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both old and new Tophat with old and new bowtie present on server

Hi everyone,

I am trying to install tophat-2.0.12.Linux_x86_64 and bowtie2-2.2.3 on a server that has an older version of these software

After unzipping the files I put it in my path by modifying .bashrc

echo $PATH shows it is in path

/home/aloo/software/bowtie2-2.2.3:/home/aloo/software/tophat-2.0.12.Linux_x86_64

Now when I type which tophat, it give me the location

/usr/local/sam/bin/tophat  
/usr/local/sam/bin/bowtie

which is the other place it is installed with older version. So when I run the command from the folder where my binaries are

./tophat2 -o shams -G Homo_sapiens.gtf -p 8 ref_ensemble/GRCh38.dna A.fastq --segmentlength 37

I get this error

Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2015-01-23 19:03:27] Checking for Bowtie
Error: TopHat requires Bowtie 2.0.5 or later

As on server old version is installed bowtie-0.12.7 while the version that I download and put in path is bowtie2-2.2.3

How can force tophat to use this new version and ignore older version installed on server

tophat linux bowtie rna-seq
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updated by Ram Ram • written by Tark • Tark

1 answer

You can add your tophat to PATH in such a way that it is found before the system wide tophat. To do that, use

PATH=/home/aloo/software/bowtie2-2.2.3:/home/aloo/software/tophat-2.0.12.Linux_x86_64:$PATH

This will use your version of tophat by default.

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written by Ram Ram

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