Re: [galaxy-dev] to put or not to put a tool suite into the toolshed
Thanks a lot for all the encouraging feedback. More than anything else the friendly atmosphere that seems to prevail on this mailing list makes me think that it may indeed be worthwhile to make the package available to this community ! I will have a closer look at the toolshed instructions and see if I get along with them. Have a nice weekend, Wolfgang ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] to put or not to put a tool suite into the toolshed
Hi Wolfgang, 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 ? Yes, it would mean extra work for you, but it is worth the effort. One main reason, you already mentioned, visibility. If done right and you are supporting your wrapper these will probably be used by many different Galaxy Servers out there. Just have a look at a few tools that are from the same field as your tools and look at the download counter. Easy installation is also one reason, as soon as you have a Galaxy server it can be trivial to install your tools, suppose you define all dependencies. -> But defining dependencies is easy nowadays, and even better, many dependencies are already available in the Tool Shed. If you depend on numpy, insert a few lines to point to the correct numpy dependency and you are done. We can help you if you encounter any problems in that step, or just drop by during the GCC developer workshop. We will give a hands-on how to wrap your tools. Reproducibility: With the Tool Shed you get reproducibility for free. You can install many different version of your tools and Galaxy will take care to select the correct one to reproduce your results. You can also share your workflows in the Tool Shed. Convince others from your tools, export your workflows and and anyone can test it with a few clicks. Be part of a very nice community, which tries hard to make bioinformatic (and more) tools accessible for everyone. Convinced? :) Cheers, Bjoern Thanks a real lot for any feedback, Wolfgang ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] to put or not to put a tool suite into the toolshed
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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] to put or not to put a tool suite into the toolshed
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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
