Error (Ubuntu 12.0.4 and Mac OS 10.10.4)

[edschen]

Current Java, Perl 5.12.4 and Perl 5.20.1 both tested, both Ubuntu 12 and Mac OS 10.10, same error.
Assistance?

setup.sh runs fine.

% perl ExCID.BatchScript_v2.1-threading_Final.pl -bam ./436164-NIPT_HJHJNBCXX-2-ID16Aligned.out.bam
Use of uninitialized value $script_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 32 (#1)
(W uninitialized) An undefined value was used as if it were already
defined. It was interpreted as a "" or a 0, but maybe it was a mistake.
To suppress this warning assign a defined value to your variables.

To help you figure out what was undefined, perl will try to tell you the
name of the variable (if any) that was undefined. In some cases it cannot
do this, so it also tells you what operation you used the undefined value
in.  Note, however, that perl optimizes your program and the operation
displayed in the warning may not necessarily appear literally in your
program.  For example, "that $foo" is usually optimized into "that "
. $foo, and the warning will refer to the concatenation (.) operator,
even though there is no . in your program.

Use of uninitialized value $script_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 33 (#1)
Use of uninitialized value $script_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 35 (#1)
grep: /Config.txt: No such file or directory
Use of uninitialized value $tmp[0] in substitution (s///) at
ExCID.BatchScript_v2.1-threading_Final.pl line 36 (#1)
Use of uninitialized value $tmp[0] in scalar chomp at
ExCID.BatchScript_v2.1-threading_Final.pl line 37 (#1)
Use of uninitialized value $database_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 40 (#1)
Use of uninitialized value $database_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 41 (#1)
Use of uninitialized value $database_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 42 (#1)
Use of uninitialized value $database_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 43 (#1)
Use of uninitialized value $database_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 44 (#1)
Use of uninitialized value $database_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 45 (#1)
Use of uninitialized value $script_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 48 (#1)
Use of uninitialized value $script_dir in concatenation (.) or string at
ExCID.BatchScript_v2.1-threading_Final.pl line 54 (#1)
grep: /Config.txt: No such file or directory
Use of uninitialized value $tmp[0] in substitution (s///) at
ExCID.BatchScript_v2.1-threading_Final.pl line 55 (#1)
Use of uninitialized value $tmp[0] in scalar chomp at
ExCID.BatchScript_v2.1-threading_Final.pl line 56 (#1)
Please input target BED file. Exiting!!

If I add the following line, it goes further, but fails when it calls other scripts.

$script_dir='/Users/myhome/ExCID-master/ExCID_v2.1';

Lock file /Users/edc/Work/ExCID-master/ExCID_v2.1/annotation/foo.bed-ouput_dir.lck
----Obtained Lock----Tue Mar 1 13:02:01 2016
Annotating Bed file...

ln: /Users/edc/Work/ExCID-master/ExCID_v2.1/annotation/foo.bed-ouput_dir//foo.bed: File exists
ln: /Users/edc/Work/ExCID-master/ExCID_v2.1/annotation/foo.bed-ouput_dir///foo.bed: File exists
Uncaught exception from user code:
No such file or directory at /Users/edc/Work/ExCID-master/ExCID_v2.1/bed_file-annotator_V2_RefSeq-VEGA.pl line 26.
ln: /Users/edc/Work/ExCID-master/ExCID_v2.1/annotation/foo.bed-ouput_dir///foo.bed: File exists
Uncaught exception from user code:
No such file or directory at /Users/edc/Work/ExCID-master/ExCID_v2.1/bed_file-annotator_V2_CCDS-miRBASE.pl line 23.
ln: /Users/edc/Work/ExCID-master/ExCID_v2.1/annotation/foo.bed-ouput_dir///foo.bed: File exists
Uncaught exception from user code:
No such file or directory at /Users/edc/Work/ExCID-master/ExCID_v2.1/bed_file-annotator_V2_RefSeq-VEGA.pl line 26.
ln: /Users/edc/Work/ExCID-master/ExCID_v2.1/annotation/foo.bed-ouput_dir///foo.bed: File exists
Uncaught exception from user code:
No such file or directory at /Users/edc/Work/ExCID-master/ExCID_v2.1/bed_file-annotator_V2_CCDS-miRBASE.pl line 23.
Uncaught exception from user code:
No such file or directory at ExCID.BatchScript_v2.1-threading_Final.pl line 262.