Question: Installing Trinity, Error with Samtools
gravatar for nikelle.petrillo
4.9 years ago by
Providence College, Providence, RI
nikelle.petrillo100 wrote:


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! 

myposts rna-seq samtools trinity • 3.5k views
ADD COMMENTlink modified 4.9 years ago by • written 4.9 years ago by nikelle.petrillo100
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4.9 years ago by
Philadelphia, PA wrote:

When installing programs with make files, like samtools, one can specify the install path for the program. To do this when typing make simply enter: 'make prefix=/path/to/dir install' when running 'make install' This will install samtools in the directory that you wish. However, as indicated by Trinity, you need to set samtools in your path. I keep a directory in my home directory called 'bin', in which I install programs such as these. Then in .bashrc, enter a line to export the path to this directory: 'export PATH=$PATH:/home/your_home/bin'. Restart the terminal, and type 'echo $PATH'. Your home directory bin folder should now show up in your path as well as any others that are being exported, plus the typical /usr/local/bin/; /usr/bin; etc.

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