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From: <no...@us...> - 2010-10-12 21:04:04
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Revision: 23956
http://gmod.svn.sourceforge.net/gmod/?rev=23956&view=rev
Author: nomi
Date: 2010-10-12 21:03:56 +0000 (Tue, 12 Oct 2010)
Log Message:
-----------
Updated the Apollo mailing list URL and a few other hardcoded URLs.
Modified Paths:
--------------
apollo/trunk/doc/html/dataadapter_cookbook.html
apollo/trunk/doc/html/tiers.html
Modified: apollo/trunk/doc/html/dataadapter_cookbook.html
===================================================================
--- apollo/trunk/doc/html/dataadapter_cookbook.html 2010-10-12 21:03:18 UTC (rev 23955)
+++ apollo/trunk/doc/html/dataadapter_cookbook.html 2010-10-12 21:03:56 UTC (rev 23956)
@@ -1388,7 +1388,7 @@
this adapter, but until we get to that point, theres no urgency to
finely configure this. So in other words if you are wanting to connect
up your chado database, please contact us
-via the <a target=_new href=http://mail.fruitfly.org/mailman/listinfo/apollo>Apollo mailing list</a>
+via the <a target=_new href=https://lists.lbl.gov/sympa/info/apollo>Apollo mailing list</a>
and we can discuss what
your chado database looks like, how much it conforms to SO, and figure
out where the fine grain configging will need to
@@ -1479,7 +1479,7 @@
</p>
<p></p>
<dd><i>Note: Lincoln's notes were written before the <a
- href="http://www.fruitfly.org/annot/apollo/game.rng.txt">RNG schema</a>
+ href="/game.rng.txt">RNG schema</a>
for GAME XML was written to replace the inaccurate DTD.</i>
<p><seq><br>
id yes<br>
Modified: apollo/trunk/doc/html/tiers.html
===================================================================
--- apollo/trunk/doc/html/tiers.html 2010-10-12 21:03:18 UTC (rev 23955)
+++ apollo/trunk/doc/html/tiers.html 2010-10-12 21:03:56 UTC (rev 23956)
@@ -16,7 +16,7 @@
etc.).
<P>
There is a good description of the Apollo tiers files in the
-<a href=http://www.fruitfly.org/annot/apollo/userguide.html#TiersFiles>Apollo user
+<a href=/userguide.html#TiersFiles>Apollo user
manual</a>--please read that section before you read this description of
how to create and change tiers files.
<P>If you edit the tiers file, be aware that each tier line and each type line must be a
@@ -29,7 +29,7 @@
<br>
<h3>Adding new types to a tiers file</h3>
Sometimes when you display a datafile, you will see messages in the
-<a href=http://www.fruitfly.org/annot/apollo/userguide.html#stdout>Apollo console</a>
+<a href=/userguide.html#stdout>Apollo console</a>
about new feature property schemes being created, e.g.
<P>
Creating new feature property scheme for Gene Prediction<br>
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|
From: <no...@us...> - 2010-10-13 00:30:28
|
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:
-----------
For some reason, these weren't in svn.
Fixed mailing list links.
Added Paths:
-----------
apollo/trunk/doc/html/faq.html
apollo/trunk/doc/html/index.html
Added: apollo/trunk/doc/html/faq.html
===================================================================
--- apollo/trunk/doc/html/faq.html (rev 0)
+++ apollo/trunk/doc/html/faq.html 2010-10-13 00:30:19 UTC (rev 23959)
@@ -0,0 +1,279 @@
+<!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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|
|
From: <no...@us...> - 2010-11-08 21:57:54
|
Revision: 24104
http://gmod.svn.sourceforge.net/gmod/?rev=24104&view=rev
Author: nomi
Date: 2010-11-08 21:57:46 +0000 (Mon, 08 Nov 2010)
Log Message:
-----------
Fixed NIH grant number
Modified Paths:
--------------
apollo/trunk/doc/html/index.html
apollo/trunk/doc/html/userguide.html
Modified: apollo/trunk/doc/html/index.html
===================================================================
--- apollo/trunk/doc/html/index.html 2010-11-08 18:55:37 UTC (rev 24103)
+++ apollo/trunk/doc/html/index.html 2010-11-08 21:57:46 UTC (rev 24104)
@@ -68,6 +68,6 @@
<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>
+This work was supported by NIH grant 1R01GM080203-03 from tne National Institute of General Medical Sciences (NIGMS).</font>
</BODY>
</HTML>
Modified: apollo/trunk/doc/html/userguide.html
===================================================================
--- apollo/trunk/doc/html/userguide.html 2010-11-08 18:55:37 UTC (rev 24103)
+++ apollo/trunk/doc/html/userguide.html 2010-11-08 21:57:46 UTC (rev 24104)
@@ -177,7 +177,7 @@
It is a Java
application that is easy to install and run on Windows, Mac OS X, or any Unix-type system
(including Linux).
-Apollo is currently supported by NIH grant 1R01GM080203-01 from the National Institute of General Medical Sciences (NIGMS).
+Apollo is currently supported by NIH grant 1R01GM080203-03 from the National Institute of General Medical Sciences (NIGMS).
</p><p>
The current Apollo team is:
</p><ul>
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