Hi Philipe

Look into the bin/deseq_config.sh and see if the path to octave and samtools have been set correctly.

I'm having problem running DESeq too. I go past this point by I get

get_reads.mex
error: path/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: failed to load: /mnt/all/cloudman/galaxy/

clare/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: undefined symbol: bam_index_destroy

error when trying to run get_reads.mex in octave.

Mahtab

On Fri, Mar 1, 2013 at 3:54 PM, Philipe Moncuquet <philippe.mcqt@gmail.com> wrote:

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

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