Skip to content

Commit

Permalink
This commit was manufactured by cvs2svn to create tag 'release-1_37'.
Browse files Browse the repository at this point in the history
  • Loading branch information
Nobody committed Jul 15, 2002
1 parent b9c4e27 commit 6c16ab6
Show file tree
Hide file tree
Showing 36 changed files with 807 additions and 14,008 deletions.
48 changes: 0 additions & 48 deletions ChangeLog
View file
Original file line number Diff line number Diff line change
@@ -1,51 +1,3 @@
1.45 Sun Jul 7 17:32:08 EDT 2002
* Major feature release.
* Added conversion script for human genome annotations from NCBI.
* New CDS/reading frame glyph.
* New 3-frame translation glyph.
* FASTA dumper now dumps out decorated FASTA files.
* Sequence dumper supports output in GenBank, EMBL, GAME, BSML and other
formats (thanks to magic of Bio::SeqIO).
* Full set of restriction enzymes in restriction enzyme annotator plugin.
* Support for named external feature tracks in popup menu.
* External feature tracks are now highlighted in selection list.
* Fixed uploaded files so that they are persistent.
* Minor aesthetic improvements.
* REQUIRES: BioPerl 1.02.
* STILL PENDING: Internationalization/localization fixes
1.44 Mon May 6 19:14:45 EDT 2002
* Bug fix that caused keyword searches to fail on case mismatch.
* Number of matches now printed at top of multiple-match page.
1.43 Mon May 6 14:38:40 EDT 2002
* Bug fix to correct a server error that occurred when multiple
features match a search term.
* Added very preliminary support for using GBrowse as a
front end for GenBank and EMBL databases.
1.42 Sun May 5 11:35:22 EDT 2002
* Fixed a bad url in the help generated by gbrowse_img.
1.41 Sat May 4 16:19:20 EDT 2002
* Added gbrowse_img script; this allows local and remote HTML pages
to inline the images generated by gbrowse.
1.40 Fri Apr 12 20:49:50 EDT 2002
* Minor documentation fixes.
* Patch file now fixes a host of small display problems in bioperl 1.0
1.39 Fri Apr 12 00:18:10 EDT 2002
* Fixed problems compiling and installing on Solaris systems.
* Added the wormbase_gene aggregator. Useful for the c. elegans gff file.
* If you pick up the latest bioperl-live (or apply extras/bioperl-1.0.patch)
there are fixes in Bio::Graphics that prevent genes from disappearing
when zoomed all the way into an intron.
1.38 Mon Apr 8 21:16:12 EDT 2002
* Previous version would crash on vanilla Bioperl 1.0 installations.
This problem has been fixed, but at the cost of disabling wildcard
searches. To get wildcard searches, upgrade to Bioperl 1.01 using
CVS or the patch file in extras/bioperl-1.0.patch.
* Fixed aesthetic problems with a phantom "plugin:Restriction Sites"
entry appearing on the key even when restriction sites are turned
off.
* Fixed intermittent "Couldn't open database" errors.
* Fixed intermittent scrambling of user settings.

1.37 Sun Mar 31 16:10:11 EST 2002
* Plugin architecture completed see README-PLUGINS
* Sample plugins provided:
Expand Down
8 changes: 3 additions & 5 deletions DISCLAIMER
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
The Generic Genome Browser package and all associated files are
Copyright (c) 2002 Cold Spring Harbor Laboratory and University of
California, Berkeley.
Copyright (c) 2002 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See the Artistic License file
Expand All @@ -20,6 +19,5 @@ nature, which may arise from your Institution's respective use,
handling or storage of the SOFTWARE.

If publications result from research using this SOFTWARE, we ask that
CSHL and University of California, Berkeley be acknowledged and/or
credit be given to CSHL/Berkeley scientists, as scientifically
appropriate.
CSHL be acknowledged and/or credit be given to CSHL scientists, as
scientifically appropriate.
196 changes: 32 additions & 164 deletions INSTALL
View file
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
This document describes how to install the Generic Genome Browser.
This document describes how to install the Generic Genome Browser
(GGB).

1. PREREQUISITES

GBrowse runs on top of several software packages. These must be
installed and configured before you can run GBrowse. Most
preconfigured Linux systems will have some of these packages installed
already.
GGB runs on top of several software packages. These must be installed
and configured before you can run it. Most preconfigured Linux
systems will have some of these packages installed already.

A) MySQL -- http://www.mysql.com
The MySQL database is a fast open source relational database
Expand All @@ -18,9 +18,10 @@ already.
C) Perl 5.005 -- http://www.cpan.org
The Perl language is widely used for web applications.
Version 5.6 is preferred, but 5.00503 or higher will work.


D) Standard Perl modules -- http://www.cpan.org
The following Perl modules must be installed for GBrowse to work.
The following Perl modules must be installed for GGB to work.
They can be found on the Comprehensive Perl Archive Network
(CPAN):

Expand All @@ -30,15 +31,16 @@ already.
Digest::MD5
Text::Shellwords

F) BioPerl version 1.02 or higher -- http://www.bioperl.org
E) Bio::DB::GFF module -- http://www.bioperl.org
This is the middleware layer that translates between
the CGI script to the database. It is part of the
bioperl package.

Optional modules:

G) XML::Parser, XML::Writer, XML::Twig, XML::DOM

If these modules are present, the "Sequence Dumper" plugin
will be able to produce GAME and BSML output. They can be
downloaded from CPAN.
F) Bio::Graphics module -- http://www.gmod.org
This is the module that renders the information in the
database into graphics. It is part of the GMOD project
and can be downloaded from the same location you got this
package.

2. INSTALLING THE BROWSER

Expand Down Expand Up @@ -111,26 +113,22 @@ files are placed in a directory named gbrowse. The install script
will detect if there are already configuration files in the selected
directory and not overwrite them if so. The same applies to the
cascading stylesheet file (gbrowse.css) located in the gbrowse
subdirectory. However, neither the GIF files in the "buttons"
subdirectory nor the plugin modules in the gbrowse.conf/plugins
directory are checked before overwriting them, so be careful to copy
the new copies somewhere safe if you have modified them.
subdirectory. However, the GIF files in the "buttons" subdirectory
are not checked before they are overwritten, so be careful to copy the
new copies somewhere safe if you have modified them.

You can always manually move the files around after install. See
docs/configuration.txt for details.

When installing the static files, the install script also creates an
empty directory named "tmp". This directory is set to be world
writable so that the GBrowse server can use it to manage temporary image
writable so that the GGB server can use it to manage temporary image
files that it creates on the fly. If you would prefer not to have a
world writable directory on your system, simply change the ownership
and permissions to allow the web server account to write into it. The
directory is located in /usr/local/apache/htdocs/gbrowse/tmp by
default.

The first time you run Makefile.PL, a file named GGB.def will be
created your file path settings. When Makefile.PL is run again, it
will ask you whether you wish to use the

3. POPULATING THE DATABASE

Expand All @@ -139,15 +137,15 @@ Synopsis:
mysql -uroot -p password -e 'create database yeast'

mysql -uroot -p password -e 'grant all privileges on yeast.* to me@localhost'
mysql -uroot -p password -e 'grant file on *.* to me@localhost'
mysql -uroot -p password -e 'grant file on *.* to yeast@localhost'
mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost'

bulk_load_gff.pl -d yeast sample_data/yeast_data.gff
make test

Details:

You will need a MySQL database in order to start using GBrowse. Using the
You will need a MySQL database in order to start using GGB. Using the
mysql command line, create a database (called "yeast" in the synopsis
above), and ensure that you have update and file privileges on it.
The example above assumes that you have a username of "me" and that
Expand Down Expand Up @@ -213,24 +211,23 @@ that massage the model-specific annotation files into GFF format
suitable for loading:

process_gadfly.pl For FlyBase D. melanogaster flat files
process_ncbi_human.pl For human annotations from NCBI
process_sgd.pl For SGD S. cerevisiae flat files
process_wormbase.pl For WormBase C. elegans flat files

You will find the scripts, along with information on downloading the
current model organism files, in the "bin" subdirectory of this
package. The scripts will also have been copied into your system
binaries directory when you made "install". Run the script with the
-h option to get some data-specific help:
current model organism files, in the bin subdirectory of this package.
The scripts will also have been copied into your system binaries
directory when you made "install". Run the script with the -h option
to get some data-specific help:

% process_gadfly.pl -h

The process_wormbase.pl script requires the AcePerl package, which is
available from CPAN. It is not strictly necessary to run this script
because the unaltered GFF files distributed from WormBase are
compatible with GBrowse. process_wormbase.pl supplements the
information with the physical positions of genetic markers, GenBank
accession numbers and functional descriptions of gene products.
compatible with GGB. process_wormbase.pl supplements the information
with the physical positions of genetic markers, GenBank accession
numbers and functional descriptions of gene products.

6. CREATING YOUR OWN GENOME DATABASE

Expand All @@ -246,141 +243,12 @@ performance of the script noticeably.

Be aware that there is a bad interaction between the Apache::DBI
module (often used to speed up database accesses) and Bio::DB::GFF.
This will cause the GFF dumper plugin to fail intermittently. GBrowse
This will result in the GFF dump feature failing intermittently. GGB
does not need Apache::DBI to achieve performance increases under
mod_perl and it is suggested that you disable Apache::DBI. If you
cannot do this, then you should remove the file GFFDumper.pm from the
gbrowse.conf/plugins directory.

8. BIOPERL VERSIONS

GBrowse requires Bioperl version 1.02. At the time this was written
(July 7, 2002), version 1.02 had not been officially released but was
expectedly imminently. Should version 1.02 not be available at the
time you read this, there are two ways to obtain it:

a. The Patch method

This distribution contains a patch file named "bioperl-101-102.patch"
located in the "extras" subdirectory. Applying it to a virgin
Bioperl-1.0.1 distribution will generate a version 1.0.2 distribution.
The steps to follow are these:

a1. unpack bioperl-1.0.1.tar.gz
gunzip -c bioperl-1.0.1.tar.gz | tar xvf -

a2. enter bioperl-1.0.1
cd bioperl-1.0.1

a3. apply the patch
patch -p1 < ../Generic-Genome-Browser-1.45/extras/bioperl-101-102.patch

Modify the last command to point to the actual location of the patch
file.

b. By anonymous CVS.

You can get the most recent version of the Bioperl 1.00 branch
using anonymous CVS. Here is the incantation:

cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl \
checkout -r branch-1-0-0 bioperl-live

When prompted, the password is "cvs". For more details, see
http://cvs.bioperl.org.

9. THE GBROWSE_IMG SCRIPT

The gbrowse_img CGI script (a new feature as of version 1.41), is a
stripped-down version of gbrowse which just generates images. It is
suitable for incorporating into <img> tags in order to make a
thumbnail of a region of interest. The thumbnail can then be linked
to the full-featured gbrowse. Here is an example of how this works
using the WormBase site:

<a href="http://www.wormbase.org/db/seq/gbrowse?source=wormbase;name=mec-3">
<img src="http://www.wormbase.org/db/seq/gbrowse_img?source=wormbase;name=mec-3;width=200">
</a>

This will generate a 200-pixel inline image of the region. Clicking
on the image will link to the fully-navigable gbrowse script.

You can also use gbrowse_img to superimpose temporary features (like
BLAST hits) on the existing genome features.

Read docs/gbrowse_img.txt for the CGI parameters and other
instructions. A copy of these instructions in HTML form will be
generated when gbrowse_img is called without any arguments. Type
http://your.host/cgi-bin/gbrowse_img into your favorite web browser.

10. THE GENBANK/EMBL PROXY

Sample configuration number 5 ("05.embl.conf") corresponds to an
experimental pass-through proxy for Genbank. At least in theory, if
you enter a landmark that isn't recognized, gbrowse will go to EMBL
using the bioperl BioFetch facility, parse the record, and enter it
into the local database. This allows you to browse arbitrary
Genbank/EMBL/Refseq entries.

You are free to experiment with this, but don't expect it to be
entirely reliable. To get it to work, you must:

a) make sure you are using Bioperl 1.02 (or a patched version of
1.01)

b) create a local database named "embl" and initialize it
this way:

perl -MBio::DB::GFF -e "Bio::DB::GFF->new('embl')->initialize(1)"

c) set up permissions for this database so that "nobody@localhost"
has SELECT, INSERT, UPDATE and DELETE privileges

d) cross your fingers

11. UPDATING THE BROWSER WITHOUT REENTERING YOUR DIRECTORY SETTINGS

When updating GBrowse to a new version of the software, you can
configure it using your preferred directory settings by making a
backup copy of the file GGB.def that was generated the first time you
installed GBrowse and using `cat GGB.def` as the argument to
Makefile.PL. Here is the recipe:

cp Generic-Genome-Browser-1.40/GGB.def Generic-Genome-Browser-1.41/GGB.def
cd Generic-Genome-Browser-1.41/
perl Makefile.PL `cat GGB.def`
make
make install

12. KNOWN BUGS

Currently there is one known bug. The navigation buttons do not
operate properly when the client is using Internet Explorer 5.1 on a
Macintosh and accessing gbrowse running on a MacOS X server running
Apache. Other combinations of clients and servers work properly.

13. FEATURE WISH LIST (updated July 7, 2002)

- Full DAS support.
- Internationalization and localization support.
- A glyph for representing cytogenetic maps.
- Multiple alignment representations.
- A percent identity (PIP) glyph.
- An XY plot glyph.
- Support for Oracle and PostgreSQL databases.

If you are interested in working on any of these features, please
contact the developers at the address given in the next section.

14. SUPPORT AND BUG REPORTS

Please send requests for help to gmod-devel@lists.sourceforge.net.
There is also a formal bug tracking and feature request system in
place at http://sourceforge.net/projects/gmod/

mod_perl and it is suggested that you disable Apache::DBI.

Have fun!

Lincoln Stein & the GMOD team
lstein@cshl.org
July 7, 2002
March 22, 2002
Loading

0 comments on commit 6c16ab6

Please sign in to comment.