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hmmer.org and eddylab.org are now commercially hosted at linode.
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cryptogenomicon committed Aug 24, 2015
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8 changes: 4 additions & 4 deletions Makefile
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Expand Up @@ -6,11 +6,11 @@ WEBDIR = /var/www/hmmer.org/public_html
LABWEB = http://eddylab.org

# Building hmmer.org pages also requires a local git working copy of "labbib", at:
LABBIB = ~/labbib
LABBIB = ${HOME}/labbib

# Building hmmer.org pages is coordinated with the lab web pages, in
# this same git repo one level up.
LABDIR = ../eddylab.org
LABDIR = ${HOME}/web/eddylab.org


# 'make all' updates the live site.
Expand All @@ -34,8 +34,8 @@ test: site/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
~/labbib/publications.pl -n -k 'hmmer' --template=selab.tt > 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
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63 changes: 21 additions & 42 deletions site/documentation.html
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Expand Up @@ -40,8 +40,8 @@ <h1>HMMER</h1>
<div class="col-sm-12">
<h3> Current user guide & release notes</h3>
<ul>
<li><a href="ftp://selab.janelia.org/pub/software/hmmer3/3.1b2/Userguide.pdf">User's Guide: [PDF, 119 pages]</a></li>
<li><a href="ftp://selab.janelia.org/pub/software/hmmer3/3.1b2/RELEASE-NOTES">Release notes</a></li>
<li><a href="http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf">User's Guide: [PDF, 119 pages]</a></li>
<li><a href="http://eddylab.org/software/hmmer3/3.1b2/RELEASE-NOTES">Release notes</a></li>
</ul>
</div>
</div>
Expand All @@ -62,23 +62,13 @@ <h3>Briefly, to compile from source:</h3>
directory containing precompiled binaries. Installing HMMER takes nothing other
than moving these binaries wherever you want them.</p>

<p>We believe HMMER compiles and runs on <em>any</em> POSIX-compliant system
<p>We believe HMMER compiles and runs on any POSIX-compliant system
with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX operating systems.
For more installation and configuration options, see the <strong>Installation</strong>
chapter of the User Guide (included in the package, and also linked
in the documentation section on this site).</p>
</div>
</div>
<div class="row">
<div class="col-xs-12">
<h3>Subversion Access</h3>

<p>Our current development trunk is available via Subversion. To get an anonymous, read-only checkout:</p>
<pre class="bold">svn checkout https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk hmmer</pre>

<p>We welcome code contributions. It's best to give us patches against the development trunk, rather than against the release code (but we'll look at whatever you give us). For developers who've been donating good patches to us for a while, we'll grant write access to the repository.</p>
</div>
</div>

<div class="row">
<div class="col-xs-12">
Expand All @@ -90,19 +80,17 @@ <h5>Blog</h5>

<h5>Papers</h5>
<ul>
<li>Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011
Oct;7(10):e1002195</li>
<li>Eddy SR. A Probabilistic Model of Local Sequence Alignment that Simplifies Statistical Significance Estimation. PLoS Comput. Biol. 2008 May 30;4(5):e1000069 </li>
<li>Eddy SR. A new generation of homology search tools based on probabilistic
inference. Genome Inform. 2009 Oct;23(1):205-11.</li>
<li>Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 7:e1002195 (2011) </li>
<li>Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol. 4:e1000069 (2008) </li>
<li>Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23:205-11 (2009).</li>
<li><a href="/publications.html">Other publications</a> about HMMER</li>
</ul>

<h5>Book</h5>
<p>
The theory behind profile HMMs:
R. Durbin, S. Eddy, A. Krogh, and G. Mitchison,
<a href="http://selab.janelia.org/cupbook.html">
<a href="http://eddylab.org/cupbook.html">
<i>Biological sequence analysis: probabilistic models of proteins
and nucleic acids</i></a>,
Cambridge University Press, 1998.
Expand All @@ -111,43 +99,34 @@ <h5>Book</h5>
</div>
</div>


<li>
<a href="http://www.ploscompbiol.org/doi/pcbi.1000069" id="Eddy08">A Probabilistic Model of Local Sequence Alignment that Simplifies Statistical Significance Estimation</a>. S. R. Eddy.
<em>PLoS Comput. Biol.</em>,
4:e1000069,
2008.
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=18516236&dopt=Abstract"><span class="glyphicon glyphicon-globe"></span> abstract</a>
<div></div></li>



<div class="row">
<div class="col-sm-12">
<h3>Support</h3>
<p>
HMMER is not intended to be commercial software. In particular, it
comes with no promise of support whatsoever. We are generally not able
Because we're an academic research group, HMMER
comes with no promise of support. We are generally not able
to respond individually to requests for help with the package, beyond
the help already provided in HMMER's documentation. We do respond
gratefully to useful suggestions for improved documentation, and to
bug reports.
the help already provided in HMMER's documentation. We do appreciate
suggestions for better documentation, improvements, and bug reports.
</p>
</div>
</div>

<div class="row">
<div class="col-sm-12">
<h3>Reporting bugs</h3>
<p><a href="http://selab.janelia.org/people/eddys/contact.html">Email me</a>
and please provide as much information as possible so that I can recreate the problem, but equally do not write
pages and pages. Useful things to include are: </p>
<p> Email <a href="mailto:&#115;&#101;&#097;&#110;&#064;&#101;&#100;&#100;&#121;&#108;&#097;&#098;&#046;&#111;&#114;&#103;">&#115;&#101;&#097;&#110;&#064;&#101;&#100;&#100;&#121;&#108;&#097;&#098;&#046;&#111;&#114;&#103;</a>
and please provide me with enough information that I can recreate the problem.
Useful things to include are: </p>
<ul>
<li>Input data (or examples, but just sufficient to recreate the problem).</li>
<li>Information about the operating system you are using (e.g. % cat /proc/cpuinfo, or % uname -a)</li>
<li>Input data (or examples, a small test case sufficient to recreate the problem).</li>
<li>Information about the operating system you are using (e.g. <code> cat /proc/cpuinfo </code> or <code> uname -a </code></li>
<li>Which version of HMMER you're using, and whether you compiled from source or used a binary distro.</li>
</ul>
<p>Without these pieces of information I have to guess or send mails back and forth to determine the cause
of the issue. Many questions are also covered in the <a href="ftp://selab.janelia.org/pub/software/hmmer3/3.1b2/Userguide.pdf">HMMER documentation</a>,
<p>Without these pieces of information I have to make guesses and send mails back and forth with you to determine the cause
of the issue, and then I get all frustrated and snippy with you because I'm usually pretty busy, and then you think I'm a jerk, and then I feel guilty and bad and have to go away and go running. Nobody wants all that drama.</p>
<p>
Also, many questions are already covered in the <a href="http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf">HMMER documentation</a>,
so it may be worth browsing there first before sending an e-mail.</p>
</div>
</div>
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