picard error in trinty pipeline

Question

[eyonesi]

Hi everybody,

I am running GATK pipeline for variant calling in trinity with following command.

/usr/local/bin/Trinityrnaseq-v2.6.6/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py --st_fa ./SuperDuper.fasta --st_gtf ./SuperDuper.gff -p ./FCHG1.fq.gz  ./FCHG.fq.gz -o ./variant_calls_outdir

But I got following error:

Error, missing path to Picard-Tools in $PICARD_HOME.

based on the instructions on the trinity web, I need to set the installation directory to the environmental variable ${PICARD_HOME}. for this purpose (adding the picard path to $PATH) I tried following command but my problem was not solved.

PATH="$PATH:$HOME/picard-2.23.0" 
echo $PATH

output

/home/ubuntu/bin:/home/ubuntu/.local/bin:/home/ubuntu/anaconda3/bin:/home/ubuntu/perl5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ubuntu/picard-2.23.0

I don’t know how can I set the installation directory to the environmental variable ${PICARD_HOME}.

best regards

Answer 1

[Ram]

Please read the error message properly. You need to set PICARD_HOME to the installation directory, not add it to PATH. Try

PICARD_HOME=$HOME/picard-2.23.0

and then run the script again.

Answer 2

[JC]

The script is asking for the $PICARD_HOME variable, then you need to create it:

export PICARD_HOME="$HOME/picard-2.23.0"