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updated GBrowse READMEs with SVN checkout instructions

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rbuels committed Sep 15, 2009
1 parent fa8e764 commit 738b0651c089a47489048e366a38c9b065990fea
Showing with 13 additions and 16 deletions.
  1. +1 −1 INSTALL
  2. +6 −7 README.IF.GBROWSE.ISNT.WORKING
  3. +6 −8 README.gff3
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@@ -110,7 +110,7 @@ Generic Genome Browser Installation
E) Bioperl version 1.5 or higher -- <http://www.bioperl.org>
GBrowse requires functionality that exists in bioperl-live (in the
- cvs repository). Please either use bioperl-live or Bioperl 1.5 when
+ svn repository). Please either use bioperl-live or Bioperl 1.5 when
it comes out. Until then, there is a release candidate of Bioperl
1.5 that is thought to be stable with regard to GBrowse. It can be
found at <http://bioperl.org/DIST/bioperl-1.5.0-RC1.tar.gz>. Other
@@ -1,12 +1,11 @@
-If you got a cvs checkout of GBrowse and it isn't working, it is probably
-because you checked out from cvs HEAD, which is the main development
-branch. Unfortunately, that branch is currently unstable due to some
-major reworking which will make GBrowse so much better. In the mean time
+If you got an svn checkout of GBrowse and it isn't working, it is probably
+because you checked out from the svn HEAD, which is the main development
+branch. Unfortunately, that branch is often unstable due to some
+major reworking which will make GBrowse much better. In the mean time
(that is, until this README disappears), please check out from the
-stable branch. You can use the same cvs commands with an added flag:
+stable branch. You can use almost the same svn command:
-cvs -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/gmod login
-cvs -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/gmod co -r stable Generic-Genome-Browser
+svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/branches/stable Generic-Genome-Browser
Thanks,
Scott Cain
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@@ -24,18 +24,16 @@ This data model is encouraged by GFF3 and is used by FlyBase;
unfortunately Bio::DB::GFF cannot store such gene features without
hacking the FlyBase GFF3 files.
-As of June 2006, the bleeding-edge (CVS) version of Bioperl has
-database support for GFF3 format via the Bio::DB::SeqFeature::Store
-module. Currently only Mysql and preliminary in-memory implementations
-are available, but a BerkeleyDB version is in progress. You are
-encouraged to install this module and test it out, but it is still a
-development project and is not guaranteed to be 100% stable.
+The most recent (1.6.x) series of Bioperl releases have support for
+the GFF3 format via the Bio::DB::SeqFeature::Store.
Here are instructions for bringing up the Fly GFF3 annotations.
-1) Get the most recent version of Bioperl via CVS:
+1) Get the most recent version of Bioperl from CPAN:
- cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl co bioperl-live
+ cpan Bio::DB::SeqFeature::Store
+ or
+ sudo cpan Bio::DB::SeqFeature::Store
2) perl Makefile.PL, make and make install in the bioperl-live
directory.

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