bashcheetah

syntax error with '$' sign ; Cheetah / bash


I work on a script running Cheetah ; at some point there are some bash commands and I got a syntax error ("Error in the Python code which Cheetah generated for this template").

The line involved is :

&& name=$(echo '\$another_variable'".phy" | cut -d _ -f 1)

The syntax error being on the very first '$' sign. It worked yesterday so I'm kind of confused ...

The whole code is wrraped in a xml tag :

<command><![CDATA[
    ln -s '$input' '$input.element_identifier' &&

    BlastAlign -i '$input.element_identifier'
    -m $advanced_option.m
    #if $advanced_option.r != ""
        -r $advanced_option.r
    #end if
    #if $advanced_option.x != ""
        -x $advanced_option.x
    #end if
    -n $advanced_option.n
    #if $advanced_option.s != 0
        -s $advanced_option.s
    #end if

    && mkdir outputs

    && name=$(echo '\$input.element_identifier'".phy" | cut -d _ -f 1)

    && number=$(grep '/' '\$input.element_identifier'".phy" | wc -l)

    && new_file=$name"_sp"$number".phy"
    && mv '\$input.element_identifier'".phy" '$new_file'
    && new_file2=$name"_sp"$number".nxs"
    && mv '\$input.element_identifier'".nxs" '$new_file2'
    && cp '$new_file' outputs/
    && cp '$new_file2' outputs/

    #if $fasta_out.value == True
        && python $__tool_directory__/scripts/S01_phylip2fasta.py /outputs/'$new_file' outputs/$name"_sp"$number".fasta"
    #end if

]]></command>

Solution

  • You have to screen (escape with a backslash) every $ sign that you want to pass to bash, else Cheetah tries to interpret them:

    && name=\$(echo '\$input.element_identifier'".phy" | cut -d _ -f 1)
    
    && number=\$(grep '/' '\$input.element_identifier'".phy" | wc -l)
    

    etc.