用于停止管道的bash中的Grep R错误消息

Question

我有一条管道在工作。我有一个wrappper.sh，它将各种.R脚本组合在一起。但是，此管道将通过错误消息运行。我想添加一种方法，grep我们的单词错误，如果真，关闭管道。我知道我需要一个if/ out状态，但是不知道如何在运行在.R中的bash.sh脚本中实现这个信息。参见一个示例错误。

当前脚本：

#!/bin/bash

#Bash script for running GeoMx Pipeline

####
# Install required R packages for pipeline
echo "installing R packages"

Rscript installPackages.R

echo "DONE! R packages installed"

#####
# Created required folders
echo "Creating Folders"

Rscript CreateFolder.R

echo "DONE! Folders created"

####
# Copy data over
cp -u -p Path/Initial\ Dataset.xlsx /PATO_TO

####
# Run Statistical Models

echo "Running Statistical Analysis"

Rscript GLM_EdgeR.R

echo "DONE! Statistical Models completed"

示例错误：

Error in glmLRT(glmfit, coef = coef, contrast = contrast) :
  contrast vector of wrong length, should be equal to number of coefficients in the linear model.
Calls: glmQLFTest -> glmLRT
Execution halted

我想要的：

#!/bin/bash

#Bash script for running GeoMx Pipeline

####
# Install required R packages for pipeline
echo "installing R packages"

Rscript installPackages.R

if grep error == TRUE
then 
   echo "Fatal Error, STOP Pipeline"
   STOP
else 
   echo "DONE! R packages installed"

#####
# Created required folders
echo "Creating Folders"

Rscript CreateFolder.R

if grep error == TRUE
then 
   echo "Fatal Error, STOP Pipeline"
   STOP
else 
   echo "DONE! Folders created"

####
# Copy data over
cp -u -p Path/Initial\ Dataset.xlsx /PATO_TO

####
# Run Statistical Models

echo "Running Statistical Analysis"

Rscript GLM_EdgeR.R

if grep error == TRUE
then 
   echo "Fatal Error, STOP Pipeline"
   STOP
else 
   echo "DONE! Statistical Models completed"

Answer 1

如果您不需要grep来查找错误，您可以测试上一次状态代码是否为非零：

#!/bin/bash

Rscript CreateFolder.R

exit_code=$?
if test $exit_code -ne 0
then
  echo "Fatal Error, STOP Pipeline"
  exit $exit_code
else
  echo "DONE! Folders created"
fi

如果Rscript CreateFolder.R失败，bash脚本将以相同的状态代码退出。

尽管如果您有更多想要检查的条件，但是使用set -e是有意义的。

如果由单个简单命令、列表或复合命令组成的管道返回非零状态，则

立即退出。

https://www.gnu.org/software/bash/manual/html_node/The-Set-Builtin.html

基本上，它会让您的脚本运行到某些东西失败为止：

#!/bin/bash
set -e
Rscript installPackages.R
echo "DONE! R packages installed"
Rscript CreateFolder.R
echo "DONE! Folders created"
Rscript GLM_EdgeR.R
echo "DONE! Statistical Models completed"

对于第二个脚本，CreateFolder.R，失败，它将如下所示：

~/r# ./wrappper.sh
[1] "OK"
DONE! R packages installed
Error: object 'will_fail' not found
Execution halted