xargs – Tumbling Oysters

Author

Affiliation

Steven Roberts

Professor, UW - School of Aquatic and Fishery Sciences

Published

May 27, 2024

find /home/shared/8TB_HDD_02/graceac9/data/pycno2021/*_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
| xargs -I{} basename -s _R1_001.fastq.gz.fastp-trim.20220810.fq.gz {} \
| xargs -I{} sh -c '/home/shared/hisat2-2.2.1/hisat2 \
-x ../analyses/10-hisat-deseq2/GCA_032158295.index \
--dta \
-p 20 \
-1 /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
-2 /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R2_001.fastq.gz.fastp-trim.20220810.fq.gz \
-S ../analyses/10-hisat-deseq2/{}_02.sam \
> ../analyses/10-hisat-deseq2/{}_hisat.stdout 2> ../analyses/10-hisat-deseq2/{}_hisat.stderr'

---
title: "xargs"
description: "now with no reason for loops"
categories: [xargs] # self-defined categories
#citation: 
date: 05-27-2024
image: http://gannet.fish.washington.edu/seashell/snaps/Monosnap_bestblogever_-_main_-_RStudio_2024-05-26_11-52-26.png # finding a good image

author:
  - name: Steven Roberts
    url: 
    orcid: 0000-0001-8302-1138
    affiliation: Professor, UW - School of Aquatic and Fishery Sciences
    affiliation-url: https://robertslab.info
  #url:  # self-defined
draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready!
format:
  html:
    code-fold: true
    code-tools: true
    code-copy: true
    highlight-style: github
    code-overflow: wrap
---



```bash
find /home/shared/8TB_HDD_02/graceac9/data/pycno2021/*_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
| xargs -I{} basename -s _R1_001.fastq.gz.fastp-trim.20220810.fq.gz {} \
| xargs -I{} sh -c '/home/shared/hisat2-2.2.1/hisat2 \
-x ../analyses/10-hisat-deseq2/GCA_032158295.index \
--dta \
-p 20 \
-1 /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
-2 /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R2_001.fastq.gz.fastp-trim.20220810.fq.gz \
-S ../analyses/10-hisat-deseq2/{}_02.sam \
> ../analyses/10-hisat-deseq2/{}_hisat.stdout 2> ../analyses/10-hisat-deseq2/{}_hisat.stderr'
```