From 90ecf5a01911f95839c1a264747e4e917a7835f1 Mon Sep 17 00:00:00 2001
From: Sebastian Mackowiak <Drmirdeep@users.noreply.github.com>
Date: Mon, 13 Nov 2017 13:24:10 +0100
Subject: [PATCH] v0.9.2

Fixed curl https bug, fixed wget recognition bug
---
 install.pl | 40 ++++++++++++++++++++++++++++++----------
 1 file changed, 30 insertions(+), 10 deletions(-)

diff --git a/install.pl b/install.pl
index 14f902b..de2e597 100755
--- a/install.pl
+++ b/install.pl
@@ -79,7 +79,7 @@
 $progs{pdf}=0;
 $progs{ttf}=0;
 
-my $wget=`which wget`;
+my $wget=`wget 2>&1`;
 my $curl=`which curl`;
 
 my $dtool='';
@@ -273,8 +273,12 @@
 				if($err){
 					die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
 				}
-			}elsif(check("https://sourceforge.net/projects/bowtie-bio/files/bowtie/$bowtie_version/$bowtie")){
-				$err=system("$dtool https://sourceforge.net/projects/bowtie-bio/files/bowtie/$bowtie_version/$bowtie $dopt");
+			}elsif(check("https://sourceforge.net/projects/bowtie-bio/files/bowtie/$bowtie_version/$bowtie",$bowtie)){
+				if(not -f $bowtie){
+					$err=system("$dtool https://sourceforge.net/projects/bowtie-bio/files/bowtie/$bowtie_version/$bowtie $dopt");
+				}else{
+					$err=0;
+				}
 				if($err){
 					die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
 				}
@@ -298,7 +302,7 @@
 
 	chdir "$install_bin_dir";
 
-	buildgood("$dir/essentials/bowtie-$bv/bowtie");
+	buildgood("$dir/essentials/bowtie-$bv/bowtie","bowtie");
 
 	if(not -f "bowtie"){
 		system("ln -s $dir/essentials/bowtie-$bv/bowtie* .");
@@ -319,8 +323,12 @@
 			print STDERR "Downloading Vienna package now\n\n";
 			my $ptc="https://www.tbi.univie.ac.at/RNA/download/sourcecode/1_8_x/ViennaRNA-1.8.4.tar.gz";
 			# if(check("http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-1.8.4.tar.gz")){ # address changed 
-			if(check($ptc)){
-				$err=system("$dtool $ptc $dopt");
+			if(check($ptc,$dfile)){
+				if(not -f $dfile){
+					$err=system("$dtool $ptc $dopt");
+				}else{
+					$err=0;
+				}
 				if($err){
 					die "Download of Vienna package not successful\n\n";
 				}
@@ -363,7 +371,7 @@
 		`make 1>> ../install.log 2>> ../install_error.log`;
 		`make install 1>> ../install.log 2>> ../install_error.log`;
 
-		buildgood("$dir/essentials/ViennaRNA-1.8.4/install_dir/bin/RNAfold");
+		buildgood("$dir/essentials/ViennaRNA-1.8.4/install_dir/bin/RNAfold","RNAfold");
 
 		chdir("..");
 		chdir "$install_bin_dir";
@@ -490,7 +498,7 @@
 		`mv Makefile_new Makefile`;
 
 		`make 1>>../install.log 2>>../install_error.log`;
-		buildgood("$dir/essentials/randfold-2.0/randfold");
+		buildgood("$dir/essentials/randfold-2.0/randfold","randfold");
 		chdir("..");
 	}
 
@@ -745,7 +753,7 @@ sub checkBIN{
 
 
 sub check{
-	my ($url) = @_;
+	my ($url,$file) = @_;
 	my $out='';
 	if($dtool =~ /wget/){
 		$out=`wget --spider -v $url 2>&1`;
@@ -754,11 +762,22 @@ sub check{
 		if($out =~ /NOT/i){
 			$out='broken';
 		}
+
+		if($url =~ /https/){
+			`curl $url > $file`;
+			if(-s "$file" < 1000){
+				$out='broken';
+				`rm -f $file`;
+			}else{
+				$out=0;
+			}
+		}
+
 	}else{
 		die "No download tool found\nplease install wget or curl\n";
 	}
 
-	if($out =~ /broken/){
+	if($out =~ /broken/i){
 		return 0;
 	}else{
 		return 1;
@@ -769,6 +788,7 @@ sub check{
 sub buildgood{
 	if(-f $_[0]){
 		print STDERR "Building of $_[0] successful\n";
+		$progs{$_[1]}=1;
 	}else{
 		die "Building of $_[0] not successful\nPlease have a look at the install.log and install_error.log in 
 		the essentials directory