Re: Status of bitseq

[Andreas Tille <andreas@an3as.eu>]

Hi Tim,

[keeping the old thread from bitseq to potentially gain more input]

On Wed, Jan 01, 2014 at 11:07:15PM +0100, Andreas Tille wrote:
> Hi Tim,
> 
> as you know I was checking the status of some packages which are
> potentially interesting for BioLinux and stumbled upon bitseq.  I have
> updated the packaging in SVN with the exception of these warnings:
> 
> W: bitseq: script-with-language-extension usr/bin/extractTranscriptInfo.py
> W: bitseq: script-with-language-extension usr/bin/getCounts.py
> W: bitseq: binary-without-manpage usr/bin/extractTranscriptInfo.py
> W: bitseq: binary-without-manpage usr/bin/getCounts.py
> 
> 
> You see we are facing another issue with language extensions in scripts
> and I wonder what might be your opinion about this in this specific case.
 

On Wed, Jan 08, 2014 at 05:41:12PM +0000, Tim Booth wrote:
> Hi Andreas,
> 
> > PS: Some clarification about bitseq (see my other mail) would be helpful
> >     as well.
> 
> OK, that one first - I packaged it by request but it turns out the user
> really wanted the R module rather than the standalone version.

You mean:

   http://www.bioconductor.org/packages/release/bioc/html/BitSeq.html

?

> I wasn't
> planning to to anything more on it for BL but I'd think that for Debian,
> given the generic command names, you'd really want a wrapper (standard
> form - like so):
> 
> ---
> cat > /usr/bin/bitseq
> #!/bin/sh
> 
> if [ $# = 0 ] ; then
>     echo "   Usage: bitseq <cmd> [args]"
>     echo "for help: bitseq <cmd> -h"
>     echo "Commands:"
>     ls /usr/lib/bitseq | sed 's/^/  /'
> fi
> 
> prog=`basename $1 .py`
> 
> PATH="/usr/lib/bitseq:$PATH"
> 
> if [ -e "/usr/lib/bitseq/$prog.py" ] ; then
>   exec "/usr/lib/bitseq/$prog.py" "$@"
> else
>   exec "$prog" "$@"
> fi
> ---
> 
> (I've not tested this - just thought it was easier to write the code
> than describe what it should do)

Yep, I understand
 
> Of course this negates your work adding manpages, but then it will keep
> Lintian happy if you just put in a single mini-manpage for bitseq.

That's correct.

So what do Debian Med readers think?  Do we need a bitseq package or
would it be better to package only / in addition r-bioc-bitseq?

Remark:  If you want me to do something, please be not to shy to answer
here.  For me it is a bit frustrating to sit and wait like in the dotur
case[2] and having no idea what might be in the interest of our users.
:-(

Kind regards

      Andreas.

[2] https://lists.debian.org/debian-med/2013/12/msg00010.html

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