Installing R in the cluster :)

I managed to install R packages inside the cluster in the local folder.


shell script to run the R install file :

packs=c("zoo","snow","caTools")

for(i in 1:length(packs)){

        install.packages(packs[i],lib="/mnt/home/sinha/Rpackages",dependencies=TRUE,repos='http://cran.us.r-project.org')

}

Then change the bashrc file by adding the following lines

if [ -n $R_LIBS ]; then

   export R_LIBS=/mnt/home/sinha/Rpackages:$R_LIBS

else

   export R_LIBS=/mnt/home/sinha/Rpackages

fi

Similar install perl packages using cpanm  and change the bashrc file by adding the following lines

eval $(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)

eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`

export MANPATH=$HOME/perl5/man:$MANPATH

Installing Repeat Enrichment Estimator in Mac OSX Yosemite

First the there was the problem of installing the Bio::DB::Fasta files and in general BioPerl
Finally was able to install it using cpanm for some reason installing inside span gave errors.

Then trying install the bwa was a mess. It constantly gave the error

ld: warning: ignoring file bwt_gen/libbwtgen.a, file was built for archive which is not the architecture being linked (i386): bwt_gen/libbwtgen.a

Undefined symbols for architecture i386:

  "_bwt_2occ", referenced from:

      _bwt_match_exact in bwt.o

      _bwt_match_exact_alt in bwt.o

      _bwt_cal_width in bwtaln.o

  "_bwt_2occ4", referenced from:

      _bwt_match_gap in bwtgap.o

  "_bwt_bwtgen", referenced from:

      _bwa_index in bwtindex.o

  "_bwt_bwtgen_main", referenced from:

      _main in main.o

ld: symbol(s) not found for architecture i386

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [bwa] Error 1

What really worked was the following:

Install Xcode, gcc(5.1) 

In the Makefile change the following flags

Originally commands

CC= gcc

CXX= g++

CFLAGS= -Wall -O3 -m64 

Modified

CC= gcc-5

CXX= g++-5

CFLAGS= -Wall -O3 -m64 -fgnu89-inline