[gt-users] Fwd: Genome tools sketch yields blank png

[Sascha Steinbiss]

Hi Mark,

> We're running CentOS-5.2 and CentOS-5.3 on the two systems we've tested. "Nearly 
> blank" means the image is all white except for a black vertical line a few 
> pixels high on the image (I'll attach an example).

I have set up a CentOS 5.3 (amd64) system in a virtualization
environment to reproduce your issue. However, I used yum to install
external library packages from the CentOS binary repositories (cairo,
ncurses, glibc-devel...). I wonder why you chose to build the pixman and
cairo libraries by hand. Did you have a specific reason to do this?

> Here are the package versions we used:
> pixman-0.16.2.tar.gz
> cairo-1.8.8.tar.gz
> genometools-1.3.3.tar.gz

My versions are a bit older (cairo 1.2.4, I did not have to install a
separate pixman package). However, I am currently preparing the same
package versions you used, to reproduce your environment as closely as
possible.

> Here is a command-line that fails. The problem seems to be with some part of the 
> build not the particular data-set, since we get the same sort of image no matter 
> what. In contrast, building on a 32-bit CentOS-5.x system gives no trouble and 
> we get the expected output.

Did you build a proper 64-bit genometools binary by adding the
'64bit=yes' option to your make call? If not, please try that first as
running a 32bit binary on a 64bit system has lead to problems before.

> gt sketch -width 1024 -force -flattenfiles -addintrons -seqid 1 -start 1 -end 
> 20000 minimal.png minimal.gff3
<snip>

This command produces, on my CentOS system, perfectly fine images with
both 32-bit and 64-bit genometools binaries (see attachment). The
introns look different in your image than in mine -- did you change
something in the default style file?

> Let me know if we can provide other details.
> Mark

Please retry with the '64bit=yes' option enabled during compilation and
report whether this has any influence on the resulting image.
I will report back when I have evaluated the current versions of cairo
and pixman.

Sascha

-- 
Sascha Steinbiss
Center for Bioinformatics
University of Hamburg
Bundesstr. 43
20146 Hamburg
Germany

Email:  steinbiss at zbh.uni-hamburg.de
URL:    http://www.zbh.uni-hamburg.de/steinbiss
Phone:  +49 (40) 42838 7322
FAX:    +49 (40) 42838 7312


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