bash - 在bash中运行CSH可执行文件会引发语法错误

Question

我需要在MacOS X High Sierra上运行NACCESS程序。

最突出的错误是if: Expression Syntax.
该错误可能是因为NACCESS可执行文件是CSH脚本，其第一行带有#!/bin/csh。

我将第一行更改为#!/bin/bash并开始收到诸如 ./naccess: line 14: syntax error near unexpected token `1' ./naccess: line 14: ` exit(1)'
再次，我认为这是发生的，因为可执行文件需要在CSH Shell中执行，而不是bash。 this resource表示，exit(1)是针对CSH shell格式化的，而bash则需要exit 1。

我尝试在Terminal中键入csh来切换 shell ，但是echo $SHELL命令只是告诉我我仍然在bash中。

我用grep '^#!' /usr/bin/*查看了我的shell选择，但是找不到任何CSH shell。我试图使用自制软件下载tcsh。但是我现在真的不知道我在做什么。

我知道不鼓励使用CSH shell，但是如何在Mac上启动并运行CSH shell，或者如何使NACCESS运行？

[EDIT] 这是NACCESS代码的前几行:

(请注意，我正在使用.pdb文件参数运行它，并且已经正确设置了path_to_naccess_repository。如果仅运行usage naccess pdb_file [-p probe_size] [-r vdw_file] [-s stdfile] [-z zslice] -[hwyfaclqb]，我确实会得到./naccess读数)

#!/bin/csh
set EXE_PATH = /path/to/repo
#naccess_start

set nargs = $#argv
if ( $nargs < 1 ) then
   echo "usage naccess pdb_file [-p probe_size] [-r vdw_file] [-s stdfile] [-z zslice] -[hwyfaclqb]"
   exit(1)
endif

set PDBFILE = 0
set VDWFILE = 0
set STDFILE = 0
set probe = 1.40
set zslice = 0.05
set hets = 0
set wats = 0
set hyds = 0
set full = 0
set asao = 0
set cont = 0
set oldr = 0
set nbac = 0

while ( $#argv )
  switch ($argv[1])
     case -[qQ]:
    echo "Naccess2.1 S.J.Hubbard June 1996"
    echo "Usage: naccess pdb_file [-p probe_size] [-r vdw_file] [-s stdfile] [-z zslice] -[hwyfaclq]"
    echo " "
    echo "Options:"
    echo " -p = probe size (next arg probe size)"
    echo " -z = accuracy (next arg is accuracy)"
    echo " -r = vdw radii file (next arg is filename)"
    echo " -s = standard accessibilities file (next arg is filename)"
    echo " -h = hetatoms ?"
    echo " -w = waters ?"
    echo " -y = hydrogens ?"
    echo " -f = full asa output format ?"
    echo " -a = produce asa file only, no rsa file ?"
    echo " -c = output atomic contact areas in asa file instead of accessible areas"
    echo " -l = old RSA output format (long)"
    echo " -b = consider alpha carbons as backbone not sidechain"
    echo " -q = print the usage line and options list"
    echo " "
        exit
        breaksw
     case -[pP]:
    shift
    set probe = $argv[1]
    breaksw
     case -[zZ]:
        shift
        set zslice = $argv[1]
    breaksw
     case -[hH]:
        set hets = 1
    breaksw
     case -[wW]:
        set wats = 1
        breaksw
     case -[yY]:
        set hyds = 1
        breaksw
     case -[rR]:
        shift
        set VDWFILE = $argv[1]
        breaksw
     case -[sS]:
        shift
        set STDFILE = $argv[1]
        breaksw
     case -[fF]:
        set full = 1
        breaksw
     case -[aA]:
        set asao = 1
        breaksw
     case -[cC]:
        set cont = 1
        breaksw
     case -[lL]:
        set oldr = 1
        breaksw
     case -[bB]:
        set nbac = 1
        breaksw
     default:
        if ( -e $argv[1] && $PDBFILE == 0 ) then
       set PDBFILE = $argv[1]
        endif
    breaksw
  endsw
  shift
end
#
if ( $PDBFILE == 0 ) then
  echo "usage: you must supply a pdb format file"
  exit(1)
endif

[编辑]我没有正确设置路径>。<所以这个问题主要是关于如何使bsh中的csh脚本运行。这个csh脚本没有问题。

Answer 1

SHELL变量仅列出您的第一个登录shell，如果您运行另一个shell则不会更改。 echo $0将显示您正在运行csh。您可以选择保留bash并将shebang更改为tcsh:

#!/usr/bin/tcsh -f

或完全删除shebang并运行

csh ./naccess

如果您要使用第一个选项，并且不确定csh在哪里，只需点击

which csh

找到路径。正如@Chepner所添加的那样，由于该文件带有csh shebang，因此请不要触摸它并按上面的方式运行它。