I am trying to install trinity on our schools server. I have installed it into my home directory since I do not have access to install it to the bin. I then ran the "make" command and "make plugins." Everything seemed to be running smoothly, however, when I went to run Trinitys sample code, I got this error:
which: no samtools in (/home/npetrill/trinityrnaseq-2.1.1/trinity-plugins/BIN:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/npetrill/bin:/usr/local/bin/trinityrnaseq-2.0.6:/usr/local/bin/bowtie-1.1.2:/home/npetrill/samtools-0.1.19:/home/npetrill/scripts) Error, cannot find samtools. Please be sure samtools is installed and included in your PATH setting.
I set my path so that it would search the directory in which samtools is in, however, I keep getting this error message. Does anyone know what I am doing wrong here?
Thank you for your help!