Trinity alignment problem

[sarika01]

Dear All
I have used trinity for assembly it run and given me trinity.fasta
after that i want to run align_and_estimate_abundance.pl it gives following error
pls rectify this problem


[user@wrk08 sarika]$ trinityrnaseq-2.0.6/util/./align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference
which: no bowtie-build in (/home/user/Desktop/sarika/trinityrnaseq-2.0.6/util/../trinity-plugins/rsem:/home/user/Desktop/sarika/tools/bowtie2-2.2.5:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/user/bin:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/rsem-1.2.21/)
ERROR, cannot find bowtie-build in PATH setting: /home/user/Desktop/sarika/trinityrnaseq-2.0.6/util/../trinity-plugins/rsem:/home/user/Desktop/sarika/tools/bowtie2-2.2.5:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/user/bin:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/rsem-1.2.21/

which: no bowtie in (/home/user/Desktop/sarika/trinityrnaseq-2.0.6/util/../trinity-plugins/rsem:/home/user/Desktop/sarika/tools/bowtie2-2.2.5:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/user/bin:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/rsem-1.2.21/)
ERROR, cannot find bowtie in PATH setting: /home/user/Desktop/sarika/trinityrnaseq-2.0.6/util/../trinity-plugins/rsem:/home/user/Desktop/sarika/tools/bowtie2-2.2.5:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/user/bin:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/bowtie2-2.2.5/:/home/user/Desktop/sarika/tools/samtools-1.2/:/home/user/Desktop/sarika/tools/rsem-1.2.21/

Please be sure bowtie and express are installed and the utilities samtools bowtie-build bowtie rsem-calculate-expression are available via your PATH setting.

[westerman]

Please be sure bowtie and express are installed and the utilities samtools bowtie-build bowtie rsem-calculate-expression are available via your PATH setting.

Do what the error message says.