Re: Packaging parsnp and harvest-tools for Debian
Hi Todd,
may be this mail was missing you somehow so I resent it hereby.
Kind regards
Andreas.
On Tue, Mar 15, 2016 at 03:01:41PM +0100, Andreas Tille wrote:
> Hi Todd,
>
> I'm writing you on behalf of the Debian Med team, a group inside Debian
> with the objective to package free software relevant in the field of
> biology and medicine for official Debian. You can find an overview of
> software that we have packaged yet on our biology tasks page[0].
>
> We intend to package parsnp[1] and when downloading the archive from
> Github[2] I realised that it contains some binaries we need to replace
> by Debian packaged binaries built from the according sources to enable a
> distribution in main Debian.
>
> This is no issue for bin/fasttree since it is packaged for Debian so
> we can take this one.
>
> I'm not sure what the source of bin/harvest might be. I have the
> suspicion that this is build from harvest-tools[3] and thus created
> all packaging stuff ready for uploading to Debian in our packaging
> git repository[4].
>
> However, when calling bin/harvest_linux and the result from packaging
> the output is different:
>
> --- harvest_linux.out 2016-03-15 14:52:04.205897606 +0100
> +++ harvesttools.out 2016-03-15 14:52:15.505733147 +0100
> @@ -1,13 +1,19 @@
> -harVest usage: harvest
> - -i <harvest input>
> +harvesttools options:
> + -i <Gingr input>
> -b <bed filter intervals>,<filter name>,"<description>"
> -B <output backbone intervals>
> -f <reference fasta>
> + -F <reference fasta out>
> -g <reference genbank>
> + -a <MAF alignment input>
> + -m <multi-fasta alignment input>
> + -M <multi-fasta alignment output (concatenated LCBs)>
> -n <Newick tree input>
> -N <Newick tree output>
> - -o <hvt output>
> + --midpoint-reroot (reroot the tree at its midpoint after loading)
> + -o <Gingr output>
> -S <output for multi-fasta SNPs>
> + -u 0/1 (update the branch values to reflect genome length)
> -v <VCF input>
> -V <VCF output>
> -x <xmfa alignment file>
>
> and thus I wonder whether there is some other tool "Harvest" that
> might be needed to run parsnp.
>
> Moreover I wonder where I can find the source for bin/Profile. That's
> quite a generic name - not a good idea in a general scope. Can you
> please point me to the sources of this tool?
>
> Finally you are shipping a copy of libMUSCLE[5] which has three changes
> applied (besides PATH changes):
>
> diff -ubrN /home/andreas/debian-maintain/alioth/debian-med_git/libmuscle/libMUSCLE/Makefile.am libMUSCLE/Makefile.am
> --- /home/andreas/debian-maintain/alioth/debian-med_git/libmuscle/libMUSCLE/Makefile.am 2015-04-17 21:54:11.587201633 +0200
> +++ libMUSCLE/Makefile.am 2015-03-24 07:34:57.000000000 +0100
> @@ -1,5 +1,5 @@
> OPTIMIZATION = -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
> -AM_CXXFLAGS = $(OPTIMIZATION) -DNDEBUG=1 @OPENMP_CXXFLAGS@
> +AM_CXXFLAGS = $(OPTIMIZATION) -DNDEBUG=1 @OPENMP_CXXFLAGS@ -fopenmp
> AM_LDFLAGS = $(OPTIMIZATION)
>
> LIBMUSCLE_H = \
> diff -ubrN /home/andreas/debian-maintain/alioth/debian-med_git/libmuscle/libMUSCLE/params.cpp libMUSCLE/params.cpp
> --- /home/andreas/debian-maintain/alioth/debian-med_git/libmuscle/libMUSCLE/params.cpp 2015-04-17 21:54:11.591201574 +0200
> +++ libMUSCLE/params.cpp 2015-03-24 07:34:57.000000000 +0100
> @@ -114,7 +114,7 @@
> //TLS<int> g_scoreGapExtend(0);
> TLS<unsigned> g_uMaxIters(8);
> TLS<unsigned long> g_ulMaxSecs(0);
> -TLS<unsigned> g_uMaxMB(500);
> +TLS<unsigned> g_uMaxMB(16000);
>
> TLS<PPSCORE> g_PPScore(PPSCORE_LE);
> TLS<OBJSCORE> g_ObjScore(OBJSCORE_SPM);
> diff -ubrN /home/andreas/debian-maintain/alioth/debian-med_git/libmuscle/libMUSCLE/threadstorage.h libMUSCLE/threadstorage.h
> --- /home/andreas/debian-maintain/alioth/debian-med_git/libmuscle/libMUSCLE/threadstorage.h 2015-04-17 21:54:11.599201455 +0200
> +++ libMUSCLE/threadstorage.h 2015-03-24 07:34:57.000000000 +0100
> @@ -9,7 +9,7 @@
> //
>
> #ifdef _OPENMP
> -#define MAX_THREAD_COUNT 16
> +#define MAX_THREAD_COUNT 64
> #define OMP_GET_THREAD_NUM omp_get_thread_num()
> #include <omp.h>
> #else
>
>
> I think upstream of libMUSCLE would be happy to profit from these
> changes as well. I plan to apply these to the official Debian package
> since it seems sensible to me and link parsnp against this library
> dynamically.
>
> What do you think?
>
> Kind regards
>
> Andreas.
>
>
> [0] http://blends.debian.org/med/tasks/bio
> [1] http://harvest.readthedocs.org/en/latest/content/parsnp.html
> [2] https://github.com/marbl/parsnp/releases
> [3] http://harvest.readthedocs.org/en/latest/content/harvest-tools.html
> [4] https://anonscm.debian.org/cgit/debian-med/harvest-tools.git
> [5] http://sourceforge.net/p/mauve/code/HEAD/tree/muscle/trunk/
>
> --
> http://fam-tille.de
--
http://fam-tille.de
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