Question: (Closed) Trinity Won'T Find Bowtie2
0
gravatar for Biojl
6.4 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

Hi,

I'm trying to run trinity and I'm getting the error:

...

which: no bowtie in (/home/josepl/Desktop/software/Version_8.97_101117/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/soft/bio/sequence/mafft-6.857/bin:/soft/bio/sequence/bowtie2-2.1.0/:/soft/bio/sequence/samtools-0.1.7a/:/soft/bio/sequence/tophat-2.0.8/bin/tophat:/home/josepl/bin)

...

I have the path exported. Presumably the error appears because he is looking for Bowtie and I have installed Bowtie2. Anyone knows if there is an option to tell trinity to use bowtie2?

Thanks

trinity • 3.9k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 6.4 years ago by Biojl1.7k
1

Even if you created a link, the syntax for using bowtie2 is slightly different from that for bowtie1, so I suspect you'd end up needing to edit the trinity.pl script anyway.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Devon Ryan94k

I think you are right, this thread from Trinity SourceForge page talks about the same thing, so I guess Biojl will need a local installation of bowtie

ADD REPLYlink written 6.4 years ago by Sudeep1.6k

Isn't it easy to create a symbolic link with name bowtie linking to bowtie2 in bowtie2 bin folder ?.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Sudeep1.6k

I can do that in my workstation but I cannot modify the software in a cluster, where everybody uses it.

ADD REPLYlink written 6.4 years ago by Biojl1.7k

Well, you could create a symbolic link in $HOME/bin and export that to your path. However, see my comment below.

ADD REPLYlink written 6.4 years ago by Devon Ryan94k

Hello Biojl!

We believe that this post does not fit the main topic of this site.

No longer relevant.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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

Cheers!

ADD REPLYlink written 2.7 years ago by Michael Dondrup47k
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