why mirnakey can't find bwa

Question

[zizigolu]

hi,

I have already installed bwa but whenver I am trying mirnakey telling Burrows-Wheeler Aligner must be installed to run miRNAkey (please see help -> requirements).

what should I do please?

[Devon Ryan]

Is bwa in your PATH?

[zizigolu]

thank you Devon,

this is path to bwa : /usr/home/izadi/Downloads/bwa-0.7.12/

this is path to mirnakey: /usr/data/nfs6/izadi/miRNAkey/

how I can put them in path please?

I did like so

export PATH=$PATH:/usr/home/izadi/Downloads/bwa-0.7.12/ /usr/data/nfs6/izadi/miRNAkey/

but error is the same

[Devon Ryan]

export PATH=$PATH:/usr/home/izadi/Downloads/bwa-0.7.12:/usr/data/nfs6/izadi/miRNAkey

Note the colon where you had a space before.

[zizigolu]

thank you

[izadi@lbox200 ~]$ cd /usr/home/izadi/Downloads/bwa-0.7.12/

[izadi@lbox200 bwa-0.7.12]$ export PATH=$PATH:/usr/home/izadi/Downloads/bwa-0.7.12:/usr/data/nfs6/izadi/miRNAkey Bad : modifier in $ '/'.

[izadi@lbox200 bwa-0.7.12]$

I also tried

echo 'export PATH=$PATH:/usr/home/izadi/Downloads/bwa-0.7.12' /usr/data/nfs6/izadi/miRNAkey

but error again

:(

[Devon Ryan]

Apparently you're not using bash, but tcsh or something like that. I think you use setenv or something like that on such shells.

[zizigolu]

DEvon I am with fedora 22 I think is bash

[GenoMax]

You are using tcshell at the moment (based on the result below).

[GenoMax]

What does echo $SHELL show? If it shows tcsh/csh in there somewhere then

setenv PATH $PATH:/path_you_want_to_add

[zizigolu]

thank you

[izadi@lbox200 izadi]$ echo $SHELL

/bin/tcsh

[izadi@lbox200 izadi]$

[zizigolu]

sorry I did like below

[izadi@lbox200 izadi]$ cd /usr/home/izadi/Downloads/bwa-0.7.12/

[izadi@lbox200 bwa-0.7.12]$ setenv PATH $PATH:/usr/data/nfs6/izadi/miRNAkey/ Bad : modifier in $ '/'.

[izadi@lbox200 bwa-0.7.12]$

Answer 1

[zizigolu]

[izadi@lbox200 ~/Downloads]$ setenv PATH $PATH\:/usr/home/izadi/Downloads/bwa-0.7.12/

[izadi@lbox200 ~/Downloads]$ setenv PATH $PATH\:/usr/data/nfs6/izadi/miRNAkey/