Question: (Closed) How to add tophat and bowtie to the path?
gravatar for mirza
2.5 years ago by
mirza80 wrote:

Hi, I am using ubuntu 16.04 and tried using a command suggested in one of the posts (C: how i can put bowtie2 with tophat2 in the path? ; by alolex) to add tophat and bowtie to my path but I think I wasn't successful.

The command I used,

$ export PATH=$PATH:$home/gjjha/Downloads/softwares/bowtie2-2.2.9/index:/home/gjjha/Downloads/softwares/tophat-2.1.1

$ which bowtie2 returns /usr/bin/bowtie2 but echo $PATH shows neither of them in the path. I also tried running tophat from a directory , it also shows that tophat can't find the b2 index files. What am I doing wrong?

ADD COMMENTlink modified 2.5 years ago by genomax68k • written 2.5 years ago by mirza80

Hello mirza!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 2.5 years ago by Pierre Lindenbaum121k

Yes, I know and I used the command from a similar post only (I have mentioned above). I tried asking there but since i didn't receive an answer so I created a new post.

ADD REPLYlink written 2.5 years ago by mirza80

Both these posts have been created an hour ago. Multiple posts for the same question don't increase your changes - in fact they only call moderator attention and decrease your chances. Please do not repeat this.

ADD REPLYlink written 2.5 years ago by RamRS22k

It appears that you are setting the PATH for bowtie2 to an "index" directory inside the "bowtie2" folder. There also appears to be a $ (before home) at the beginning of your PATH command as typed above.

You have a bowtie2 in /usr/bin, which may be an older version. You would need to deal with that if you want to use the one in your Downloads directory.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax68k
Please log in to add an answer.
The thread is closed. No new answers may be added.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1142 users visited in the last hour