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export function in linux

Hello,

I have a file containing the reads and reference genome. How I can tell bowtie2 where are the which it need now?

[izadi@lbox161 ~]$ pwd
/usr/people/home/izadi

[izadi@lbox161 ~]$ ls
0-coot-history.py   fereshteh              snapshot2.png
0-coot-history.scm  Music                  sratoolkit.2.5.2-centos_linux64
Desktop             ncbi_error_report.xml  Templates
Documents           Pictures               Videos
Downloads           Public

[izadi@lbox161 ~]$ cd fereshteh/

[izadi@lbox161 ~/fereshteh]$ ls
bedtools2      cutadapt-1.8.3  pip-7.1.0     sratoolkit.2.5.2-centos_linux64
bowtie2-2.2.5  FILES           samtools-1.2

[izadi@lbox161 ~/fereshteh]$ cd bowtie2-2.2.5/
[izadi@lbox161 bowtie2-2.2.5]$ ls
AUTHORS                bowtie2-build-s          LICENSE
bowtie2                bowtie2-build-s-debug    MANUAL
bowtie2-align-l        bowtie2-inspect          MANUAL.markdown
bowtie2-align-l-debug  bowtie2-inspect-l        NEWS
bowtie2-align-s        bowtie2-inspect-l-debug  scripts
bowtie2-align-s-debug  bowtie2-inspect-s        TUTORIAL
bowtie2-build          bowtie2-inspect-s-debug  VERSION
bowtie2-build-l        doc
bowtie2-build-l-debug  example

[izadi@lbox161 bowtie2-2.2.5]$ pwd
/usr/people/home/izadi/fereshteh/bowtie2-2.2.5

[izadi@lbox161 bowtie2-2.2.5]$ bash

[izadi@lbox161 bowtie2-2.2.5]$ export BT2/usr/people/home/izadi/fereshteh/bowtie2-2.2.5
bash: export: `BT2/usr/people/home/izadi/fereshteh/bowtie2-2.2.5': not a valid identifier

[izadi@lbox161 bowtie2-2.2.5]$ echo $BT2

[izadi@lbox161 bowtie2-2.2.5]$ pwd
/usr/home/izadi/fereshteh/bowtie2-2.2.5
[izadi@lbox161 bowtie2-2.2.5]$ cd /usr/people/home/izadi/fereshteh/FILES

[izadi@lbox161 FILES]$ pwd
/usr/people/home/izadi/fereshteh/FILES

[izadi@lbox161 FILES]$ ls
Coli_Protein_Coding_genes.fa      coding_genes.2.bt2       rRNA.1.bt2
Ecoli_rRNA.fa                     coding_genes.3.bt2       rRNA.2.bt2
SRR493748.fastq                   coding_genes.4.bt2       rRNA.3.bt2
SRR493748_trimmed.fastq           coding_genes.rev.1.bt2   rRNA.4.bt2
SRR493748_trimmed_unmapped.fastq  coding_genes.rev.2.bt2   rRNA.rev.1.bt2
coding_genes.1.bt2                mapped_and_unmapped.sam  rRNA.rev.2.bt2

[izadi@lbox161 FILES]$ $BT2/bowtie2-build Ecoli_rRNA.fa rRNA
bash: /bowtie2-build: No such file or directory
bowtie2 fedora
• 161 views • link
updated by Ram Ram • written by zizigolu zizigolu

1 answer 

export BT2="/usr/people/home/izadi/fereshteh/bowtie2-2.2.5"
• 0 views • link
updated by Ram Ram • written by russhh russhh

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