Subversion to git conversion, and the move to commercial hosting.

00README

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+HMMER's web server
+
+"make" installs at:      [email protected]
+in directory:            /var/html/hmmer.org/public_html
+
+
+
+################################################################
+# Making and testing a change
+################################################################
+In a git working directory:
+
+
+  git pull origin
+     [make edits]
+  make test
+     [test site is: ---]
+  make
+     [real site is: http://hmmer.org/, which is 96.126.110.11]
+  make clean
+  git commit -a
+  git push origin
+
+
+
+################################################################
+# Commercially hosted at Linode
+################################################################
+
+Linode management dashboard :
+  https://manager.linode.com/linodes/dashboard/linode1257886
+  user = cryptogenomicon
+
+hmmer.org is currently hosted at linode.com, on a single node:
+  linode1257886 running Ubuntu 14.04 LTS
+  96.126.110.11 
+  archangel
+
+The machine has a single user, seddy. 
+The public_html directory is chown seddy.
+
+The installation scripts use rsync and ssh, and assume that seddy has
+passwordless SSH access configured.
+
+
+
+################################################################
+# Under Git revision control
+################################################################
+
+Git repository for Eddy lab web projects, on Odyssey:
+   /n/eddy_lab/gitrepo/web.git
+
+To get a copy remotely:
+   git clone [email protected]:/n/eddy_lab/gitrepo/web.git
+or:
+   git clone seddy@ody:/n/eddy_lab/gitrepo/web.git
+
+Replace "seddy" with your username. You need appropriate permissions
+in our lab to access the lab gitrepo. Some of us have an "ody"
+nickname set up for our preauthenticated ssh access.
+
+
+
+################################################################
+# The HMMER logo
+################################################################
+
+The HMMER logo was produced by David Deen (www.daviddeen.com).
+
+The logo with "HMMER" text is hmmer_small.ai
+The square logo without text is hmmer_square.ai
+
+My web page titlebar is hmmer_titlebar.ai
+
+
+
+
+

Makefile

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+# Public installation site; where we'll rsync and ssh to: 
+WEBHOST  =  [email protected]
+WEBDIR   =  /var/www/hmmer.org/public_html
+
+# hmmer.org makes crossreferences to our publications, on lab web site rooted at:
+LABWEB   =  http://eddylab.org
+
+# Building hmmer.org pages also requires a local git working copy of "labbib", at:
+LABBIB   =  ~/labbib
+
+# Building hmmer.org pages is coordinated with the lab web pages, in
+# this same git repo one level up.
+LABDIR   =  ../eddylab.org
+
+
+# 'make all' updates the live site.
+# The -C option to rsync makes it not copy .svn stuff.
+#
+all:    site/publications-inc.html
+	rsync -Cavuz site/ ${WEBHOST}:${WEBDIR}/
+	ssh ${WEBHOST} chmod +x ${WEBDIR}/publications.html
+
+# Install/update the test site
+# Having everything in site/ lets us do one rsync.
+#
+test:    site/publications-inc.html
+	ssh ${WEBHOST} mkdir -p ${TESTDIR}
+	rsync -Cavuz site/ ${WEBHOST}:${TESTDIR}/
+	ssh ${WEBHOST} chmod +x ${TESTDIR}/publications.html
+
+# Below is an example of using the boolean search with keywords. It will search for all entries
+# tagged with 'hmmer', but not 'lab'.
+# ~/labbib/publications.pl -k 'hmmer NOT lab' ~/labbib/master.bib > site/others-publications-inc.html
+site/publications-inc.html:   ${LABBIB}/lab.bib ${LABBIB}/master.bib
+	rm -f site/publications
+	ln -s ${LABDIR}/site/publications site/publications
+	~/labbib/publications.pl -k 'hmmer' --template=selab.tt --url='${LABWEB}' > site/publications-inc.html
+	~/labbib/publications.pl -k 'hmmer' --template=selab.tt master.bib > site/others-publications-inc.html
+	rm -f site/publications
+
+# Clean up this source directory
+#
+clean:
+	rm -f *~ \
+		site/*~ \
+		site/publications-inc.html \
+		site/others-publications-inc.html
+
+# Delete the test site.
+#
+testdelete:
+	ssh ${WEBHOST} rm -rf ${TESTDIR}
+
+

selab.tt

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+[%- BLOCK title -%]
+[%- title_link = entry.title_link -%]
+[%- IF title_link %]
+  <a href="[% title_link %]" id="[% entry.key %]">
+[%- END -%]
+[% entry.cleaned('title') %]
+[%- IF title_link %]</a>.[%- END -%]
+[%- END -%]
+[%- BLOCK notes -%]
+<div>
+[%- FOREACH key IN entry.links.keys.sort -%]
+  [%- IF entry.links.$key.0.label -%]
+  [% entry.links.$key.0.label %] :
+  [%- END -%]
+  [%- FOREACH link IN entry.links.$key -%]
+    [%- IF link.type == "CORRECTION" -%]
+    There is a <a href="[% link.url %]">[[% link.text %]]</a> for this publication.
+    [%- ELSE -%]
+    <a href="[% link.url %]">[[% link.text %]]</a>
+    [%- END -%]
+  [%- END -%]
+  <br/>
+[%- END -%]
+</div>
+[%- END -%]
+
+[%- year = 0000 -%]
+
+[%- FOREACH entry IN entries -%]
+[%- IF ! nodiv -%]
+[%- IF entry.year != year -%]
+  [%- year = entry.year -%]
+  <div class="row">
+    <div class="col-sm-12">
+      <h2>[% year%]</h2>
+    </div>
+  </div>
+[%- END -%]
+[%- END -%]
+
+[%- IF entry.type == 'ARTICLE' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+[%- PROCESS title -%]
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%].
+<em>[% entry.cleaned_field('journal') %]</em>,
+[% IF entry.volume && entry.pages %][% entry.volume %]:[% entry.pages %],[% END %]
+[% entry.year %].
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.pubmedlink %]
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- ELSIF entry.type == 'PHDTHESIS' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+<em>[%- PROCESS title -%]</em>
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%].
+PhD Thesis:[% entry.field('school') %], [% entry.year %].
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- ELSIF entry.type == 'BOOK' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+<em>[%- PROCESS title -%]</em>
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%].
+[% entry.publisher %], [% entry.year %].
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- ELSIF entry.type == 'INCOLLECTION' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+[%- PROCESS title -%]
+In: <em>[% entry.cleaned('booktitle') %]</em>[%- IF entry.pages -%], [% entry.pages %][%- END -%].
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%].
+[% entry.publisher %], [% entry.year %].
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- ELSIF entry.type == 'INPROCEEDINGS' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+[%- PROCESS title -%]
+In: <em>[% entry.cleaned('booktitle') %]</em>,
+[% entry.pages %].
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%],
+[% entry.year %].
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- ELSIF entry.type == 'MASTERSTHESIS' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+<em>[%- PROCESS title -%]</em>
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%].
+Masters Thesis: [%entry.school %], [% entry.year %].
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- ELSIF entry.type == 'TECHREPORT' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+[%- PROCESS title -%]
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%].
+[% entry.year %]
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- ELSIF entry.type == 'UNPUBLISHED' -%]
+<div class="row">
+  <div class="col-md-9 col-sm-8">
+[%- PROCESS title -%]
+[%- FOREACH author IN entry.cleaned_author -%]
+  [% author.first %] [% author.last %][% IF ! loop.last %],[% END %]
+[%- END -%].
+[% entry.note %], [% entry.year %].
+[%- PROCESS notes -%]
+  </div>
+  <div class="col-md-3 col-sm-4">
+[% entry.reprint_link -%]
+  </div>
+</div>
+
+[%- END -%]
+[%- END -%]
+</ul>

site/404.html

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+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <title>HMMER</title>
+
+    <!-- Bootstrap -->
+    <link href="/css/bootstrap.min.css" rel="stylesheet">
+
+    <!-- HTML5 Shim and Respond.js IE8 support of HTML5 elements and media queries -->
+    <!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+    <link href="/css/hmmer.css" rel="stylesheet">
+  </head>
+  <body>
+    <div class="container">
+      <div class="row header">
+        <div class="col-sm-2 logo">
+          <a href="/">
+            <img id="hmmerLogo" src="/images/hmmer_title.png" alt="HMMER"/>
+            <h1>HMMER</h1>
+          </a>
+        </div>
+        <div class="col-sm-10 nav">
+          <ul>
+            <li><a href="/download.html">Download</a></li>
+            <li><a href="/documentation.html">Documentation</a></li>
+            <li><a href="http://www.ebi.ac.uk/Tools/hmmer/">Search</a></li>
+            <li><a href="/publications.html">Publications</a></li>
+            <li><a href="http://cryptogenomicon.org/category/hmmer/">Blog</a></li>
+          </ul>
+        </div>
+      </div>
+
+      <div class="row">
+        <div class="col-xs-12">
+          <h2 class="text-center">404: Not Found</h2>
+        </div>
+      </div>
+      <div class="row">
+        <div class="col-sm-12 text-center">
+          <h3>We're sorry, but that page could not be found.</h3>
+          <p>It is possible that the page was part of the web based hmmer search system,
+          which has been moved to <a href="http://www.ebi.ac.uk/Tools/hmmer/">http://www.ebi.ac.uk/Tools/hmmer/</a>.</p>
+        </div>
+      </div>
+      <div class="row footer">
+        <div class="col-sm-12"></div>
+      </div>
+
+
+    </div>
+
+    <!-- jQuery (necessary for Bootstrap's JavaScript plugins) -->
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
+    <!-- Include all compiled plugins (below), or include individual files as needed -->
+    <script src="js/bootstrap.min.js"></script>
+    <script src="js/main.js"></script>
+  </body>
+</html>