Use portable shebangs instead of hardcoding interpreters See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ --- a/scripts/dnadiff.pl +++ b/scripts/dnadiff.pl @@ -1,4 +1,4 @@ -#!__PERL_PATH -w +#!/usr/bin/env perl #------------------------------------------------------------------------------- # Programmer: Adam M Phillippy, University of Maryland --- a/scripts/exact-tandems.csh +++ b/scripts/exact-tandems.csh @@ -1,4 +1,4 @@ -#!__CSH_PATH -f +#!/usr/bin/env csh # # Find exact tandem repeats in specified file involving an # exact duplicate of at least the specified length --- a/scripts/mapview.pl +++ b/scripts/mapview.pl @@ -1,4 +1,4 @@ -#!__PERL_PATH +#!/usr/bin/env perl use lib "__SCRIPT_DIR"; use Foundation; --- a/scripts/mummerplot.pl +++ b/scripts/mummerplot.pl @@ -1,4 +1,4 @@ -#!__PERL_PATH +#!/usr/bin/env perl ################################################################################ # Programmer: Adam M Phillippy, The Institute for Genomic Research --- a/scripts/nucmer2xfig.pl +++ b/scripts/nucmer2xfig.pl @@ -1,4 +1,4 @@ -#!__PERL_PATH +#!/usr/bin/env perl # (c) Steven Salzberg 2001 # Make an xfig plot for a comparison of a reference chromosome (or single # molecule) versus a multifasta file of contigs from another genome. --- a/scripts/nucmer.pl +++ b/scripts/nucmer.pl @@ -1,4 +1,4 @@ -#!__PERL_PATH +#!/usr/bin/env perl #------------------------------------------------------------------------------- # Programmer: Adam M Phillippy, The Institute for Genomic Research --- a/scripts/promer.pl +++ b/scripts/promer.pl @@ -1,4 +1,4 @@ -#!__PERL_PATH +#!/usr/bin/env perl #------------------------------------------------------------------------------- # Programmer: Adam M Phillippy, The Institute for Genomic Research --- a/scripts/run-mummer1.csh +++ b/scripts/run-mummer1.csh @@ -1,4 +1,4 @@ -#!__CSH_PATH -f +#!/usr/bin/env csh # # **SEVERELY** antiquated script for running the mummer 1 suite # -r option reverse complements the query sequence, coordinates of the reverse --- a/scripts/run-mummer3.csh +++ b/scripts/run-mummer3.csh @@ -1,4 +1,4 @@ -#!__CSH_PATH -f +#!/usr/bin/env csh # # for running the basic mummer 3 suite, should use nucmer instead when possible # to avoid the confusing reverse coordinate system of the raw programs.