Trinity Won'T Find Bowtie2
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
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Isn't it easy to create a symbolic link with name
bowtielinking tobowtie2in bowtie2 bin folder ?.I can do that in my workstation but I cannot modify the software in a cluster, where everybody uses it.
Well, you could create a symbolic link in $HOME/bin and export that to your path. However, see my comment below.
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.
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
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