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Difference between revisions of "SourceCode"

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=Anonymous access to the latest hosted source code repositories=
 
=Anonymous access to the latest hosted source code repositories=
  
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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.  
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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.  
  
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== Note to casual users ==
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The following OBF supported projects are now using git hosted on [http://github.com github.com]:
  
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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.  
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    * [http://www.bioruby.org BioRuby] uses http://github.com/bioruby/bioruby
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    * [http://www.biopython.org Biopython] uses http://github.com/biopython/biopython
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    * [http://www.bioperl.org BioPerl] uses http://github.com/bioperl
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    * [http://www.biosql.org 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.
 
For downloads of tested and released software, please visit the official [[Projects]] page for links to the project websites and download locations.
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== Note to developers ==
 
== Note to developers ==
  
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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.
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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].
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==How to browse our latest source code repositories via the web==
 
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Projects using CVS repositories:  http://code.open-bio.org/cgi/viewcvs.cgi
 
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Projects using Subversion repositories:  http://code.open-bio.org/svnweb/
 
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==Downloading and updating code via Anonymous CVS==
 
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* Make sure that [[wp:Concurrent_Versions_System | CVS]] is installed on your system.
 
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* Pick the repository that you wish to use
 
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'''IMPORTANT NOTE (Starting in 2008): BioPerl and BioJava are switching from CVS to Subversion for source code version control management. At some point the CVS links below for BioPerl and BioJava will be removed.
 
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'''
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biopython /home/repository/biopython]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biojava /home/repository/biojava]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=bioperl /home/repository/bioperl]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biodas /home/repository/biodas]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biomoby /home/repository/moby]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biocorba /home/repository/biocorba]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=biosql /home/repository/biosql]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=bioruby /home/repository/bioruby]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=emboss /home/repository/emboss]
 
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    * [http://code.open-bio.org/cgi/viewcvs.cgi/?cvsroot=obf-common /home/repository/obf-common]
 
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* Use the following command (all on one line) to login to the server. The example below shows how to login to the bioperl repository. To login to other repositories simply alter the /home/repository/(project) information.
 
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    cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl login
 
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* When prompted, the password is 'cvs'
 
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* 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.
 
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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.
 
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    cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl checkout bioperl-live
 
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* 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:
 
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    cvs update
 
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==Downloading and updating code via Anonymous Rsync==
 
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The code.open-bio.org server also offers up read-only copies of source code repositories via anonymous [[wp:Rsync | rsync]].
 
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To see a list of available rsync modules, try this command:
 
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  rsync rsync://code.open-bio.org
 
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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.
 
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The following example shows how to obtain the latest Bioperl codebase snapshot using anonymous rsync:
 
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  rsync -av code.open-bio.org::cvsbioperl .
 
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==Downloading and updating code via Anonymous SVN==
 
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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
 
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''Example Usage'':
 
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To see what SVN modules the BioJava project is making available, try this command:
 
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  svn list svn://code.open-bio.org/biojava
 
  
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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:
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== Past archives ==
  
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  svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live
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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 00:40, 31 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.

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