NBIC Galaxy Server: Galaxy Module Repository
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To add your modules, you could upload the source code and wrapper file to the galaxytools repository (https://trac.nbic.nl/galaxytools). This repository (nbic_gmr) is mirrored to the NBIC Galaxy server. The following picture explains its location at NBIC Galaxy server and how it is organized.
galaxy-dist | |-----tools/ | | | |-----nbic_gmr/ (A customized directory links to NBIC Galaxy repository) | | | |-----tools/ | | | | | |-----general/ | | | | | |-----ngs/ | | | |----Alignment/ (all modules for sequence alignments) | | | |----De novo/ (all modules for de novo alignments) | | | |----Benchmarking/ (all modules for benchmarking) | | | | | | | ... | | | | | |-----proteomics/ | | | |----Peak finder/ | | ... |---- | | |---- | | | | | ... | | | |-----pipelines/ | | | | | |-----general/ | | | | | |-----ngs/ | | | |----GAPSS/ | | | |----ChipSeq/ | | | |----Benchmarking/ (all pipelines for benchmarking) | | | | | | | ... | | | | | |-----proteomics/ | | | |----msCompare/ | | ... |---- | | |---- | | | | | ... | | | |-----Data/ | | | | | ... | | | |-----Documentations/ | | | | | ... | | | |----LICENSE | |----README | |---- tool-data | |---- ...
Please add your program at an appropriate task force location, e.g. ngs, proteomics, etc. The choice of associating your program to either tools or pipelines depends on how you can position your program. If your program is developed to offer an end to end service (e.g., GAPSS that offers alignment, SNP calling, and annotations), then it can be located in pipelines. If your program is developed to support a specific function (e.g. converting file format), then it is best to be located in tools.
To make the installation easier, please create a small README file to explain a bit your tool and how to set it up. Please also try to avoid any hard coded links to libraries/modules/data files in your code. Please also refer to a list of currently supported tools and their versions to adjust your module.
Once you uploaded the files, please send the maintenance team an email and we will install the code at the NBIC Galaxy server accordingly. Of course, if you need any question or require any technical assistance, you are also welcome to contact us.
