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Merge upstream

Merged Merge upstream
dev into master
Merged Loraine Gueguen requested to merge dev into master
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templates/page--front.tpl.php
+ 56
− 13
@@ -147,17 +147,43 @@
<?php endif; ?>
<?php if (getenv('ENABLE_BLAST')): ?>
<?php
if (getenv('ENABLE_BLAST') == "1")
$url = $GLOBALS['base_url'].'/blast';
else
$url = getenv('ENABLE_BLAST');
$blast_list = explode("&", getenv('ENABLE_BLAST'));
$blast_urls = array();
foreach ($blast_list as $item){
list($str1,$str2) = explode('=', $item, 2);
$name = "Blast";
if (strlen($str2) == 0){
if ($str1 == "1"){
$url = $GLOBALS['base_url'].'/blast';
}else{
$url = $str1;
}
}else{
$name = $str1;
$url = $str2;
}
$blast_urls[$name] = $url;
}
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Blast</a></li>
<?php if (count($blast_urls) > 1): ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46">
<a href="#">Blast</a>
<ul class="sub-menu">
<?php endif; ?>
<?php foreach ($blast_urls as $name => $url): ?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46">
<a href="<?php echo $url; ?>" target="_blank"><?php echo "$name"; ?>
</a></li>
<?php endforeach; ?>
<?php if (count($blast_urls) > 1): ?>
</ul>
</li>
<?php endif; ?>
<?php endif; ?>
<?php if (getenv('ENABLE_JBROWSE')): ?>
<?php
if (getenv('ENABLE_JBROWSE') == "1")
$url = '/jbrowse';
$url = '/jbrowse/';
else
$url = getenv('ENABLE_JBROWSE');
?>
@@ -165,14 +191,29 @@
<?php endif; ?>
<?php if (getenv('ENABLE_APOLLO')): ?>
<?php
if (getenv('ENABLE_APOLLO') == "1")
$url = '/apollo';
else
if (getenv('ENABLE_APOLLO') == "1") {
$url = $GLOBALS['base_url'] . '/apollo';
$url_report = $GLOBALS['base_url'] . '/apollo_report';
}
else {
$url = getenv('ENABLE_APOLLO');
$url_report = $url . 'report';
}
foreach ($page['organisms'] as $org_id => $org) {
if (isset($org->version)) {
$apollo_org = $org->genus . ' ' . $org->species . ' ' . $org->version;
if (strpos($url, '?') !== false)
$url .= '&organism=' . $apollo_org;
else
$url .= 'annotator/loadLink?organism=' . $apollo_org;
break;
}
}
?>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url'].$url; ?>">Apollo</a>
<li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $url; ?>">Apollo</a>
<!-- <ul class="sub-menu">
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="<?php echo $GLOBALS['base_url'].'/apollo_report'; ?>">Annotation report</a></li>
<li id="menu-item-43" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-43"><a href="<?php echo $url_report; ?>">Annotation report</a></li>
</ul>-->
</li>
<?php endif; ?>
@@ -229,7 +270,9 @@
<li id="menu-item-78" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-78"><a href="https://bipaa.genouest.org/is/lepidodb/">LepidoDB</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/coleoptera/">Coleoptera</a></li>
<li id="menu-item-44" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-44"><a href="https://bipaa.genouest.org/is/crustacea/">Crustacea</a></li>-->
<li id="menu-item-130" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-130"><a href="http://galaxy.sb-roscoff.fr/">Galaxy</a></li>
<li id="menu-item-130" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-130"><a href="https://phaeoexplorer.sb-roscoff.fr">Phaeoexplorer</a></li>
<li id="menu-item-130" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-130"><a href="https://abims.sb-roscoff.fr/resources/genomic_resources">Other genomic resources</a></li>
<!--<li id="menu-item-130" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-130"><a href="https://galaxy.sb-roscoff.fr/">Galaxy</a></li>-->
<!--<li id="menu-item-138" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-138"><a href="https://bipaa.genouest.org/account/">BIPAA account</a></li>-->
</ul>
</li>
@@ -321,7 +364,7 @@
<?php include('/var/www/html/species_legend.html'); ?>
<?php endif; ?>
<p style="font-style:italic; margin:0; padding:0">Other organisms are available on the <a href="http://abims.sb-roscoff.fr/">ABiMS website</a>.</p>
<!--<p style="font-style:italic; margin:0; padding:0">Other organisms are available on the <a href="http://abims.sb-roscoff.fr/">ABiMS website</a>.</p>-->
</div>
<div id="front_analyses">