Hi Wolfgang
short answer:
Please, put your package into the Galaxy Tool Shed. This makes it
visible to the whole Galaxy community and everybody can profit from it.
long answer:
I have been in the same boat. We never put the Galaxy wrappers and the
perl scripts of our old NGS pipeline into the Tool Shed. I do feel bad
about this. My excuse has always been that too much local customization
would be necessary, eg making possible to store data outside the Galaxy
directory tree. Hence, we only distributed the package as bunch of files
on request. Obviously, there were hardly any requests.
Now we are in a similar situation. We are in the process of making our
new R/Bioconductor based NGS pipeline available on our internal Galaxy
server. And the code is far from being ready to be put into the Tool
Shed. But this time we will make the effort. So the Galaxy community can
benefit from it (@Dave Clements: Unfortunately, it won't be ready for
Baltimore).
Regards, Hans-Rudolf
On 06/05/2014 11:52 PM, Wolfgang Maier wrote:
Dear all,
I am maintaining a (still young) suite of command line tools (written in
Python) for identification of mutations in model organism genomes
through whole-genome sequencing (https://sourceforge.net/projects/mimodd/).
MiModD aims at geneticists that do not have much background in
bioinformatics, and it's supposed to make WGS analysis for small model
organism genomes (anything from yeast to fish) possible on regular PCs,
so it's not a cloud/cluster solution.
We do support Galaxy though through a complete set of tool wrappers for
three reasons:
- to provide a graphical user interface
- to offer labs the possibility to install the software on one dedicated
machine, but run analyses from any machine (typically with Windows
installed)
- to keep analysis workflows documented and reproducible.
Currently, we advise users to take advantage of these features and
install a local instance of Galaxy even though it will be running then
only on a single desktop PC (or even just a notebook). After
installation of Galaxy our software simply copies its wrapper xmls over
to the tools folder and modifies the tool_conf file to integrate itself.
In addition, users have to install a bit of other third-party software
(samtools, snap aligner, optionally snpeff) that our code relies on.
[End of lengthy introduction]
So my question is: in what way could the package profit from being
uploaded to a Galaxy toolshed ? I guess it would mean quite some extra
work from my side since I'm not familiar with the whole procedure, so
are there benefits (visibility, ease of installation, etc.) that are
worth the effort ?
Thanks a real lot for any feedback,
Wolfgang
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