picard: command not found

[jphe]

Hi,

I'm running MAESTRO scATAC-seq with bam file according to the manual, and it reports an error: /bin/bash: picard: command not found.

Does the picard represents the javar picard (https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-)? if so, seems it need to be run with "java -jar"? And I find another python picard (https://pypi.org/project/picard/) in pip, but it seems a music tagger and none business with bam files.

Bellow is my script:

MAESTRO scatac-init --platform 10x-genomics --format bam --species GRCh38 \ --bam ../atac_pbmc_10k_v1_possorted_bam.bam \ --cores 10 --directory PBMC_10k_MAESTRO_bam --outprefix 10X_PBMC_10k \ --peak-cutoff 100 --count-cutoff 1000 --frip-cutoff 0.2 --cell-cutoff 50 \ --rpmodel Enhanced \ --giggleannotation ../giggle.all \ --annotation --method both --signature human.immune.CIBERSORT --clusterpeak

Thanks, Jphe

[crazyhottommy]

Hi, Did you install MAESTRO by conda? If so, picard should be on your $PATH

conda activate MAESTRO1.3.2
(MAESTRO1.3.2) [mtang@kraken1 singularity_images]$ which picard
~/anaconda3/envs/MAESTRO1.3.2/bin/picard

[jphe]

Thanks, I have found picard under conda: https://anaconda.org/bioconda/picard

I have tried to install MAESTRO( https://anaconda.org/liulab-dfci/maestro) conda: conda install -c liulab-dfci maestro。 But it reports

[crazyhottommy]

oh, can you do

$ conda config --add channels defaults
$ conda config --add channels liulab-dfci
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
# To make the installation faster, we recommend using mamba
$ conda install mamba -c conda-forge
$ mamba create -n MAESTRO maestro=1.3.2 -c liulab-dfci
# Activate the environment
$ conda activate MAESTRO

[f6v]

@jphe Mac OS isn't supported, only Linux.