So one of my colleagues has a script he wants to turn into a  Galaxy
tool. The twist is that script:


1.       Looks for files with a fixed name (e.g. "params.txt")

2.       Accepts other file names as commandline arguments, but the
actual names of those files has arguments embedded in it  (e.g.
"nuc_100iter_b.fasta" for nucleotide data in fasta format to be run
against model b for 100 iterations.)


I know, awkward and clumsy. But hardly unique for many historical
bioinformatic tools. Anyway, the challenge for me is to pick the easiest
path to port this script to a tool. And it seems to be fairly awkward
under the Galaxy model as I understand it. Possibilities:


1.       Rewrite the script argument parsing and invocation. Obviously,
there will be resistance to this and with some justification ("I thought
you said this could wrap any command line program ...")

2.       Write a script that calls the original script after moving and
renaming files according to desired arguments. Any problems with a
two-script/executable tool like this? How do I specify the interpreter
for both parts of the script?

3.       Use config files for the fixed name files. But configuration
files seem to be given a random not fixed name, correct?

4.       For the file names with semantic content, extract that from the
dataset metadata. Of course, then it still has to be passed to the
original script somehow.

5.       Use <code>


Ideas, suggestions? Obviously a rewrite is the "best" solution, but in
this case we might be looking for the quickest ...



Paul Agapow (

Bioinformatics, Centre for Infections, Health Protection Agency


The information contained in the EMail and any attachments is
confidential and intended solely and for the attention and use of
the named addressee(s). It may not be disclosed to any other person
without the express authority of the HPA, or the intended
recipient, or both. If you are not the intended recipient, you must
not disclose, copy, distribute or retain this message or any part
of it. This footnote also confirms that this EMail has been swept
for computer viruses, but please re-sweep any attachments before
opening or saving. HTTP://
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

Reply via email to