[EMBOSS] Where can I found the source code repository?

[David Bauer]

Hi Adam,

if cvs is not working, you can also just get the sources from the ftp server:
ftp://emboss.open-bio.org/pub/EMBOSS/

With regard to the isoelectric point, this is not a change to the code but there is just an additional data file with the new values.
Programs which use these data (e.g. iep) have an advanced qualifier -pkdata.
This defaults to Epk.dat if nothing is specified. 
If you specify "-pkdata Epkexpasy.dat" the program will use the alternative data file with the Expasy values.
The program embossdata will tell you where you can find the data files on your system.

David.

-----Ursprüngliche Nachricht-----
Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Peter Cock
Gesendet: 31 March 2014 17:12
An: Adam Sjøgren
Cc: root-l at lists.open-bio.org; emboss at emboss.open-bio.org
Betreff: Re: [EMBOSS] Where can I found the source code repository?

On Mon, Mar 31, 2014 at 3:44 PM, Adam Sjøgren <asjo at koldfront.dk> wrote:
>   Hi.
>
> I wanted to look up what the code changes corresponding to "Calculation
> of isoelectric point has been updated to use the same data values as
> Expasy and the Open Bio packages." in the ChangeLog (on
> http://emboss.sourceforge.net/developers/changelog.html#0) were.
>
> So I tried checking out the source code, using the instructions found on
> http://emboss.sourceforge.net/developers/cvs.html - but failed:
>
>   $ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login
>   Logging in to :pserver:cvs at cvs.open-bio.org:2401/home/repository/emboss
>   CVS password:
>   cvs [login aborted]: reading from server: Connection reset by peer
>   $
>
> Am I using the wrong instructions, or has the repository moved (perhaps
> to git? :-))?

There is a tentative plan to move the EMBOSS repository to git
hosted on GitHub (I've been meaning to talk with Peter Rice
about this). This might start with the git repository being used
as a read only mirror...

However, for now EMBOSS is still using CVS on *.open-bio.org,
which has a read/write live server for the developers, and a read
only CVS mirror for end users. It looks like there is a problem
with the CVS mirror cvs.open-bio.org aka code.open-bio.org :(

I presume (perhaps wrongly), that the development CVS server
is still fine...

Peter

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