Toolshed repository update error

2 Aug 2013


      I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing my script to fail of course. How can I prevent this from happening?

Saskia


snippet of the code:


    if [[ ! -s $rfile ]]
    then
        dummycol=${addcols:2}
        outputcol=${dummycol//",B."/"    "}
<<<<<<< local
        echo -e "${col_chr_name}\t${col_start_name}\t${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile
        cat $rfile
=======
        numcommas=`echo "$addcols" | grep -o "," | wc -l`
        echo "numcolums: $numcommas"

        awk 'BEGIN{FS="\t";OFS="\t"}{
                if(FNR==1)
                    print $0,"'"$outputcol"'";
                else{
                    printf $0
                    for(i=0;i<="'"$numcommas"'"+1;i++)
                        printf "\t"
                    printf "\n"
                }
            }END{}' $ofile > tempofile

            mv tempofile $ofile

        return
...
...
...
...
...
...
> other
    fi

S.D. Hiltemann

Bjoern Gruening

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