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.m...@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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