Question: both old and new Tophat with old and new bowtie present on server
0
gravatar for Tark
5.2 years ago by
Tark50
japan
Tark50 wrote:

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 uzipping 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

linux bowtie rna-seq tophat • 2.6k views
ADD COMMENTlink modified 5.2 years ago by RamRS26k • written 5.2 years ago by Tark50
0
gravatar for RamRS
5.2 years ago by
RamRS26k
Houston, TX
RamRS26k wrote:

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.

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by RamRS26k
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