Question: How to make bowtie available via PATH settings ?
0
gravatar for iamtuttu5
3.9 years ago by
iamtuttu540
United States
iamtuttu540 wrote:

Dear all,

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

/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 (yellow):

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,

assembly rna-seq bowtie ubuntu • 4.0k views
ADD COMMENTlink modified 3.9 years ago by biocyberman800 • written 3.9 years ago by iamtuttu540
1
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Devon Ryan92k
1
gravatar for biocyberman
3.9 years ago by
biocyberman800
Denmark
biocyberman800 wrote:

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/

ADD COMMENTlink written 3.9 years ago by biocyberman800
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