you can specify your samtools as part of your path in your bashrc or
profile or equiv. shell file.

e.g.
PATH=$PATH:location of Samtool
export PATH

> Hello all,
>
> Please forgive me if this seems like an obvious question, but when I try
> running the alignReads.pl script I get the following error:
>
> Error, path to required samtools cannot be found at
> /Users/wolniaklab/desktop/Bioinfromatic/trinityrnaseq_r2011-11-26/util/alignReads.pl
> line 182.
>
> Can somebody give me a hint as to how I need to specify where samtools is
> for this script? Or, am I supposed to put my samtools directory in a
> certain location?
>
> Thank you,
> T
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> Trinityrnaseq-users mailing list
> Trinityrnaseq-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/trinityrnaseq-users
>
>
>



------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Trinityrnaseq-users mailing list
Trinityrnaseq-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/trinityrnaseq-users