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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