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 -- http://fam-tille.de -- http://fam-tille.de -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
