command -v fix ubuntu

Author: Pombert-JF

Tools/MASH/run_Mash.pl

@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert JF, Illinois Tech - 2019
-my $version = '1.1';
+my $version = '1.1a';
 my $name = 'run_Mash.pl';
-my $updated = '2021-03-14';
+my $updated = '2021-12-21';
 
 use strict; use warnings; use Getopt::Long qw(GetOptions);
 
@@ -39,7 +39,7 @@
 );
 
 ## Checking if Mash is installed
-my $prog = `command -v mash`;
+my $prog = `echo \$(command -v mash)`;
 chomp $prog;
 if ($prog eq ''){
 	die "\nERROR: Cannot find Mash. Please install Mash in your \$PATH\n\n";

bam2fastq.pl

@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert Lab, IIT, 2019
 my $name = 'bam2fastq.pl';
-my $version = '0.3b';
-my $updated = '2021-03-22';
+my $version = '0.3c';
+my $updated = '2021-12-21';
 
 use strict; use warnings; use Getopt::Long qw(GetOptions); use File::Basename;
 
@@ -53,7 +53,7 @@
 );
 
 ## Program + option check
-my $samtools = `command -v samtools`;
+my $samtools = `echo \$(command -v samtools)`;
 chomp $samtools;
 if ($samtools eq ''){
 	die "\nERROR: Cannot find Samtools. Please install Samtools in your path\n\n";

get_SNPs.pl

@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert JF, Illinois Tech - 2020
-my $version = '2.0';
+my $version = '2.0a';
 my $name = 'get_SNPs.pl';
-my $updated = '2021-03-16';
+my $updated = '2021-12-21';
 
 use strict; use warnings; use File::Basename; use Getopt::Long qw(GetOptions);
 
@@ -414,7 +414,7 @@
 # sub to check if programs are installed
 sub chkinstall{
 	my $exe = $_[0];
-	my $prog = `command -v $exe`;
+	my $prog = `echo \$(command -v $exe)`;
 	chomp $prog;
 	if ($prog eq ''){die "\nERROR: Cannot find $exe. Please install $exe in your \$PATH\n\n";}
 }