amazon-ec2 - snakemake 集群命令中的括号问题

Question

我使用以下命令在 aws cfncluster 上使用 snakemake 4.0.0。

rule fastq_to_counts:
input: fastql="/shared/dbGAP/sras2/fastq.gz/{sample}_1.fastq.gz", fastqr="/shared/dbGAP/sras2/fastq.gz/{sample}_2.fastq.gz"
output: "/shared/counts/{sample}"
shell: '/shared/packages/sailfish-master/bin/sailfish quant -i /shared/packages/gencode26/gencode26 -l IU -p 1  -1 <(zcat {input.fastql})  -2 <(zcat {input.fastqr})       --output  {output}'

它在头节点上运行良好，但是当我提交到头节点时，出现以下错误。

    /shared/packages/sailfish-master/bin/sailfish quant -i /shared/packages/gencode26/gencode26 -l IU -p 1  -1 <(zcat /shared/dbGAP/sras2/fastq.gz/xxx.fastq.gz)  -2 <(zcat /shared/dbGAP/sras2/fastq.gz/xxx.fastq.gz)       --output  /shared/counts/SRR1075530 
/bin/sh: 1: Syntax error: "(" unexpected
Error in job fastq_to_counts while creating output file /shared/counts/xxx.

规则异常：

问题是“sh”命令不支持“（”的“bashism”有没有办法强制snakemake使用/bin/bash？谢谢

Answer 1

发现解决方案是将以下内容添加到snakefile shell.executable('bash')