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
Hi Bjoern,
Ross just gave me some pointers and I realised that I could just set these
environment variables myself by doing
action type=set_environment
environment_variable action=prepend_to
name=PATH$INSTALL_DIR/bin/environment_variable
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
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
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
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
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
