How to make bowtie available via PATH settings ?

Question

[iamtuttu5]

Dear all,

I'm trying to run the script align_and_estimate_abundance.pl with the command:

/usr/local/trinityrnaseq-2.0.6/util/align_and_estimate_abundance.pl \
  --transcripts ./Step_2_Assembled/Trinity.fasta \
  --est_method RSEM \
  --aln_method bowtie \
  --trinity_mode \
  --prep_reference

but is showing the following error message:

ERROR, cannot find rsem-calculate-expression in PATH setting: /usr/local/trinityrnaseq-2.0.6/util/../trinity-plugins/rsem-1.2.19/./rsem-calculate-expression:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/cd-hit:/usr/lib/cd-hit
Please be sure bowtie and express are installed and the utilities samtools bowtie-build bowtie rsem-calculate-expression are available via your PATH setting

I can not understand why the error. Please any suggestions?

Thanks for your attention,

Answer 1

[Devon Ryan]

You meant to add

/usr/local/trinityrnaseq-2.0.6/trinity-plugins/rsem-1.2.19

rather than

/usr/local/trinityrnaseq-2.0.6/util/../trinity-plugins/rsem-1.2.19/./rsem-calculate-expression

Answer 2

[biocyberman]

First, identify the path you want to add that contains bowtie. Let's say it is in /usr/local/trinityrnaseq-2.0.6/util/

Then add that path to PATH by adding the following lines to .bashrc (I assume you are using bash shell) under your home directory.

PATH=$PATH:/usr/local/trinityrnaseq-2.0.6/util
export PATH

You need to logout and login again to have the new PATH loaded

This is very simple instruction for beginer. Read more in this page if you want to understand more: http://www.cyberciti.biz/faq/unix-linux-adding-path/