[Bioperl-l] github -- pull request for adding bp_ to scripts

Carnë Draug carandraug+dev at gmail.com
Mon Jul 25 14:34:42 UTC 2011

Hi everyone

I made a pull request to the bioperl repo a few days ago (
https://github.com/bioperl/bioperl-live/pull/17 ) but got no answer
yet. The changes are on the scripts directory.

During installation, the scripts have their names changed to
bp_something. Some of them already have the bp_ prefix on them and
those are not changed. I simply changed the filename of all of them so
there's no need to make changes by the install script. Also, since
after installation all of them are named bp_something, it makes sense
that their documentation (and man pages generated from the POD)
reflect this. As such, I also changed their names on the

I asked at #bioperl back then and people seemed positive about this change:

<carandraug>  I noticed that the scripts have their names changed to
bp_scriptname during install. Any reason why not to have the files
already with bp? I noticed the man pages refer to the scripts without
the bp. I forked it and was planning on fix that
<rbuels> carandraug: i'm not sure what the logic is behind having it
that way.  pyrimidine is likely to be in the channel pretty soon, he
would probably know
<rbuels> carandraug: i agree with you that it's silly
<pyrimidine> carandraug: yes, it is silly.  I recall there being a
reason for this at some point, but I slept since then.  I think it's
safe to go ahead and change them.

Could someone comment on the pull request?


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