Off topic:Trinity Won'T Find Bowtie2
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7.5 years ago
Biojl ★ 1.7k

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 • 4.3k views
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