How to set or change the default software path in R -

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i have program called "bowtie2" , changed default path in terminal:

$export path=/opt/ngs/bowtie2-2.2.8:/usr/local/sbin:/usr/local/bin:/usr/sbin $bowtie2 --version /opt/ngs/bowtie2-2.2.8/bowtie2-align-s version 2.2.8

but when call r it's still old version other path:

> bowtie2="bowtie2" > system2(bowtie2,"--version",stdout=true)[1] [1] "/usr/bin/bowtie2-align version 2.1.0"

my question how change default path program in r (so version "/opt/ngs/bowtie2-2.2.8/bowtie2-align-s version 2.2.8" rather "/usr/bin/bowtie2-align version 2.1.0")

you need add export path=/opt/ngs/bowtie2-2.2.8:/usr/local/sbin:/usr/local/bin:/usr/sbin end of .bashrc(linux) or .bash_profile(mac) file in home folder.

vi ~/.bash_profile

and add export command @ end of file, otherwise work current shell session. when use system command in r, launches new shell session, export command won't apply to.

see this link find out more export command


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