Plink (genetics) and PuTTY Link confusion in linux

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9.4 years ago

Varun ▴ 30

Hello,

I am trying to run a gene based analysis using VEGAS using a linux terminal (ubuntu precise). The programme require plink to be installed and called accordingly. However, the computer also has PuTTY Link which is also called plink installed, and now when I run the programme, it's not calling the correct plink (the genetic version). Does anyone know how I can work around this?

Thanks,
Varun

snp software-error • 3.5k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by Varun ▴ 30

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Why don't you just use the full path?

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by GouthamAtla 12k

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I am not familiar with VEGAS software. If this software calls plink, then there should be a line in the VEGAS or VEGAS configuration file for the default path to plink. Edit that line and add the full path to plink.

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by Siva ★ 1.9k

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Thanks both. I renamed plink in the config file and the executable file. So it works now.

Cheers,
Varun

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by Varun ▴ 30

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Renaming a binary is not a good idea. configuring it properly.

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.4 years ago by GouthamAtla 12k

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How can I install Plink in the server and how to change its name in the configuration file?

ADD REPLY • link 7.4 years ago by forever ▴ 80

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