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- 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.
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