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[Gmod-apollo-cmts] SF.net SVN: gmod:[23959] apollo/trunk/doc/html
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From: <no...@us...> - 2010-10-13 00:30:28
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Revision: 23959
http://gmod.svn.sourceforge.net/gmod/?rev=23959&view=rev
Author: nomi
Date: 2010-10-13 00:30:19 +0000 (Wed, 13 Oct 2010)
Log Message:
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For some reason, these weren't in svn.
Fixed mailing list links.
Added Paths:
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apollo/trunk/doc/html/faq.html
apollo/trunk/doc/html/index.html
Added: apollo/trunk/doc/html/faq.html
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--- apollo/trunk/doc/html/faq.html (rev 0)
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+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<HTML>
+<HEAD>
+</HEAD>
+
+<TITLE>Apollo FAQ</TITLE>
+
+<BODY BGCOLOR=#FFFFFF TEXT=#000000 LINK=#0033CC VLINK=#CC3300 ALINK=#9900CC>
+
+<H1 ALIGN=CENTER>
+Apollo Frequently Asked Questions
+</H1>
+<H3 ALIGN=CENTER>
+(Also see the <a href=userguide.html>Apollo Userguide</a>)
+</H3>
+
+<B>Q:</B> What is Apollo?
+<BR><B>A:</B> Apollo is a genome annotation viewer and editor.
+<P>
+<B>Q:</B> What isn't Apollo?
+<BR><B>A:</B> Apollo will not analyze your sequence for you. It will not
+directly help you find sequencing errors or SNPs. And it doesn't toast bread.
+<P>
+<B>Q:</B> Why is it called Apollo?
+<BR><B>A:</B> Apollo was the Greek god of the sun, music, poetry, prophecy,
+agriculture, and pastoral life. Sounds good to us. Or, at any rate,
+better than another possible name for our annotation tool: GOAT (GenOme
+Annotation Tool).
+<P>
+<B>Q:</B> Is Apollo an applet?
+<BR><B>A:</B> No, Apollo is a Java application--you can <a
+href=install.html>download</a> the software and install it on your
+computer and run it locally.
+<P>We have recently enabled Apollo to run as a Web start application
+(which can be launched from a browser, much like an applet), but we
+have not yet made this publicly available due to limitations from
+the data server side.
+<P>
+<B>Q:</B> What platforms does Apollo run on?
+<BR><B>A:</B> Windows (98, 2000, XP, etc.), Mac OS X (please note that
+Apollo is <b>not</b> intended for use on pre-OS X Macs), and any Unix-type
+system (Solaris, Linux, etc.).
+<P>
+<B>Q:</B> Do I need to install Java on my computer in order to run Apollo?
+<BR><B>A:</B> Probably not. If you don't already have Java installed, you can <a
+href=install.html>download</a> Apollo packaged with the appropriate Java
+Virtual Machine (JVM) for your platform. However, if you are running Mac
+OS X, you may need to update your JVM--see the next question.
+<P>
+<B>Q:</B> What version of Java does Apollo require?
+<BR><B>A:</B> JDK1.5+ is required for all platforms.
+Please see <a href=http://www.apple.com/softwareupdate>Apple's instructions on downloading the latest JDK (currently 1.6)</a>, using Software Updates.
+<P>
+<B>Q:</B> How much memory does Apollo need?
+<BR><B>A:</B> Apollo uses a lot of memory, largely due to
+the sheer size of the annotation data.
+In order to use Apollo, your computer will need to have at least 164Mb of
+RAM. Moreover, even if you have that much memory, you will probably find that if you try
+to run more than one instance of Apollo at the same time, performance
+will suffer. Also note that if you load a very
+large region, Apollo will use up more memory. Keep in mind that other applications running on your
+computer also use memory, so you will get better performance if you shut down other applications (Photoshop, Word, etc.) before you launch Apollo.
+<P>
+
+<B>Q:</B> The installer is not working for me.
+<BR><B>A:</B> The installer software (a third-party product) has been
+problematic on some varieties of Unix and Mac OS X.
+If you are on Linux and are having trouble running the installer, try downloading the Linux installer
+<i>without</i> Java VM (and make sure you have Java version 1.5+ installed
+ on your computer). If the installer still doesn't work, <a href=/annot/apollo/apollo-zip.html>click here</a> for an alternative way to install Apollo.<P>
+
+<B>Q:</B> I am having trouble getting Apollo to run on my 64-bit Linux system.
+<BR><B>A:</B> See the answer to the previous question. Also, try installing
+a different Java Virtual Machine. One 64-bit Linux user reported trouble using Red Hat's Java, and was
+only able to get Apollo to work when he used Sun's Java.
+<P>
+
+<B>Q:</B> I am having trouble getting Apollo to run on my Mac--the Apollo icon
+bounces a few times, but Apollo does not come up.
+<BR><B>A:</B> Some security-related software updates on Panther (v10.3) interfere
+with Java and prevent Apollo from launching from the shortcut. We are looking into
+how to address that, but there are two workarounds:
+<BR>
+<LI> Upgrade your Mac to Tiger (10.4) or later (Leopard or Snow Leopard); or<BR>
+<LI> Launch Apollo from the command line. First, start a Terminal window (Applications -> Utilities -> Terminal). In the Terminal window, cd to the directory where you installed Apollo, usually /Applications/Apollo, and type ./bin/apollo (note the lowercase a):<BR>
+<pre><dd>cd /Applications/Apollo
+<dd>./bin/apollo</pre>
+</dd>
+You will see the text output from Apollo in the Terminal window, and an Apollo
+window should come up.
+<P>
+<B>Q:</B> I want to see the text output from Apollo on my Mac running Tiger. I opened a Console window, as it says in the userguide, but I don't see output there.
+<BR><B>A:</B> Something in Tiger has stopped this from working. We are investigating this. For now, you can see the text output by launching Apollo from a Terminal window (see the previous question) rather than by clicking on the icon.
+
+<P>
+<B>Q:</B> Is there an Apollo mailing list?
+<BR><B>A:</B> Yes; you can <a
+href=https://lists.lbl.gov/sympa/info/apollo>subscribe here</a>.
+In order to reduce spam, only members can send messages to the list.
+This mailing list has low traffic and is not used for any purpose other than
+Apollo updates and questions. (If you receive spam that appears to be from
+the apollo mailing list, it is not really--the address is forged.)
+<P>
+<B>Q:</B> What data formats does Apollo read?
+<BR><B>A:</B>The most robust Apollo data adapters read <a href=game.rng.txt>GAME XML</a> (the format used for the
+Drosophila annotations), ChadoXML (the version used at FlyBase Harvard) and the <a
+href=http://www.sanger.ac.uk/Software/formats/GFF/>Ensembl version of
+GFF</a>. The <a href=http://www.ensembl.org>Ensembl</a> group has enabled Apollo to read data
+via the Ensembl CGI and directly from Ensembl databases, with the EnsJ/Otter
+adapter.
+<P>
+There are also two useful data adapters currently under development.
+The Analysis adapter lets you read raw analysis results (BLAST, sim4,
+GENSCAN, etc.) into Apollo. This is mostly working, although the GUI
+needs work. The GenBank adapter is also mostly working but needs
+more testing.
+<P>
+New in Release 1.5.0 is a Chado XML adapter. Right now, it is very
+FlyBase-specific and needs to be generalized, but it would be a good starting
+point for a group that is using a Chado database.
+<P> We recently did some preliminary work towards enabling Apollo to act
+as a client for <a target=_new href=http://biodas.org/documents/das2/das2_protocol.html>DAS/2</a> servers. It can now read simple DAS2XML files.
+<P>
+<B>Q:</B> Is there a schema for GAME XML?
+<BR><B>A:</B>Yes, <a href=game.rng.txt>game.rng</a>. If you find a
+game.dtd, please disregard it--it was not a good schema description for GAME XML.
+For more about the GAME schema, please see doc/schema-notes in the Apollo
+distribution.
+<P>
+<B>Q:</B> Apollo is not working for me--I tried to get Drosophila
+melanogaster data and got the error message "Can't connect to URL--server not responding."
+<BR><B>A:</B>This is not an Apollo problem--this is a problem with the
+FlyBase server that supplies the D. melanogaster annotation data. The server
+or the database it accesses may be down, or the traffic may be too heavy.
+<P>
+Another possible issue is that you might have a firewall that prevents the data from getting to
+your computer. If you use a proxy, be sure to set the proxy by clicking the "Proxy settings"
+button before trying to load data.
+<P>
+<B>Q:</B> How can I download and run the latest in-development version
+of Apollo?
+<BR><B>A:</B>
+Keep in mind that if you try to run the very latest Apollo, there are no
+guarantees that it will work correctly. We are actively developing it,
+and often there are many bugs that crop up between releases and then are
+fixed. So on any given day, it's possible that the up-to-the-minute
+Apollo won't run at all (though that is rare) or that various aspects of
+it will be broken.
+<P>
+Occasionally, someone will check in code that doesn't compile; when this
+happens, it's always fixed quickly (within a day). But if you get lots
+and lots of errors when you try to make, there's probably something wrong
+with your environment (not having APOLLO_ROOT set properly is the most
+common mistake).
+<P>
+Here is the command I use for checking out the whole Apollo
+distribution from sourceforge:
+<pre>
+setenv CVS_RSH ssh
+cvs -z3 -d:ext:mya...@gm...:/cvsroot/gmod checkout -d apollo apollo
+</pre>
+For "myaccount", substitute your own SourceForge account name. (It's a good
+idea to get a SourceForge account if you're going to be doing this--it's
+quick, free, and they don't send you spam.) If you don't want to get an
+account on SourceForge, you can do an anonymous checkout; however,
+anonymous checkouts give you a version that's a few days out of date.
+To check out an anonymous version:
+<pre>
+cvs -d:pserver:ano...@gm...:/cvsroot/gmod login
+cvs -d:pserver:ano...@gm...:/cvsroot/gmod checkout -d apollo apollo
+</pre>
+<P>
+The "-d apollo" specifies the directory name you want the Apollo stuff to
+go in, so you can change that if you want to put it somewhere else.
+<P>
+After you've checked out the code, compiling it is straightforward:
+<pre>
+ cd apollo
+ setenv APOLLO_ROOT `pwd`
+ cd src/java
+ make clean [only necessary if you've already compiled and then updated]
+ make jar
+</pre>
+You can also use <a target=ant href=http://ant.apache.org/>Ant</a> to
+compile the source.<P>
+To run your newly compiled apollo:
+<pre>
+ ~/apollo/bin/apollo
+</pre>
+(where ~/apollo is the directory where you've installed apollo--change
+as appropriate).
+<P>
+Note that all my instructions assume that you're on a Unix-y system
+(which includes Macs).
+If you're on Windows, I have no idea what to do. I've never tried to
+compile on Windows, nor to run anything other than the installed version
+of Apollo. I gather you can use Ant to compile on Windows.
+<P>
+<B>Q:</B> Can I customize Apollo for my own use?
+<BR><B>A:</B> Yes. There are many user-customizable options; see the <a
+href=userguide.html#configuration>user guide</a> for more information.
+<BR>
+If you are a Java developer and wish to customize the Apollo code (for
+example, by adding a new data adapter to read a different data format),
+you can download the source from <a
+href=http://www.sourceforge.net/projects/gmod/>SourceForge</a> (see
+instructions above).
+<P>
+<B>Q:</B> Where can I find Apollo developer documentation?
+<BR><B>A:</B>
+Although Apollo has extensive user documentation,
+the documentation for developers is more spotty.
+You can look at the <a target=_new href=javadoc/>javadocs</a>,
+which are a bit sparse but might still be helpful. If you are
+interested in data adapters, look at the data adapter "cookbook"
+(<a href=dataadapter_cookbook.html>doc/html/dataadapter_cookbook.html</a>).
+Also, the <a href=http://genomebiology.com/2002/3/12/research/0082 target=_paper>Genome Biology
+paper about Apollo</a> has a diagram and discussion of the Apollo architecture.
+<P>
+<B>Q:</B> I would like to annotate the <a href=http://www.lpzoo.com/tour/factsheets/mammals/naked_mole_rat.html>naked mole rat</a> genome using
+Apollo. What do I need to do?
+<BR><B>A:</B> Well, first you need to run some sequence analysis tools
+(such as <a href=http://www.ncbi.nlm.nih.gov/BLAST/>BLAST</a>, <a href=http://genes.mit.edu/GENSCAN.html>GENSCAN</a>, etc.) on your sequence data. We are currently developing
+a raw analysis results output loader that can load BLAST results and some
+other output formats.
+<P>
+The only data formats that fully support editing right now are <a href=game.rng.txt>GAME XML</a>
+and Chado XML
+(<a href=example.xml>Here</a> is an example of annotations and results stored in GAME XML format.)
+<P>
+At the BDGP, we run sequences through an analysis pipeline that finishes
+with a program called BOP, which parses the output from the various
+analysis programs and does some filtering and then saves the results as
+GAME XML. BOP is now part of the Apollo codebase--however, BOP has not been debugged
+and robustified the way Apollo has, so you'll be navigating rougher
+terrain if you try to use it. If you've checked out the
+Apollo code from SourceForge, you can run BOP from the command line by using the bin/apollo
+shell script with the "-bop" option. BOP is also used in the
+Analysis Adapter, which lets you read raw analysis results (BLAST, sim4,
+GENSCAN, etc.) into Apollo. We are still debugging this.
+
+<P>
+<B>Q:</B> Can I add annotations to the human genome using Apollo?
+<BR><B>A:</B> At the moment, the interface to the <a href=http://www.ensembl.org/Homo_sapiens/>human genome
+annotations</a> at <a href=http://www.ensembl.org/>Ensembl</a> is
+read-only: you can view the annotations but you can't edit them or add
+new annotations. We hope to provide that capability soon.
+<P>You can, however, edit the Drosophila annotations (or any other
+annotations that are stored in GAME XML or Chado XML format, or in
+a Chado database). If you wish to submit corrections to our Drosophila
+annotations, you can do so at <A
+HREF=http://flybase.org/cgi-bin/mailto-fbhelp.html>http://flybase.org/cgi-bin/mailto-fbhelp.html</a>.
+<P>
+<B>Q:</B> I found a bug in Apollo.
+<BR><B>A:</B> We are shocked and horrified; Apollo is 100% bug-free.
+Well, ok, that's completely untrue. You can report your bug using the <a href=http://sourceforge.net/tracker/?func=add&group_id=27707&atid=462763>
+SourceForge Apollo bug tracker</a>.
+Please be as specific as possible when you
+report bugs--tell us what dataset you were looking at, what operating system
+you're on (e.g. Mac OS X), and what you did that caused the bug. Also send us the
+output from the Java console (see <a href=userguide.html#stdout>the userguide</a> for instructions
+on accessing the console).
+Be sure to include your email address so we can contact you for more information about the
+bug and notify you when we fix it.
+<BR>
+We periodically (every month or two) release a new and improved version of Apollo;
+visit the <a href=install.html>download page</a> to get the latest version.
+<P>
+<B>Q:</B> I have made some changes to Apollo that I would like to commit
+to the main codebase.
+<BR><B>A:</B> We are happy to look at bug fixes and new additions made by
+members of the community, and in fact have already incorporated several of
+these. Please send your proposed changes to the Apollo mailing list (include any
+classfiles or other files that have changed, as well as a description of
+what you've changed) and we will review your changes and, if they seem good,
+incorporate them into the codebase. (Before sending your changes, please
+do a cvs update to make sure your version of apollo is completely up to date.)
+</BODY>
+</HTML>
Added: apollo/trunk/doc/html/index.html
===================================================================
--- apollo/trunk/doc/html/index.html (rev 0)
+++ apollo/trunk/doc/html/index.html 2010-10-13 00:30:19 UTC (rev 23959)
@@ -0,0 +1,73 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<HTML>
+<link REL="SHORTCUT ICON" href="/favicon.ico">
+<HEAD>
+<BASEFONT FACE="Geneva,Arial,Helvetica" SIZE=3>
+</HEAD>
+
+<TITLE>Apollo Genome Annotation Curation Tool</TITLE>
+
+<BODY BGCOLOR=#FFFFFF TEXT=#000000 LINK=#0033CC VLINK=#CC3300 ALINK=#9900CC>
+
+<CENTER>
+<!-- <IMG SRC="/pics/apollosplash.gerry.jpg" BORDER=0 width=529 height=240 hspace=5 vspace=5 ALT="APOLLO"> -->
+<H1>Apollo Genome Annotation Curation Tool</H1>
+<IMG SRC="images/cropped-mainwindow-for-web.gif" BORDER=0 width=499 height=274 hspace=5 vspace=5 ALT="APOLLO">
+</CENTER>
+
+<P>
+Apollo is a genome annotation viewer and editor. It was
+developed as a collaboration between the <a href=/>Berkeley Drosophila Genome
+Project</a> (part of the <a
+href=http://flybase.bio.indiana.edu/>FlyBase</a> consortium) and <a href=http://www.ensembl.org>The Sanger Institute</a> in
+Cambridge, UK.
+Apollo allows researchers to explore genomic
+annotations at many levels of detail, and to perform expert annotation
+curation, all in a graphical environment. It was used by the
+FlyBase biologists to construct the <a href=/annot/release3.html>Release 3 annotations</a> on the finished
+<i>Drosophila melanogaster</i> genome, and is also a primary vehicle
+for sharing these annotations with the community.
+The <a href=http://www.gmod.org>Generic Model Organism Database (GMOD) project</a>, which
+aims to provide a complete ready-to-use toolkit for analyzing whole
+genomes, has adopted Apollo as its annotation workbench.
+Apollo is a Java
+application that can be downloaded and run on Windows, Mac OS X, or any Unix-type system
+(including Linux).
+
+<P><HR><P>
+
+<UL>
+<LI> <a href="install.html">Download Apollo</a> (Version 1.11.6, last updated May, 2010)
+<P>
+<LI> How to cite Apollo:<br>
+<a href=http://genomebiology.com/2002/3/12/research/0082 target=_paper>
+Apollo: a sequence annotation editor</a>.
+Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J,
+Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS,
+Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S,
+Mungall CJ, Clamp ME (2002).
+<a href=http://genomebiology.com/><i>Genome Biology</i></a> 2002, 3(12):research0082
+<P>
+<LI> Frequently Asked Questions <a href="faq.html">(FAQ)</a>
+<P>
+<LI> <a href="userguide.html">Apollo userguide</a> (also included when you
+download Apollo)
+<P>
+<LI> <a href=https://lists.lbl.gov/sympa/info/apollo>Subscribe to
+the apollo mailing list</a>
+<P>
+<LI> If you are a developer, you may wish to <a target=_sf
+href=http://sourceforge.net/project/showfiles.php?group_id=27707>download the Apollo source
+from SourceForge</a>.<BR>
+Like many <a href=http://www.gmod.org/>GMOD</a> components, Apollo is distributed under the terms of the
+<a href=http://www.opensource.org/licenses/artistic-license.php>Artistic
+License</a>.<P>
+<LI> For developers: <a target=_sf href=javadoc>Apollo javadocs</a>
+</UL>
+
+<P><HR><P>
+<P>
+<font size=2>
+This work was supported by NIH grant 1R01GM080203-01 from tne National Institute of General Medical Sciences (NIGMS).</font>
+</BODY>
+</HTML>
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