Bash 脚本在 Windows 10 中的 Ubuntu 中不起作用

Question

Ubuntu 和 Mac 上的 Linux 有什么不同？抱歉，如果这是一个基本问题...我是新手。我正在尝试运行一个 bash 脚本，该脚本会从一些 FASTQ 文件创建一个 .sh 脚本。这在 Mac OS 的终端中有效。我试图在我的 Windows 笔记本电脑上运行它，但它忽略了我对 #s 的转义，只是说找不到几个命令。我尝试使用dos2unix并仔细检查过，cat -A file.sh但没有帮助。

我尝试运行的代码将所有 fastq 文件放在一个文件夹中，并使用它们的文件名创建一个 .sh 文件用于 SLURM 作业提交（这是我大学的计算机集群所需要的，我需要制作 100 多个作业脚本）。因此，Mac OS 版本如下：

for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)
do echo -e \
\#\!/bin/bash \
\\n\#SBATCH --partition=nonpre  \# Partition \(job queue\) \
\\n\#SBATCH --requeue                 \# Return job to the queue if preempted \
\\n\#SBATCH --job-name=samples      \# Assign a short name to your job \
\\n\#SBATCH --nodes=1                 \# Number of nodes you require \
\\n\#SBATCH --ntasks=1                \# Total \# of tasks across all nodes \
\\n\#SBATCH --cpus-per-task=64        \# Cores per task \(\>1 if multithread tasks\) \
\\n\#SBATCH --mem=180000              \# Real memory \(RAM\) required \(MB\) \
\\n\#SBATCH --time=72:00:00           \# Total run time limit \(HH:MM:SS\) \
\\n\#SBATCH --output=slurm.%N.${FILE}.out  \# STDOUT output file \
\\n\#SBATCH --error=slurm.%N.${FILE}.err   \# STDERR output file \(optional\) \
\\n \
\\n\#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION \
\\n \
\\nsacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future submissions \
> ${FILE}.sh; 
done

在 Windows 上运行此程序时，我得到：

Slurm_Generator.sh: line 13: #!/bin/bash: No such file or directory
Slurm_Generator.sh: line 14: \n#SBATCH: command not found
Slurm_Generator.sh: line 16: \n#SBATCH: command not found
Slurm_Generator.sh: line 18: \n#SBATCH: command not found
Slurm_Generator.sh: line 20: \n#SBATCH: command not found
Slurm_Generator.sh: line 22: \n#SBATCH: command not found
Slurm_Generator.sh: line 24: \n#SBATCH: command not found
Slurm_Generator.sh: line 26: \n#SBATCH: command not found
Slurm_Generator.sh: line 28: \n#SBATCH: command not found
Slurm_Generator.sh: line 30: \n#SBATCH: command not found
Slurm_Generator.sh: line 32: \n#SBATCH: command not found
Slurm_Generator.sh: line 35: \n: command not found
Slurm_Generator.sh: line 36: \n#ADD: command not found
Slurm_Generator.sh: line 39: \n: command not found
Slurm_Generator.sh: line 40: \nsacct: command not found

任何帮助都将不胜感激，并解释一下 Windows 上的 Ubuntu 与 Mac 上的终端之间的区别。我尝试研究过这个问题，但我总是发现建议的代码没有任何解释，或者这不是我的问题。谢谢！

编辑：我尝试运行chmod +x script.sh，但会出现上述错误。我运行“echo”是否错误？即使运行：“for FILE in *fastq; do echo -e hello; done”也说Command 'hello' not found

编辑：运行“bash file.sh”会产生以下结果： bash file.sh会产生以下结果（对于我的目录中的每个 5 个 .fastq 文件）：

Slurm_Generator.sh: line 8: #!/bin/bash: No such file or directory
Slurm_Generator.sh: line 9: \n#SBATCH: command not found
Slurm_Generator.sh: line 11: \n#SBATCH: command not found
Slurm_Generator.sh: line 13: \n#SBATCH: command not found
Slurm_Generator.sh: line 15: \n#SBATCH: command not found
Slurm_Generator.sh: line 17: \n#SBATCH: command not found
Slurm_Generator.sh: line 19: \n#SBATCH: command not found
Slurm_Generator.sh: line 21: \n#SBATCH: command not found
Slurm_Generator.sh: line 23: \n#SBATCH: command not found
Slurm_Generator.sh: line 25: \n#SBATCH: command not found
Slurm_Generator.sh: line 27: \n#SBATCH: command not found
Slurm_Generator.sh: line 30: \n: command not found
Slurm_Generator.sh: line 31: \n#ADD: command not found
Slurm_Generator.sh: line 34: \n: command not found
Slurm_Generator.sh: line 35: \nsacct: command not found

如果我运行，cat -A file.sh我会$在每行末尾看到一个。即使我去掉这些，我也会得到与上面相同的结果。运行结果ls -al script.sh为：-rwxrwxrwx 1 cerberus cerberus 1209 Jun 16 00:17 Slurm_Generator.sh

编辑：我将脚本更改为：

#! /bin/bash
for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)
do echo -e \
"
#\!/bin/bash
#SBATCH --partition=nonpre  # Partition (job queue)
#SBATCH --requeue              # Return job to the queue if preempted
#SBATCH --job-name=samples     # Assign a short name to your job
#SBATCH --nodes=1              # Number of nodes you require
#SBATCH --ntasks=1             # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000           # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00        # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.${FILE}.out # STDOUT output file
#SBATCH --error=slurm.%N.${FILE}.err  # STDERR output file (optional)

#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION \

sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future subm$" \
> ${FILE}.sh;
done

我的新输出如下（好多了）：

#\!/bin/bash
#SBATCH --partition=nonpre  # Partition (job queue)
#SBATCH --requeue           # Return job to the queue if preempted
#SBATCH --job-name=samples      # Assign a short name to your job
#SBATCH --nodes=1                 # Number of nodes you require
#SBATCH --ntasks=1                # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000              # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00           # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.Sample1.fastq.out  # STDOUT output file
#SBATCH --error=slurm.%N.Sample1.fastq.er  # STDERR output file (optional)


#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION

sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j $SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future submissions

我遇到的唯一问题是，虽然它会为每个 .fastq 文件打印出这些信息（这正是我想要的），但它写出的最终 .sh 文件是空白的。所以它无法识别> ${File}.sh脚本的这一部分。

谢谢大家！

Answer 1

使用 heredoc 代替：

for FILE in *fastq; #change file type when needed (e.g., fasta, fastq, fastq.gz)
do

cat <<-EOF > ${FILE}.sh
#!/bin/bash

#SBATCH --partition=nonpre             # Partition (job queue)
#SBATCH --requeue                      # Return job to the queue if preempted
#SBATCH --job-name=samples             # Assign a short name to your job
#SBATCH --nodes=1                      # Number of nodes you require
#SBATCH --ntasks=1                     # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64             # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000                   # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00                # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.${FILE}.out  # STDOUT output file
#SBATCH --error=slurm.%N.${FILE}.err   # STDERR output file (optional)

#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION

nsacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID #this will get job run stats from SLURM; use these to help designate memory of future submissions
EOF

done

Answer 2

我意识到我必须\在 之前添加一个> ${File}.sh。所以答案是：

#! /bin/bash
for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)
do echo -e \
"
#\!/bin/bash
#SBATCH --partition=nonpre  # Partition (job queue)
#SBATCH --requeue              # Return job to the queue if preempted
#SBATCH --job-name=samples     # Assign a short name to your job
#SBATCH --nodes=1              # Number of nodes you require
#SBATCH --ntasks=1             # Total # of tasks across all nodes
#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)
#SBATCH --mem=180000           # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00        # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.${FILE}.out # STDOUT output file
#SBATCH --error=slurm.%N.${FILE}.err  # STDERR output file (optional)

#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION \

sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j \$SLURM_JOBID \#this will get job run stats from SLURM\; use these to help designate memory of future subm$" \
> ${FILE}.sh;
done