set variable name containing '>' in bash [duplicate]

Question

I have to use a bash script (I'm not familiar with bash) for submitting a HPC job. The job-submission script template sets the command and options and then combines them in the end:

input="file_name"
name="simulation1"

application=my_app
options="in=$input.h5 out=$name.h5 param1=foo"

cmd="$application $options"

this all works okay, i.e. eval $cmd executes

my_app in=$input.h5 out=$name.h5 param1=foo

until I need the character '>' in the options. In particular, I want to add the option absrad="mass>1?H:0", but if I simply set

options="in=$input.h5 out=$name.h5 param1=foo absrad=mass>1?H:0"

then bash truncates that at the '>', so that eval $cmd executes

my_app in=$input.h5 out=$name.h5 param1=foo absrad=mass

instead. How to fix that such that eval $cmd executes

my_app in=$input.h5 out=$name.h5 param1=foo absrad="mass>1?H:0"

EDIT. Note that this is similar to, but not a duplicate of this post, where a single-quoted argument is the problem. Moreover, the answers there only consider solutions using an array for the options. I would like alternatives w/o array.

Is your command called like $cmd or "$cmd" because the latter should work. — Olli K
– Olli K, Commented Apr 28, 2017 at 18:47
FYI - eval is not truncating per se, but scanning the string and performing variable substitution and when it gets to the '>' it sees the redirection character and will create a file called '1?H:0'. Then it passes the line to the shell for execution. Another reason to avoid using eval which can be dangerous if the variables it is operating on can be manipulated. — Gary_W
– Gary_W, Commented Apr 28, 2017 at 18:53
By closing this question you deprive the chance for an alternative (to arrays) answer. — Walter
– Walter, Commented Apr 29, 2017 at 11:50

Jeffrey Cash · Accepted Answer · 2017-04-28 18:47:19Z

1

You could always use an array for options:

declare -a options=("in=$input.h5" "out=$name.h5" "param1=foo" "absrad=\"mass>1?H:0\"");
declare -a cmd=(my_app "${options[@]}");

Then when you want to expand cmd the following should give you the correct expansion:

"${cmd[@]}"

Additionally, this gets rid of the need to use eval, which I tend to avoid whenever possible.

answered Apr 28, 2017 at 18:47

Jeffrey Cash

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