Packaging parsnp and harvest-tools for Debian
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
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