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