command -v fix ubuntu

PombertLab · Dec 21, 2021 · 3cad3ee · 3cad3ee
1 parent ab7f680
commit 3cad3ee
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Showing 4 changed files with 15 additions and 15 deletions.
diff --git a/Homology_search/run_GESAMT.pl b/Homology_search/run_GESAMT.pl
@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert Lab 2020
-my $version = '0.5e';
+my $version = '0.5f';
 my $name = 'run_GESAMT.pl';
-my $updated = '2021-09-11';
+my $updated = '2021-12-21';
 
 use strict;
 use warnings;
@@ -87,7 +87,7 @@
 print LOG "Started on: $start\n";
 
 ## Program check
-my $prog = `command -v gesamt`;
+my $prog = `echo \$(command -v gesamt)`;
 chomp $prog;
 if ($prog eq ''){ 
 	die "\nERROR: Cannot find gesamt. Please install GESAMT in your path\n\n";

diff --git a/create_3DFI_db.pl b/create_3DFI_db.pl
@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert Lab, Illinois Tech, 2021
 my $name = 'create_3DFI_db.pl';
-my $version = '0.4';
-my $updated = '2021-11-23';
+my $version = '0.4a';
+my $updated = '2021-12-21';
 
 use strict;
 use warnings;
@@ -129,7 +129,7 @@
 # Checking for aria2, unpigz and gesamt
 
 # Aria2
-my $aria2 = `command -v aria2c`;
+my $aria2 = `echo \$(command -v aria2c)`;
 chomp $aria2;
 if ($aria2 eq ''){
 	print "[E] aria2c not found in the \$PATH. Please check if aria2 is installed\n";
@@ -140,13 +140,13 @@
 
 # Pigz
 my $decompression_tool = 'gunzip';
-my $unpigz = `command -v unpigz`;
+my $unpigz = `echo \$(command -v unpigz)`;
 chomp $unpigz;
 unless ($unpigz eq ''){ $decompression_tool = 'unpigz'; }
 
 # GESAMT
 if ($make_gesamt or $update_gesamt){ 
-	my $gesamt_prog = `command -v gesamt`;
+	my $gesamt_prog = `echo \$(command -v gesamt)`;
 	chomp $gesamt_prog;
 	if ($gesamt_prog eq ''){ 
 		print "[E] Cannot find gesamt but --make_gesamt/--update_gesamt was requested. Please install GESAMT in your \$PATH\n\n";

diff --git a/run_3DFI.pl b/run_3DFI.pl
@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert Lab, Illinois Tech, 2021
 my $name = 'run_3DFI.pl';
-my $version = '0.4.1';
-my $updated = '2021-09-27';
+my $version = '0.4b';
+my $updated = '2021-12-21';
 
 use strict;
 use warnings;
@@ -207,7 +207,7 @@
 	$pred = lc($pred);
 
 	if ($pred eq 'raptorx'){
-		my $check_modeller = `command -v $modeller`;
+		my $check_modeller = `echo \$(command -v $modeller)`;
 		chomp $check_modeller;
 		unless ($check_modeller =~ /$modeller/){
 			print "\n[E] Cannot find MODELLER version: $modeller in your \$PATH. Please check if MODELLER is installed.\n\n";
@@ -218,14 +218,14 @@
 }
 
 unless ($tdo){
-	my $gesamt_check = `command -v gesamt`;
+	my $gesamt_check = `echo \$(command -v gesamt)`;
 	chomp $gesamt_check;
 	if ($gesamt_check eq ''){ 
 		print "\n[E]: Cannot find gesamt. Please install GESAMT in your \$PATH. Exiting..\n\n";
 		exit;
 	}
 
-	my $chimerax_check = `command -v chimerax`;
+	my $chimerax_check = `echo \$(command -v chimerax)`;
 	chomp $chimerax_check;
 	if ($chimerax_check eq ''){ 
 		print "\n[E]: Cannot find chimerax. Please install ChimeraX in your \$PATH. Exiting..\n\n";

diff --git a/setup_3DFI.pl b/setup_3DFI.pl
@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert Lab, Illinois Tech, 2021
 my $name = 'setup_3DFI.pl';
-my $version = '0.5a';
-my $updated = '2021-09-23';
+my $version = '0.5b';
+my $updated = '2021-12-21';
 
 use strict;
 use warnings;