From ffa215ec34076b6fcb5c61d73cff2e1c0eaafb10 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 29 Dec 2020 19:35:32 +0100
Subject: [PATCH] shebang and argument parsing improvements

the removed test allows the --help and --version flags to work as
expected.

the change to the shebang lines allow to run the scripts on systems
where python/perl is installed in different locations
---
 MITObim.pl                                 | 6 ++----
 misc_scripts/circules.py                   | 2 +-
 misc_scripts/downsample.py                 | 2 +-
 misc_scripts/get_wiggle.pl                 | 2 +-
 misc_scripts/interleave-fastqgz-MITOBIM.py | 2 +-
 5 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/MITObim.pl b/MITObim.pl
index 0ab9346..2aa6ea8 100755
--- a/MITObim.pl
+++ b/MITObim.pl
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 #
 # MITObim - mitochondrial baiting and iterative mapping
 # wrapper script version 1.9.1
@@ -71,9 +71,7 @@
 #		--insert <int>		insert size of illumina library, default=300, relevant only for proofreading
 
 
-if (scalar @ARGV < 2){
-	die "$PROGRAM\n$VERSION\n$USAGE";
-}
+
 my $command = $0;
 for (@ARGV){
        	$command .= " $_";
diff --git a/misc_scripts/circules.py b/misc_scripts/circules.py
index a1372df..bd6765e 100755
--- a/misc_scripts/circules.py
+++ b/misc_scripts/circules.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 
 import sys,warnings
 import argparse
diff --git a/misc_scripts/downsample.py b/misc_scripts/downsample.py
index 9581ac1..2507fda 100755
--- a/misc_scripts/downsample.py
+++ b/misc_scripts/downsample.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 
 
 """downsample
diff --git a/misc_scripts/get_wiggle.pl b/misc_scripts/get_wiggle.pl
index e09287d..ec616c6 100755
--- a/misc_scripts/get_wiggle.pl
+++ b/misc_scripts/get_wiggle.pl
@@ -1,4 +1,4 @@
-#! /usr/bin/perl
+#!/usr/bin/env perl
 #
 # script to extract per base coverage info for unpadded
 # assembly result from MIRA wiggle file
diff --git a/misc_scripts/interleave-fastqgz-MITOBIM.py b/misc_scripts/interleave-fastqgz-MITOBIM.py
index e9c5beb..11051f2 100755
--- a/misc_scripts/interleave-fastqgz-MITOBIM.py
+++ b/misc_scripts/interleave-fastqgz-MITOBIM.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 # encoding:utf8
 # authors: Erik Garrison, Sébastien Boisvert
 # modified by github@cypridina on 20151104 to work with MITObim