Fix URLs

cgi-bin/EPD2NICE.pl

@@ -43,8 +43,8 @@ elsif (hostname eq ""){
   $DB="/db";
   $epd2fasta = ' /home/vital-it/gambrosi/ssa/linux/EPDtoFA';
   $epd2embl = ' /home/vital-it/gambrosi/ssa/linux/FROMFPS';
-  $ENV{'SSA2DBC'} = "/home/local/ccg/etc/SSA2DBC.def";
-  $WWWTmpDir = "/home/local/www-ccg/hourly";
+  $ENV{'SSA2DBC'} = "/home/local/ssa/data/SSA2DBC.def";
+  $WWWTmpDir = '/var/tmp/hourly';
   $R_cmd = "R --no-save > /dev/null";
 }
 
@@ -466,7 +466,7 @@ ALT:	    print "\t\t\t\t\t<td bgcolor\=\"\#FFFFCC\"><a href=\"$URLs{GENOME}$GE_S
 		if ((split(/\n/,$test))[0]=~ (/chr([0-9YXLRIV]+)\t(\d+)\t/)){
 		    $chro=$1;
 		    $gpos=$2;
-		    print "ENSEMBL <a href\=\"",$ENSEMBL{$OS1},"?h=URL:ftp://ccg.vital-it.ch/epd/BED/";
+		    print "ENSEMBL <a href\=\"",$ENSEMBL{$OS1},"?h=URL:https://epd.expasy.org/ftp/epd/BED/";
 		    print $BEDE{$OS1};
 		    print ";chr=$chro&amp;region=&amp;start=",$gpos-200,"&amp;end=",$gpos+200,"\">ContigView<\/a>\n ";
 		}
@@ -480,7 +480,7 @@ ALT:	    print "\t\t\t\t\t<td bgcolor\=\"\#FFFFCC\"><a href=\"$URLs{GENOME}$GE_S
 		if ((split(/\n/,$test))[0]=~ (/chr([0-9YXLRIV]+)\t(\d+)\t/)){
 		    $chro=$1;
 		    $gpos=$2;
-		    print "<br>UCSC <a href\=\"",$UCSC{$OS1},"&position=chr$chro:",$gpos-200,"-",$gpos+200,"&amp;hgt.customText=ftp://ccg.vital-it.ch/epd/BED/";
+		    print "<br>UCSC <a href\=\"",$UCSC{$OS1},"&position=chr$chro:",$gpos-200,"-",$gpos+200,"&amp;hgt.customText=https://epd.expasy.org/ftp/epd/BED/";
 		    print $BEDU{$OS1};
 		    print "&ct_TSSinEPD=full\">Genome Browser<\/a>\n ";
 		}

cgi-bin/fetch_biomart.cgi

@@ -203,7 +203,7 @@ if ($ENV{'REQUEST_METHOD'} eq 'POST') {
 		    #push(@page, "&clade=mammal&org=Human");
 		    #push(@page, "&db=hg18&position=$chromosome:$start-$stop");
 		    push(@page, "&position=$chromosome:$start-$stop");
-		    #push(@page, "&hgt.customText=https://epd.epfl.ch/ucsc/hg18.wig");
+		    #push(@page, "&hgt.customText=https://epd.expasy.org/epd/ucsc/hg18.wig");
 		    push(@page, "\" title='Genome Browser view'> <img border='0' bordercolor='black' src='/epd/icons/GB_small.png' width='20' height='15'> </></td></tr>");
 
 		}elsif($FORM{"query_db"} eq "mm.epdnew"){
@@ -224,7 +224,7 @@ if ($ENV{'REQUEST_METHOD'} eq 'POST') {
 		    push(@page, "https://genome.ucsc.edu/cgi-bin/hgTracks?");
 		    push(@page, "&clade=mammal&org=Mouse");
 		    push(@page, "&db=mm9&position=$chromosome:$start-$stop");
-		    push(@page, "&hgt.customText=https://epd.epfl.ch/ucsc/mm9.wig");
+		    push(@page, "&hgt.customText=https://epd.expasy.org/epd/ucsc/mm9.wig");
 		    push(@page, "\" title='Genome Browser view'> <img border='0' bordercolor='black' src='/epd/icons/GB_small.png' width='20' height='15'> </></td></tr>");
 
                 }elsif($FORM{"query_db"} eq "dm.epdnew"){
@@ -245,7 +245,7 @@ if ($ENV{'REQUEST_METHOD'} eq 'POST') {
 		    push(@page, "https://genome.ucsc.edu/cgi-bin/hgTracks?");
 		    push(@page, "&clade=insect&org=D.+melanogaster");
 		    push(@page, "&db=dm3&position=$chromosome:$start-$stop");
-		    push(@page, "&hgt.customText=https://epd.epfl.ch/ucsc/dm3_test.wig");
+		    push(@page, "&hgt.customText=https://epd.expasy.org/epd/ucsc/dm3_test.wig");
 		    push(@page, "\" title='Genome Browser view'> <img border='0' bordercolor='black' src='/epd/icons/GB_small.png' width='20' height='15'> </></td></tr>");
                 }elsif($FORM{"query_db"} eq "dr.epdnew"){
                     $count++;
@@ -265,7 +265,7 @@ if ($ENV{'REQUEST_METHOD'} eq 'POST') {
 		    push(@page, "https://genome.ucsc.edu/cgi-bin/hgTracks?");
 		    push(@page, "&clade=vertebrate&org=Zebrafish");
 		    push(@page, "&db=danRer7&position=$chromosome:$start-$stop");
-		    push(@page, "&hgt.customText=https://epd.epfl.ch/ucsc/danRer7.wig");
+		    push(@page, "&hgt.customText=https://epd.expasy.org/epd/ucsc/danRer7.wig");
 		    push(@page, "\" title='Genome Browser view'> <img border='0' bordercolor='black' src='/epd/icons/GB_small.png' width='20' height='15'> </></td></tr>");
 		}elsif($FORM{"query_db"} eq "ens"){
 		    $count++;