I am trying to install the "all_cufflinks" repository on a local Galaxy install on a Mac running El Capitan. We want to do some RNAseq analysis. I have set up a user "galaxy" with limited permissions for the install. The Galaxy install worked, i am an admin user, and we can see the Galaxy install from other computer browsers.
It was not completing cummeRbund and Cuffdiff install because of failure to install dependencies. When examined a bit closer the failure was to install the package_R_3_1_2 (R 3.1.2).
here is what i learned: R needs a few things that are not that well documented and that don't necessarily come as part of El Capitan with Developer tools installed. You need a fortran compiler (gfortran), a Java Development kit (JDK) and it helps I think to install Autoconf and Automake and libtool which are not now normally installed on Mac OS X.
So i installed all these things and was able to sucessfully compile R (independently of galaxy) as a separate download and install.
However when I then tried to reinstall the "all_cufflinks" repository using Admin in Galaxy it still did not complete the install saying the C compiler failed to compile the R source. Most other things were sucessfully installed.
Does the "galaxy" user need to have Admin privileges ? This is what i will try next. However i thought this is not what you want on a Galaxy install for security purposes.
Any tips appreciated.