a fresh
checkout of galaxy. After install of this tool
http://testtoolshed.g2.bx.psu.edu/view/iracooke/package_protk_1_2_5
I have an env.sh that looks like
GEM_PATH=/home/vagrant/tool_dependencies/protk/1.2.5/ira
Hi Ira,
> Hi Bjoern,
>
> I've just done some more testing of my tool with a fresh install and a fresh
> checkout of galaxy. After install of this tool
>
> http://testtoolshed.g2.bx.psu.edu/view/iracooke/package_protk_1_2_5
>
> I have an env.sh that looks like
>
> GEM_PATH=/home/vagrant/tool
