-

Difference between revisions of "SourceCode"

From Open Bioinformatics Foundation
Jump to: navigation, search
(github link typo)
(Update to remove mention of CVS/SVN)
 
Line 1: Line 1:
 
=Anonymous access to the latest hosted source code repositories=
 
=Anonymous access to the latest hosted source code repositories=
  
The following OBF supported projects originally used CVS and/or SVN hosted by the OBF, but are now using git hosted on [http://github.com github.com]:
+
The methods described here grant access to live snapshots of our current code repositories. The files may be in constant flux and certainly do not reflect official packages and supported releases.
 +
 
 +
The following OBF supported projects are now using git hosted on [http://github.com github.com]:
  
 
     * [http://www.bioruby.org BioRuby] uses http://github.com/bioruby/bioruby
 
     * [http://www.bioruby.org BioRuby] uses http://github.com/bioruby/bioruby
Line 7: Line 9:
 
     * [http://www.bioperl.org BioPerl] uses http://github.com/bioperl
 
     * [http://www.bioperl.org BioPerl] uses http://github.com/bioperl
 
     * [http://www.biosql.org BioSQL] uses http://github.com/biosql/biosql
 
     * [http://www.biosql.org BioSQL] uses http://github.com/biosql/biosql
 
This page documents the process of obtaining anonymous [[wp:Concurrent_Versions_System | CVS]], [[wp:SVN | SVN]] or [[wp:Rsync | RSYNC]] based access to the source code repositories hosted by the Open Bioinformatics Foundation. These methods are useful for obtaining cutting edge sourcecode and developer snapshots:
 
 
== Note to casual users ==
 
 
The methods described here grant access to live snapshots of our current code repositories. The files may be in constant flux and certainly do not reflect official packages and supported releases.
 
  
 
For downloads of tested and released software, please visit the official [[Projects]] page for links to the project websites and download locations.
 
For downloads of tested and released software, please visit the official [[Projects]] page for links to the project websites and download locations.
Line 18: Line 14:
 
== Note to developers ==
 
== Note to developers ==
  
This page describes methods for obtaining '''read only''' access to the latest snapshots of our source code. Updates, fixes and new code '''can not''' be committed or uploaded using the methods described here. The exceptions are [http://github.com/bioruby/bioruby/tree/master BioRuby] and [http://github.com/biopython/biopython/tree/master Biopython], which can be [http://github.com/pjotrp/bioruby-testing-central/wikis forked] on github (allowing you to modify you own personal repository).
+
This page describes methods for obtaining '''read only''' access to the latest snapshots of our source code. Updates, fixes and new code '''can not''' be committed, but you can create a [https://help.github.com/articles/fork-a-repo fork] of the repository on github (allowing you to modify you own personal repository), and changes resubmitted to the projects as a [https://help.github.com/articles/about-pull-requests/ pull request].
 
 
==How to browse our latest source code repositories via the web==
 
 
 
Projects using CVS repositories:  http://code.open-bio.org/cgi/viewcvs.cgi (includes legacy repositories no longer used)
 
 
 
Projects using Subversion repositories:  http://code.open-bio.org/svnweb/  (includes legacy repositories no longer used)
 
 
 
==Downloading and updating code via Anonymous CVS==
 
 
 
* Make sure that [[wp:Concurrent_Versions_System | CVS]] is installed on your system.
 
* Pick the repository that you wish to use
 
 
 
    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biodas /home/repository/biodas]
 
    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biomoby /home/repository/moby]
 
    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biocorba /home/repository/biocorba]
 
    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=emboss /home/repository/emboss]
 
    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=obf-common /home/repository/obf-common]
 
* Use the following command (all on one line) to login to the server. The example below shows how to login to the emboss repository. To login to other repositories simply alter the /home/repository/(project) information.
 
    cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl login
 
* When prompted, the password is 'cvs'
 
* Each project CVS repository can have many different packages available for download. You may need to browse the web interface for a bit to determine the packages of interest. After a successful login you may "checkout" the project package you are interested in.
 
The following command should be executed as one line. The specific example shows how to check out the primary bioperl codebase which is contained in the "bioperl-live" package.
 
    cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl checkout bioperl-live
 
* The login and checkout procedure should only have to be done once. To update the source directories in the future it should be possible just to enter the top level directory and issue the following command:
 
    cvs update
 
 
 
==Downloading and updating code via Anonymous Rsync==
 
 
 
The code.open-bio.org server also offers up read-only copies of source code repositories via anonymous [[wp:Rsync | rsync]].
 
 
 
To see a list of available rsync modules, try this command:
 
 
 
  rsync rsync://code.open-bio.org
 
 
 
The server will echo back the list of configured repositories. The module name is appended to the "::" pattern to indicate to the rsync server that a module is being requested.
 
 
 
The following example shows how to obtain the latest Bioperl codebase snapshot using anonymous rsync:
 
 
 
  rsync -av code.open-bio.org::cvsbioperl .
 
 
 
 
 
==Downloading and updating code via Anonymous SVN==
 
 
 
The code.open-bio.org server also offers up read-only copies of source code repositories via anonymous [[wp:SVN | SVN]]. A list of code repositories available via SVN can be seen here: http://code.open-bio.org/svnweb/index.cgi
 
 
 
''Example Usage'':
 
 
 
To see what SVN modules the BioJava project is making available, try this command:
 
 
 
  svn list svn://code.open-bio.org/biojava
 
 
 
The following example shows how to obtain the latest Bioperl codebase snapshot using anonymous SVN, it will check out the latest copy of bioperl-live/ from the "SVN trunk" and will locally store it in a directory named "bioperl-live" on your system:
 
 
 
  svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live
 
 
 
==Troubleshooting Anonymous SVN==
 
 
 
If you encounter an error while using the SVN client or SVN Web interface, the likely cause is that our server is in the middle of replicating the repository from the primary source. While the mirror and replication process occurs, it is not unusual for SVN client functionality to break temporarily.
 
 
 
The final step of our codebase replication process is to explicitly re-verify the health and status of each repository, this process takes a few moments but while it occurs the repository is "locked" and unavailable for access.
 
  
* Anonymous SVN repositories are updated/mirrored hourly from the primary developer server
+
== Past archives ==
* Anonymous SVN repositories are verified and repaired (if necessary) every 20 minutes
 
  
If a SVN client error occurs for longer than 20 minutes, please report this to: support@helpdesk.open-bio.org
+
The above projects have previously used CVS and/or SVN hosted on OBF-maintained hardware, but these resources are no longer available.

Latest revision as of 19:40, 30 October 2016

Anonymous access to the latest hosted source code repositories

The methods described here grant access to live snapshots of our current code repositories. The files may be in constant flux and certainly do not reflect official packages and supported releases.

The following OBF supported projects are now using git hosted on github.com:

   * BioRuby uses http://github.com/bioruby/bioruby
   * Biopython uses http://github.com/biopython/biopython
   * BioPerl uses http://github.com/bioperl
   * BioSQL uses http://github.com/biosql/biosql

For downloads of tested and released software, please visit the official Projects page for links to the project websites and download locations.

Note to developers

This page describes methods for obtaining read only access to the latest snapshots of our source code. Updates, fixes and new code can not be committed, but you can create a fork of the repository on github (allowing you to modify you own personal repository), and changes resubmitted to the projects as a pull request.

Past archives

The above projects have previously used CVS and/or SVN hosted on OBF-maintained hardware, but these resources are no longer available.