Hi,

I have tried to follow instructions provided with this installation

a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts.

I successfully ran the setup scrip but is there other path and conf that need to be done apart from those done by this script ?

b) Inside the mex folder execute the make file to create platform dependent .mex files
cd mex/Makefile
make [interpreter]
make octave for octave
make matlab for matlab

make all for octave and matlab

When I run make octave I get the following error message :

/usr/bin/mkoctfile -g --mex get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp -I/mnt/galaxyTools/tools/samtools/0.1.16 -L/mnt/galaxyTools/tools/samtools/0.1.16 -lbam -lz -lcurses

get_reads_direct.cpp:14:17: fatal error: sam.h: No such file or directory

compilation terminated.

make: *** [get_reads.mex] Error 1

It feels like this is link to samtools, when browsing on the web I found information about SAMTOOLS_ROOT env variable but changing this one doesn't solve my problem.

As anyone else encounter this kind of things ?

Regards,

Philippe