Jellyfish missing?

[sr320]

When I run trinity of raven I get the following error..

Maybe an update would remedy?

Trinity version: Trinity-v2.12.0
** NOTE: Latest version of Trinity is Trinity-v2.15.1, and can be obtained at:
    https://github.com/trinityrnaseq/trinityrnaseq/releases

Error, cannot find jellyfish installed on this system. Be sure to install it. You can get it here: http://www.genome.umd.edu/jellyfish.html at /home/shared/trinityrnaseq-v2.12.0/Trinity line 4017.

[kubu4]

It's installed, but you have to add it to your $PATH.

It's here: /home/shared/jellyfish-2.3.0/bin/jellyfish

You can add something like this to your ~/.bashrc file:

export PATH=${PATH}:/home/shared/jellyfish-2.3.0/bin/

[sr320]

thanks - in raven terminal would not hold nor once in chunk - but ftr got it run within chunk as:

export PATH=${PATH}:/home/shared/bowtie2-2.4.4-linux-x86_64/
export PATH=${PATH}:/home/shared/jellyfish-2.3.0/bin/
export PATH=${PATH}:/home/shared/salmon-1.4.0_linux_x86_64/bin/

/home/shared/trinityrnaseq-v2.12.0/Trinity \
--seqType fq \
--max_memory 300G \
--CPU 24 \
--left ../analyses/10-hisat-deseq2/PSC-35_unmapped_reads.1.fastq \
--right ../analyses/10-hisat-deseq2/PSC-35_unmapped_reads.2.fastq \
--output ../analyses/10-hisat-deseq2/trinity