How to add tophat and bowtie to the path?
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?
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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.
Cheers!
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.
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.
It appears that you are setting the PATH for
bowtie2to 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.