Question: Emboss Programs With Graphical Output(S)
0
Martin Senger • 50 wrote:
Hi,
I am new to Galaxy (but not to EMBOSS :-)) - so I may be doing
something
stupid. Sorry if I do. I am referring to my own local Galaxy
installation.
1) I noticed that most of the emboss graphical programs (e.g. plotorf)
are
executed from/by the perl interpreter, e.g.:
perl /home/galaxy/galaxy-dist/tools/emboss_5/
emboss_single_outputfile_wrapper.pl plotorf -sequence ...
These programs are working fine.
2) There are few other programs that could produce a graphical output
(freak, hmoment, iep) but they don't because the toggle "-plot" is not
used
in their command line. Therefore, strictly speaking, they are also
working
fine (producing tables instead of graphs).
3) But there are two programs, prettyplot and pepnet, that are called
without any wrapper (no perl interpreter), e.g.
pepnet -sequence ...
and they produce graph (as PNG), indeed, but this graphical result is
not
shown in Galaxy. Instead, I am getting there an image showing just the
text
of a URL (attached). And metadata/report on this result says:
114: prettyplot on data 1
empty
format: png, database: ?
Info: Created
/home/galaxy/galaxy-dist/database/files/000/dataset_116.dat.1.png
I do not know why there is an "empty" remark - because the PNG file is
created, and it is a PNG file, it is just not shown in the Galaxy.
I wonder what I have wrongly configured...?
Thanks for any help,
Martin
--
Martin Senger
email: martin.senger@gmail.com,martin.senger@kaust.edu.sa
skype: martinsenger