MG-RAST · teharrison · Jul 1, 2015 · Jun 26, 2015 · Jun 29, 2015 · Jun 29, 2015
diff --git a/dockerfiles/api/Dockerfile b/dockerfiles/api/Dockerfile
@@ -1,3 +1,5 @@
+# MG-RAST API
+
 FROM httpd:2.4.12

 # MG-RAST dependencies
@@ -6,6 +8,7 @@ RUN apt-get update && apt-get install -y \
  libpq-dev \
  make \
  curl \
+  r-base \
  perl-modules \
  liburi-perl \
  libwww-perl \
@@ -40,10 +43,8 @@ RUN apt-get install -y \
  libtemplate-perl

 RUN pip install gspread xlrd openpyxl lepl
-
 RUN cd / && git clone https://github.com/MG-RAST/pipeline.git

-
 RUN mkdir -p /sites/1/ && \
  cd /sites/1/ && \
  ln -s /MG-RAST/
@@ -58,4 +59,4 @@ RUN mkdir -p /m5nr && \
  ln -s /api-server-data/20131215 /m5nr/20131215

 # Execute:
-# /usr/local/apache2/bin/httpd -DFOREGROUND -f /MG-RAST/conf/httpd.conf
+# /usr/local/apache2/bin/httpd -DFOREGROUND -f /api-server-conf/httpd.conf
diff --git a/dockerfiles/web/Dockerfile b/dockerfiles/web/Dockerfile
@@ -64,6 +64,7 @@ RUN cd / && \
 # certificates need to be in daemon home directory
 RUN ln -s /config/postgresql/ /usr/sbin/.postgresql

+# docker run -t -i --name web -v /home/core/mgrast-config/services/web_v3/:/config -p 80:80 httpd:2.4.12 bash
 # Start
-#bash -c "/bin/chmod 600 /config/postgresql/* ; /bin/chown daemon:daemon /config/postgresql/* ; /usr/local/apache2/bin/apachectl -f /config/httpd.conf -D FOREGROUND"
+# bash -c "/bin/chmod 600 /config/postgresql/*; /bin/chown daemon:daemon /config/postgresql/*; /usr/local/apache2/bin/apachectl -f /config/httpd.conf -D FOREGROUND"

diff --git a/src/MGRAST/Schema/m5nr_copy.cql.tt b/src/MGRAST/Schema/m5nr_copy.cql.tt
@@ -0,0 +1,17 @@
+
+use m5nr_v[% version %];
+
+COPY ontologies (source, name, level1, level2, level3, level4) FROM '[% data_dir %]/m5nr_v[% version %].ontology.all';
+COPY ont_level1 (source, level1, name) FROM '[% data_dir %]/m5nr_v[% version %].ontology.level1';
+COPY ont_level2 (source, level2, name) FROM '[% data_dir %]/m5nr_v[% version %].ontology.level2';
+COPY ont_level3 (source, level3, name) FROM '[% data_dir %]/m5nr_v[% version %].ontology.level3';
+COPY ont_level4 (source, level4, name) FROM '[% data_dir %]/m5nr_v[% version %].ontology.level4';
+
+COPY organisms_ncbi (name, tax_domain, tax_phylum, tax_class, tax_order, tax_family, tax_genus, tax_species, ncbi_tax_id) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.all';
+COPY tax_domain (tax_domain, name) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.domain';
+COPY tax_phylum (tax_phylum, name) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.phylum';
+COPY tax_class (tax_class, name) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.class';
+COPY tax_order (tax_order, name) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.order';
+COPY tax_family (tax_family, name) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.family';
+COPY tax_genus (tax_genus, name) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.genus';
+COPY tax_species (tax_species, name) FROM '[% data_dir %]/m5nr_v[% version %].taxonomy.species';
diff --git a/src/MGRAST/Schema/m5nr_v4.cql → src/MGRAST/Schema/m5nr_table.cql.tt b/src/MGRAST/Schema/m5nr_v4.cql → src/MGRAST/Schema/m5nr_table.cql.tt
@@ -1,10 +1,10 @@

-CREATE KEYSPACE IF NOT EXISTS m5nr_v1
-    WITH REPLICATION = { 'class' : 'SimpleStrategy', 'replication_factor' : 2 };
+CREATE KEYSPACE IF NOT EXISTS m5nr_v[% version %]
+    WITH REPLICATION = { 'class' : 'SimpleStrategy', 'replication_factor' : [% replication %] };

-use m5nr_v1;
+use m5nr_v[% version %];

-CREATE TABLE IF NOT EXISTS md5_id_annotation (
+CREATE TABLE IF NOT EXISTS id_annotation (
    id int,
    source text,
    md5 text,
@@ -16,20 +16,18 @@ CREATE TABLE IF NOT EXISTS md5_id_annotation (
    organism list<text>,
    PRIMARY KEY (id, source)
 );
-COPY md5_id_annotation (id, source, md5, is_protein, single, lca, accession, function, organism) FROM '/mnt/src/m5nr_v1.annotation.id';

 CREATE TABLE IF NOT EXISTS md5_annotation (
    md5 text,
    source text,
    is_protein boolean,
    single text,
-    lca text,
+    lca list<text>,
    accession list<text>,
    function list<text>,
    organism list<text>,
    PRIMARY KEY (md5, source)
 );
-COPY md5_annotation (md5, source, is_protein, single, lca, accession, function, organism) FROM '/mnt/src/m5nr_v1.annotation.md5';

 CREATE TABLE IF NOT EXISTS ontologies (
    source text,
@@ -40,39 +38,34 @@ CREATE TABLE IF NOT EXISTS ontologies (
    level4 text,
    PRIMARY KEY (source, name)
 );
-COPY ontologies (source, name, level1, level2, level3, level4) FROM '/mnt/src/m5nr_v1.ontology.all';

 CREATE TABLE IF NOT EXISTS ont_level1 (
    source text,
    level1 text,
    name text,
    PRIMARY KEY (source, level1, name)
 );
-COPY ont_level1 (source, level1, name) FROM '/mnt/src/m5nr_v1.ontology.level1';

 CREATE TABLE IF NOT EXISTS ont_level2 (
    source text,
    level2 text,
    name text,
    PRIMARY KEY (source, level2, name)
 );
-COPY ont_level2 (source, level2, name) FROM '/mnt/src/m5nr_v1.ontology.level2';

 CREATE TABLE IF NOT EXISTS ont_level3 (
    source text,
    level3 text,
    name text,
    PRIMARY KEY (source, level3, name)
 );
-COPY ont_level3 (source, level3, name) FROM '/mnt/src/m5nr_v1.ontology.level3';

 CREATE TABLE IF NOT EXISTS ont_level4 (
    source text,
    level4 text,
    name text,
    PRIMARY KEY (source, level4, name)
 );
-COPY ont_level4 (source, level4, name) FROM '/mnt/src/m5nr_v1.ontology.level4';

 CREATE TABLE IF NOT EXISTS organisms_ncbi (
    name text,
@@ -86,53 +79,45 @@ CREATE TABLE IF NOT EXISTS organisms_ncbi (
    ncbi_tax_id int,
    PRIMARY KEY (name)
 );
-COPY organisms_ncbi (name, tax_domain, tax_phylum, tax_class, tax_order, tax_family, tax_genus, tax_species, ncbi_tax_id) FROM '/mnt/src/m5nr_v1.taxonomy.all';

 CREATE TABLE IF NOT EXISTS tax_domain (
    tax_domain text,
    name text,
    PRIMARY KEY (tax_domain, name)
 );
-COPY tax_domain (tax_domain, name) FROM '/mnt/src/m5nr_v1.taxonomy.domain';

 CREATE TABLE IF NOT EXISTS tax_phylum (
    tax_phylum text,
    name text,
    PRIMARY KEY (tax_phylum, name)
 );
-COPY tax_phylum (tax_phylum, name) FROM '/mnt/src/m5nr_v1.taxonomy.phylum';

 CREATE TABLE IF NOT EXISTS tax_class (
    tax_class text,
    name text,
    PRIMARY KEY (tax_class, name)
 );
-COPY tax_class (tax_class, name) FROM '/mnt/src/m5nr_v1.taxonomy.class';

 CREATE TABLE IF NOT EXISTS tax_order (
    tax_order text,
    name text,
    PRIMARY KEY (tax_order, name)
 );
-COPY tax_order (tax_order, name) FROM '/mnt/src/m5nr_v1.taxonomy.order';

 CREATE TABLE IF NOT EXISTS tax_family (
    tax_family text,
    name text,
    PRIMARY KEY (tax_family, name)
 );
-COPY tax_family (tax_family, name) FROM '/mnt/src/m5nr_v1.taxonomy.family';

 CREATE TABLE IF NOT EXISTS tax_genus (
    tax_genus text,
    name text,
    PRIMARY KEY (tax_genus, name)
 );
-COPY tax_genus (tax_genus, name) FROM '/mnt/src/m5nr_v1.taxonomy.genus';

 CREATE TABLE IF NOT EXISTS tax_species (
    tax_species text,
    name text,
    PRIMARY KEY (tax_species, name)
 );
-COPY tax_species (tax_species, name) FROM '/mnt/src/m5nr_v1.taxonomy.species';
diff --git a/src/MGRAST/Schema/mgrast_analysis_v4.cql b/src/MGRAST/Schema/mgrast_analysis_v4.cql
@@ -12,9 +12,15 @@ CREATE TYPE source_info (

 CREATE TYPE md5_info (
    abundance int,
+    exp_avg float,
+    ident_avg float,
+    len_avg float,
+    exp_stdv float,
+    ident_stdv float,
+    len_stdv float,
    seek bigint,
    length int,
-    annotation map<text, frozen <source_info>>
+    is_protein boolean
 );

 CREATE TYPE lca_info (
@@ -42,6 +48,7 @@ INSERT INTO job_test (version, job, exp_avg, md5, data) VALUES (1, 20, 60, 'foo'
 INSERT INTO job_test (version, job, exp_avg, md5, data) VALUES (1, 20, 70, 'foo', 'hello world');
 INSERT INTO job_test (version, job, exp_avg, md5, data) VALUES (1, 20, 70, 'bar', 'hello world');

+### version 1 ###
 CREATE TABLE IF NOT EXISTS job_md5s (
    version int,
    job int,
@@ -70,6 +77,7 @@ CREATE TABLE IF NOT EXISTS job_lcas (

 # see: http://docs.datastax.com/en/cql/3.1/cql/cql_using/use-slice-partition.html

+### version 2 ###
 CREATE TABLE IF NOT EXISTS job_md5s (
    version int,
    job int,
@@ -107,3 +115,17 @@ CREATE TABLE IF NOT EXISTS job_lcas (
    PRIMARY KEY ((version, job), exp_avg, ident_avg, len_avg, lca)
 );

+### version 3 ###
+CREATE TABLE IF NOT EXISTS job_md5s (
+    version int,
+    job int,
+    source text,
+    md5 text,
+    data frozen<md5_info>,
+    accession list<text>,
+    function list<text>,
+    organism list<text>,
+    PRIMARY KEY ((version, job), source, md5)
+);
+
+
diff --git a/src/MGRAST/html/MGRAST-frontpage.tmpl b/src/MGRAST/html/MGRAST-frontpage.tmpl
@@ -8,7 +8,7 @@
 <div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=MetagenomeSearch"><img src='./Html/lupe.png' style='width: 20px; height: 20px;' title='Search'></a></div>
 	<br>
 	<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=DownloadMetagenome"><img src='./Html/mg-download.png' style='width: 20px; height: 20px;' title=Download></a></div>
-    	<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
+    	<div id="top_nav_links"><a class= "nav_top" href="./Html/mgmain.html?mgpage=upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
 	<div id="top_nav_links"><a class= "nav_top" href="http://blog.metagenomics.anl.gov/howto/" target="blank"><img src='./Html/mg-help.png' style='width: 20px; height: 20px;' title='Support'></a></div>
 	<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Contact"><img src='./Html/mg-contact.png' style='width: 20px; height: 20px;' title='Contact'></a></div>
      </div>

diff --git a/src/MGRAST/html/MGRAST.tmpl b/src/MGRAST/html/MGRAST.tmpl
@@ -14,7 +14,7 @@
 	<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=MetagenomeSearch"><img src='./Html/lupe.png' style='width: 20px; height: 20px;' title='Search'></a></div>
 	<br>
 	<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=DownloadMetagenome"><img src='./Html/mg-download.png' style='width: 20px; height: 20px;' title=Download></a></div>
-    	<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
+    	<div id="top_nav_links"><a class= "nav_top" href="./Html/mgmainv3.html?mgpage=upload"><img src='./Html/mg-upload.png' style='width: 20px; height: 20px;' title='Upload'></a></div>
 	<div id="top_nav_links"><a class= "nav_top" href="http://blog.metagenomics.anl.gov/howto/" target=_blank><img src='./Html/mg-help.png' style='width: 20px; height: 20px;' title='Support'></a></div>
 	<div id="top_nav_links"><a class= "nav_top" href="metagenomics.cgi?page=Contact"><img src='./Html/mg-contact.png' style='width: 20px; height: 20px;' title='Contact'></a></div>
      </div>

diff --git a/src/MGRAST/html/js/MetagenomeSearch.js b/src/MGRAST/html/js/MetagenomeSearch.js
@@ -1,4 +1,4 @@
-var api_url = 'http://api.metagenomics.anl.gov/1/metagenome?verbosity=mixs&';
+var api_url = RetinaConfig ? RetinaConfig.mgrast_api + "/metagenome?verbosity=mixs&" : 'http://api.metagenomics.anl.gov/1/metagenome?verbosity=mixs&';
 var datastore = {};
 var result = 'result'; // div where results are to be displayed
 var saved_params = {};

diff --git a/src/MGRAST/lib/JobDB/Metadata.pm b/src/MGRAST/lib/JobDB/Metadata.pm
@@ -2,6 +2,7 @@ package JobDB::Metadata;

 use strict;
 use warnings;
+use Conf;

 1;

@@ -130,7 +131,7 @@ sub get_data {
    $obj->{id} = "mgm".$job->{metagenome_id};
    $obj->{about} = "mobedac metagenome";
    $obj->{name} = $job->{name};
-    $obj->{url} = 'http://metagenomics.anl.gov/linkin.cgi?id='.$obj->{id};
+    $obj->{url} = $Conf::cgi_url.'linkin.cgi?id='.$obj->{id};
    $obj->{version} = $job->{server_version};
    $obj->{creation} = $job->{created_on};
 #    $obj->{sample} = $job->sample->{ID};

diff --git a/src/MGRAST/lib/WebPage/Analysis.pm b/src/MGRAST/lib/WebPage/Analysis.pm
@@ -6603,8 +6603,8 @@ sub selectable_metagenomes {
      push @{$collections->{$name}}, [ $pj->{metagenome_id}, $pj->{name} ];
    }
    foreach my $coll ( sort keys %$collections ) {
-      if ( @{$collections->{$coll}} == 0 ) { next; }
-      push(@$colls, { label => $coll." [".scalar(@{$collections->{$coll}})."]", value => join('||', map { $_->[0]."##".$_->[1] } @{$collections->{$coll}}) });
+      if ( (! $coll) || (! $collections->{$coll}) || (@{$collections->{$coll}} == 0) ) { next; }
+      push(@$colls, { label => $coll." [".scalar(@{$collections->{$coll}})."]", value => join('||', map { ($_->[0] || "")."##".($_->[1] || "") } @{$collections->{$coll}}) });
    }
  }    


diff --git a/src/MGRAST/lib/WebPage/DownloadMetagenome.pm b/src/MGRAST/lib/WebPage/DownloadMetagenome.pm
@@ -73,7 +73,7 @@ sub init {
  $self->data('default', $default);

  # api info for download
-  $self->data('api', "http://api.metagenomics.anl.gov");
+  $self->data('api', $Conf::api_url || "http://api.metagenomics.anl.gov");

  # get to metagenome using the metagenome ID
  if ( $cgi->param('metagenome') ) {

diff --git a/src/MGRAST/lib/WebPage/Home.pm b/src/MGRAST/lib/WebPage/Home.pm
@@ -58,7 +58,7 @@ sub output {
  if ($is_old) {
    $content .= qq~<script>
 function bookmark(url, title) {
-   if (confirm('The URL you are using to reach this page is deprecated.\\nThe new URL is:\\n\\n\\thttp://metagenomics.anl.gov/\\n\\nWould you like to bookmark the new location?')) {
+   if (confirm('The URL you are using to reach this page is deprecated.\\nThe new URL is:\\n\\n\\t~.$Conf::cgi_url.qq~\\n\\nWould you like to bookmark the new location?')) {
     var url = url || location.protocol + '//' + location.host;
     var title = title || location.host;
     if(document.all) {
@@ -69,7 +69,7 @@ sub output {
   }
   return false;
 }
- </script><img src='./Html/clear.gif' onload='bookmark("http://metagenomics.anl.gov/", "MG-RAST");'>~;
+ </script><img src='./Html/clear.gif' onload='bookmark("~.$Conf::cgi_url.qq~", "MG-RAST");'>~;
  }

  $content .= "<div class='clear' style='height:30px;'></div>";
@@ -117,7 +117,7 @@ function forward_to_search (e) {
  $content .= "<a href='?page=Register' title='Register a new account'><div style='float:left; cursor: pointer;padding-top:5px;'>".$register."</div></a>";  
  $content .= "<a href='?page=Contact' title='Click here for contact information'><div style='float:left; cursor: pointer;padding-top:5px;'>".$contact."</div></a>";
  $content .= "<a href='http://blog.metagenomics.anl.gov' title='Click here for support and FAQs'><div style='float:left; cursor: pointer;padding-top:5px;'>".$help."</div></a>";
-  $content .= "<a href='?page=Upload' title='Upload a new metagenome'><div style='float:left; cursor: pointer;padding-top:5px; margin-right:20px;'>".$upload."</div></a>";
+  $content .= "<a href='./Html/mgmainv3.html?mgpage=upload' title='Upload a new metagenome'><div style='float:left; cursor: pointer;padding-top:5px; margin-right:20px;'>".$upload."</div></a>";
  $content .= "<a href='http://blog.metagenomics.anl.gov/' target=_blank><div style='float:left; cursor: pointer;padding-top:5px;'>".$news."</div></a>";
  $content .= "</div>";
  $content .= "<div class='clear'></div>";
@@ -176,13 +176,7 @@ END

  $content .= "<a href=\"http://www.biomedcentral.com/1471-2105/9/386\" target=\"_blank\"><p style='border-radius: 5px; -webkit-border-radius: 5px; -moz-border-radius: 5px; color: white; padding: 5px 0px 3px 10px; color: white; font-size:14; background-color: #5281B0; width: 100px; float: left; margin-right: 10px; top: -12px; position: relative;'>cite MG-RAST</p></a><a href=\"http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004008\" target=\"_blank\" style=\"float: right;\"><p style='border-radius: 5px; -webkit-border-radius: 5px; -moz-border-radius: 5px; color: white; padding: 5px 0px 3px 10px; color: white; font-size:14; background-color: #5281B0; width: 120px; float: left; margin-right: 10px; top: -12px; position: relative;'>cite MG-RAST API</p></a>";

-  #$content .= "<p style='color:#8FBC3F;text-align:left;font-size:9px;margin-top:3px;'><em>The Metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes</em> F. Meyer, D. Paarmann, M. D'Souza, R. Olson , E. M. Glass, M. Kubal, T. Paczian , A. Rodriguez , R. Stevens, A. Wilke, J. Wilkening, R. A. Edwards<br/><em>BMC Bioinformatics 2008, 9:386
-#, [<a href=\"http://www.biomedcentral.com/1471-2105/9/386\" target=\"_blank\">article</a>]</em></p>";
-
-  #$content .= "<p style='text-align: center; float: right;'><span style='font-size: 11px; color: white;'>powered by</span><br><img style='width: 50px;' src='./Html/kbase_logo.png'></p>";
-
  my $logos = "<img src='./Html/argonne_header_logo.jpg' style='padding-top: 15px; width: 150px;'>";
-  # news - logos

  return $content;
 }
@@ -198,36 +192,6 @@ sub speedometer {
    my ($speed, $mileage, $trip, $togo) = split(/\t/, $line);

    $content .= "<table style='background-color: #2f2f2f; position: absolute; right: 22px; top: 78px; color: rgb(143, 188, 63); font-family: Verdana,Arial,sans-serif;'><tr><td colspan=3 align=center style='font-size: 9pt;font-weight: bold;'>pipeline status</td></tr><tr title='analysis speed in basepairs/second'><td align=right style='font-size: 8pt;'>$speed</td><td align=left style='font-size: 8pt;'>bp/s</td><td align=left style='font-size: 8pt;'>speed</td></tr><tr title='data analyzed in the last 30 days'><td align=right style='font-size: 8pt;'>$trip</td><td align=left style='font-size: 8pt;'>Mbp</td><td align=left style='font-size: 8pt;'>last 30 days</td></tr><tr title='data left to be processed'><td align=right style='font-size: 8pt;'>$togo</td><td align=left style='font-size: 8pt;'>Mbp</td><td align=left style='font-size: 8pt;'>in queue</td></tr><tr title='total amount of data analyzed'><td align=right style='font-size: 8pt;'>$mileage</td><td align=left style='font-size: 8pt;'>Mbp</td><td align=left style='font-size: 8pt;'>total</td></tr></table>";
-
-    # my @trip1 = split(//, $trip);
-#     while (scalar(@trip1) < 7) {
-#       unshift(@trip1, "0");
-#     }
-#     $trip = '<table><tr>';# style="margin-left: 36px;"
-#     foreach my $t (@trip1) {
-#       $trip .= "<td style='font-size: 10px; border: 1px solid black; background-color: white; font-weight: bold; width: 12px; text-align: center;'>$t</td>";
-#     }
-#     $trip .= '</tr></table>';  
-#     my @togo1 = split(//, $togo);
-#     while (scalar(@togo1) < 7) {
-#       unshift(@togo1, "0");
-#     }
-#     $togo = '<table><tr>';# style="margin-left: 36px;"
-#     foreach my $t (@togo1) {
-#       $togo .= "<td style='font-size: 10px; border: 1px solid black; background-color: white; font-weight: bold; width: 12px; text-align: center;'>$t</td>";
-#     }
-#     $togo .= '</tr></table>';
-#     my @mileage1 = split(//, $mileage);
-#     while (scalar(@mileage1) < 7) {
-#       unshift(@mileage1, "0");
-#     }
-#     $mileage = '<table><tr>';
-#     foreach my $t (@mileage1) {
-#       $mileage .= "<td style='font-size: 10px; border: 1px solid black; background-color: white; font-weight: bold; width: 12px; text-align: center;'>$t</td>";
-#     }
-#     $mileage .= '</tr></table>';
-
-#     $content .= "<table style='background-color: #2f2f2f; position: absolute; right: 22px; top: 79px; color: rgb(143, 188, 63); font-weight: bold; font-family: Verdana,Arial,sans-serif;'><tr title='analysis speed in basepairs/second'><td style='font-size: 10px; text-align: right;'>$speed</td><td style='font-size: 10px; vertical-align: middle;'>bp/s</td><td style='font-size: 10px; vertical-align: middle;'>speed</td></tr><tr title='data analyzed in the last 30 days'><td>$trip</td><td style='font-size: 10px; vertical-align: middle;'>Mbp</td><td style='font-size: 10px; vertical-align: middle;'>last 30 days</td></tr><tr title='data left to be processed'><td>$togo</td><td style='font-size: 10px; vertical-align: middle;'>Mbp</td><td style='font-size: 10px; vertical-align: middle;'>in queue</td></tr><tr title='total amount of data analyzed'><td>$mileage</td><td style='font-size: 10px; vertical-align: middle;'>Mbp</td><td style='font-size: 10px; vertical-align: middle;'>total</td></tr></table>";
  }

  return $content;

diff --git a/src/MGRAST/lib/WebPage/MetagenomeOverview.pm b/src/MGRAST/lib/WebPage/MetagenomeOverview.pm
@@ -146,7 +146,7 @@ sub output {
  my $mddb = $self->data('mddb');
  my $user = $self->application->session->user;
  my $job_id  = $job->job_id;
-  my $mg_link = "http://metagenomics.anl.gov/linkin.cgi?metagenome=$mgid";
+  my $mg_link = $Conf::cgi_url."linkin.cgi?metagenome=$mgid";

  # get project information
  my $project_link   = "";

diff --git a/src/MGRAST/lib/WebPage/MetagenomeProject.pm b/src/MGRAST/lib/WebPage/MetagenomeProject.pm
@@ -129,7 +129,7 @@ sub output {
      $self->{is_editor} = 1;
    }

-    my $proj_link = "http://metagenomics.anl.gov/linkin.cgi?project=".$self->{project_id};
+    my $proj_link = $Conf::cgi_url."linkin.cgi?project=".$self->{project_id};
    $html .= "<h1 style='display: inline;'>".$project->name.(($user and $user->has_right(undef, 'edit', 'user', '*')) ? " (ID ".$project->id.")": "")."</h1>";
    $html .= "<p><table>";
    $html .= "<tr><td><b>Visibility</b></td><td style='padding-left:15px;'>".($project->public ? 'Public' : 'Private')."</td></tr>";