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[Gmod-apollo-cmts] CVS: apollo/doc/html userguide.html,1.62,1.63
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From: Nomi H. <no...@us...> - 2003-02-27 23:06:06
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Update of /cvsroot/gmod/apollo/doc/html
In directory sc8-pr-cvs1:/tmp/cvs-serv7224/html
Modified Files:
userguide.html
Log Message:
added info about creating ~/.apollo
added warning about writing to otter not working
Index: userguide.html
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/html/userguide.html,v
retrieving revision 1.62
retrieving revision 1.63
diff -C2 -d -r1.62 -r1.63
*** userguide.html 27 Feb 2003 18:13:55 -0000 1.62
--- userguide.html 27 Feb 2003 23:06:02 -0000 1.63
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*** 418,422 ****
</div>
<br>
! At time of writing, ensembl data for a particular species is organised
into clusters of databases - a "core" database (containing the essential
analyses and annotations), supported by a "sequence" database (which might
--- 418,422 ----
</div>
<br>
! At this time, ensembl data for a particular species is organised
into clusters of databases - a "core" database (containing the essential
analyses and annotations), supported by a "sequence" database (which might
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*** 502,505 ****
--- 502,509 ----
publically available one please refer to the <a href="http://www.ensembl.org/otter">otter web site</a>.
+ <P><B>Please note:</B> Some users have reported trouble writing to otter servers.
+ For some reason, when you use the installer to install Apollo, Apollo can't figure out where
+ to find the XML parser. We are working to resolve this problem.
+
<h3><a NAME="Styles"></a>Styles</h3>
Apollo has a configuration file for each known data source. This file is
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*** 508,512 ****
want to change some of the display parameters (e.g. the background color, names
of data types, etc.) be sure to change the appropriate style file--e.g. the style file
! for GAME XML is called game.style. The style files all live in the conf directory.
See the section on <a href=#Configuration>configuration files</a> for more about what's
in style files and how you can change it.
--- 512,516 ----
want to change some of the display parameters (e.g. the background color, names
of data types, etc.) be sure to change the appropriate style file--e.g. the style file
! for GAME XML is called game.style. By default, the style files all live in the conf directory.
See the section on <a href=#Configuration>configuration files</a> for more about what's
in style files and how you can change it.
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*** 1733,1738 ****
<P>
The main configuration file that Apollo reads when it starts up is called
! apollo.cfg. The usual location for apollo.cfg is in the conf directory
! inside Apollo's home directory.
Note that if you make changes to your apollo.cfg file, you will need to shut
down Apollo and restart it to see the changes.
--- 1737,1748 ----
<P>
The main configuration file that Apollo reads when it starts up is called
! apollo.cfg. The default location for apollo.cfg is in the conf directory
! inside Apollo's home directory. If you create a .apollo directory in
! your home directory and place an apollo.cfg there, Apollo will use that
! one instead of the one in APOLLO_ROOT/conf. (You can also put personal
! copies of the style and tiers file in your .apollo directory. This is
! useful on multi-user systems where many people are sharing the same
! Apollo installation.)
! <P>
Note that if you make changes to your apollo.cfg file, you will need to shut
down Apollo and restart it to see the changes.
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*** 1741,1745 ****
There is a configuration "style" file and a tiers file for each data source
(called a Data Adapter) that Apollo knows about. These are in the conf directory
! as well. The style file for the
Drosophila annotations, which are in GAME XML format, is called game.style; the
style file for Ensembl is ensembl.style. The style file specifies the name of
--- 1751,1755 ----
There is a configuration "style" file and a tiers file for each data source
(called a Data Adapter) that Apollo knows about. These are in the conf directory
! as well (though, as above, you can put them in ~/.apollo). The style file for the
Drosophila annotations, which are in GAME XML format, is called game.style; the
style file for Ensembl is ensembl.style. The style file specifies the name of
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for human. This may all sound complicated, but most users shouldn't need to do
anything to these files.
- <P> If you are on a multi-user system and want to have your own personal
- style files, you can create a .apollo subdirectory in your home directory (~/.apollo),
- copy the style files to it,
- and change apollo.cfg so it says, e.g.,
- <pre>
- DataAdapterInstall "apollo.dataadapter.GAMEAdapter" "~/.apollo/game.style"
- </pre>
<P>
The first column of each line in a style file contains property names that are recognized by Apollo.
--- 1757,1760 ----
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*** 1936,1940 ****
<td>Types</td>
<td>The location of the tiers file (usually called <i>stylename</i>.tiers) describing how to display the different feature
! types, including their order and colors. Expected to be in the conf directory,
along with the style files and apollo.cfg.</td>
</tr>
--- 1939,1944 ----
<td>Types</td>
<td>The location of the tiers file (usually called <i>stylename</i>.tiers) describing how to display the different feature
! types, including their order and colors. Expected to be in either the user's ~/.apollo
! directory or in Apollo's conf directory,
along with the style files and apollo.cfg.</td>
</tr>
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*** 2276,2280 ****
<HR><P>
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! Last modified: Wed Feb 26 16:35:19 PST 2003
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<HR><P>
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! Last modified: Thu Feb 27 15:04:52 PST 2003
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