I want to integrate tool MuSiC 2 into Galaxy NGS.
Music tool website: http://gmt.genome.wustl.edu/genome-shipit/genome-music/0.4/install.html and Galaxy website: https://usegalaxy.org/
I am considering 3 commands for now to integrate into galaxy.
calc-covg need it input from ./roi_covgs/samplename.extension . This checking is done by software itself and we not provide file name while running command. calc-bmr creates another folder ./gene_covgs/ . While integrating music i don't know which location to use as galaxy follow its own file format and directory structure.
I have uploaded files using admin section by linking files from hard disk location. Also to collect output at a particular location, I have changed galaxy config file to store output at particular location. Yet i don't know which is file what, because galaxy have its own file name.
But while running these command, I don't know which is the base folder where these commands are running. Also If I get to know, accordingly to that I have to change its file name each time the result produce by command (as galaxy gives its own file name and extension).
In short : I don't know how can I force galaxy to use particular location and how i can tell galaxy that, tool is creating folders and files too. i just need interface to run the command, hence i wish for normal structure which we observe after running through command line.
Waiting for positive reply.