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Old 03-11-2014, 09:39 PM   #1
dokadya
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Location: bangalore

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Posts: 5
Default MuSiC tool integration to Galaxy NGS

Hi, I want to integrate tool MuSiC 2 into Galaxy NGS.
Music tool website: http://gmt.genome.wustl.edu/genome-s...4/install.html and Galaxy website: https://usegalaxy.org/

I am considering 3 commands for now to integrate into galaxy.

calc-covg-helper
calc-covg
calc-bmr
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.
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Old 03-13-2014, 01:36 PM   #2
nnutter
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Location: Illinois, United States

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Default

Was also crossposted on Biostar: http://www.biostars.org/p/95051/#95250
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Old 03-23-2014, 10:40 PM   #3
dokadya
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Location: bangalore

Join Date: Mar 2014
Posts: 5
Unhappy

i have seen both, and i was unable to watch video i tried to download video its just 200kb. May be video was moved to new place.

i have made xml files xml accourdingly, but due to folder issue i am creating local scripts which i can say patch for current problem and not solution. Because script need changes whenever you change folder location. Also as I mentioned earlier, Galaxy write its input in some other folder, its little hard to get last written file by galaxy, and if we get also we have to move it to main location so that MuSiC can goto specific location and fetch it again.

Why MuSiC is not asking files directly ? I tried contacting MuSiC 2 developers but no reply from them regarding tool integration to Galaxy (MuSiC 2 research paper says, they have integrated tool to galaxy).

Tool integration is little difficult due to MuSiC 2 is fetching files from specific location.
Do anyone have answer for that ?
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