Question: R installation for cufflinks failure
gravatar for idrummond
2.7 years ago by
idrummond0 wrote:

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.

rna-seq cufflinks • 739 views
ADD COMMENTlink modified 2.6 years ago • written 2.7 years ago by idrummond0
gravatar for idrummond
2.6 years ago by
idrummond0 wrote:

here is the relevant error:

tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:R DEBUG 2016-04-05 15:16:38,318 checking for gcc... gcc

install_environment.STDOUT DEBUG 2016-04-05 15:16:39,636 checking whether the C compiler works... no

tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:R DEBUG 2016-04-05 15:16:39,666 checking whether the C compiler works... no

it finds gcc but says it does not work.

however gcc works for all the other repository programs and for installs independent of Galaxy.

giving the "galaxy" user admin privileges did not help.

maybe its finding a different gcc? I don't think there is a different gcc on this computer.


ADD COMMENTlink written 2.6 years ago by idrummond0
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