pkgsrc-WIP-changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
muscle: MUltiple Sequence Comparison by Log-Expectation
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Fri Oct 26 17:36:01 2018 -0500
Changeset: 4fe394efdd38a5120f5ee7ef0073f1f7238c1711
Modified Files:
Makefile
Added Files:
muscle/DESCR
muscle/Makefile
muscle/PLIST
muscle/distinfo
muscle/patches/patch-globalslinux.cpp
muscle/patches/patch-mk
Log Message:
muscle: MUltiple Sequence Comparison by Log-Expectation
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4fe394efdd38a5120f5ee7ef0073f1f7238c1711
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
muscle/DESCR | 15 ++++++
muscle/Makefile | 45 ++++++++++++++++
muscle/PLIST | 1 +
muscle/distinfo | 8 +++
muscle/patches/patch-globalslinux.cpp | 96 +++++++++++++++++++++++++++++++++++
muscle/patches/patch-mk | 29 +++++++++++
7 files changed, 195 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 83a93cb0cc..6067d2fa23 100644
--- a/Makefile
+++ b/Makefile
@@ -2210,6 +2210,7 @@ SUBDIR+= mupen64-plugin-sound
SUBDIR+= mupen64-plugin-video
SUBDIR+= mupen64plus
SUBDIR+= mupen64plus-extraplugins
+SUBDIR+= muscle
SUBDIR+= muscle-cflexplugin
SUBDIR+= muscle-mcardplugin
SUBDIR+= muscle-pam
diff --git a/muscle/DESCR b/muscle/DESCR
new file mode 100644
index 0000000000..6bf4b68cdd
--- /dev/null
+++ b/muscle/DESCR
@@ -0,0 +1,15 @@
+MUSCLE is multiple alignment software for protein and nucleotide sequences.
+The name stands for multiple sequence comparison by log-expectation.
+A range of options is provided that give you the choice of optimizing
+accuracy, speed, or some compromise between the two. Default parameters are
+those that give the best average accuracy in the published tests. MUSCLE
+can achieve both better average accuracy and better speed than CLUSTALW or
+T-Coffee, depending on the chosen options.
+Citation:
+Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
+and high throughput. Nucleic Acids Research 32(5): 1792-1797.
+Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
+reduced time and space complexity. BMC Bioinformatics 5(1): 113.
+The NAR paper gives only a brief overview of the algorithm and
+implementation details. For a full discussion of the method and many of
+the non-default options that it offers, please see the BMC paper.
diff --git a/muscle/Makefile b/muscle/Makefile
new file mode 100644
index 0000000000..5f7d39b7d1
--- /dev/null
+++ b/muscle/Makefile
@@ -0,0 +1,45 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Fri Oct 26 17:22:43 CDT 2018 #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+#ONLY_FOR_ARCHS_REASON= Fails to install: tries to modify /dev/tty
+
+DISTNAME= muscle${PV}_src
+PKGNAME= muscle-${PV}
+CATEGORIES= biology
+MASTER_SITES= http://www.drive5.com/muscle/downloads${PV}/
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= http://www.drive5.com/muscle/
+COMMENT= MUltiple Sequence Comparison by Log-Expectation
+
+DEPENDS+= dos2unix:../../converters/dos2unix
+
+# LICENSE=
+
+ONLY_FOR_PLATFORM= *-*-x86_64 *-*-i386
+
+USE_LANGUAGES= c c++
+
+WRKSRC= ${WRKDIR}/muscle${PV}/src
+BUILD_TARGET= muscle
+
+PV= 3.8.31
+
+INSTALLATION_DIRS= bin
+
+pre-patch:
+ dos2unix ${WRKSRC}/*.cpp
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/muscle ${DESTDIR}${PREFIX}/bin
+
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/muscle/PLIST b/muscle/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/muscle/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/muscle/distinfo b/muscle/distinfo
new file mode 100644
index 0000000000..13accfe49a
--- /dev/null
+++ b/muscle/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+SHA1 (muscle3.8.31_src.tar.gz) = 2fe55db73ff4e7ac6d4ca692f8f213d1c5071dac
+RMD160 (muscle3.8.31_src.tar.gz) = 18c9cf465f330a77d6a06ff9323c311a6f6be662
+SHA512 (muscle3.8.31_src.tar.gz) = 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce
+Size (muscle3.8.31_src.tar.gz) = 515267 bytes
+SHA1 (patch-globalslinux.cpp) = 6d6d531400ce120603e9759d571396869b864a9c
+SHA1 (patch-mk) = 1f257ec0272ed1b8630c1506180b357c702226cc
diff --git a/muscle/patches/patch-globalslinux.cpp b/muscle/patches/patch-globalslinux.cpp
new file mode 100644
index 0000000000..13e0efc6aa
--- /dev/null
+++ b/muscle/patches/patch-globalslinux.cpp
@@ -0,0 +1,96 @@
+$NetBSD$
+
+--- globalslinux.cpp.orig Tue Nov 30 05:09:50 2004
++++ globalslinux.cpp Mon Jul 4 11:13:18 2005
+@@ -7,6 +7,12 @@
+ #include <errno.h>
+ #include <stdio.h>
+ #include <fcntl.h>
++#if __FreeBSD__ > 2
++#include <kvm.h>
++#include <sys/param.h>
++#include <sys/sysctl.h>
++#include <sys/user.h>
++#endif // __FreeBSD__ > 2
+
+ const int ONE_MB = 1000000;
+ const int MEM_WARNING_THRESHOLD = 20*ONE_MB;
+@@ -39,6 +45,34 @@
+ return szCmdLine;
+ }
+
++#if __FreeBSD__ > 2
++double GetMemUseMB()
++ {
++ kvm_t *kd;
++ struct kinfo_proc *ki;
++ vm_size_t size;
++ int nproc;
++
++ kd = kvm_open(NULL, "/dev/null", NULL, O_RDONLY, "kvm_open");
++ if (kd == NULL)
++ {
++ static bool Warned = false;
++ if (!Warned)
++ {
++ Warned = true;
++ Warning("*Warning* Cannot open KVM");
++ }
++ return 0;
++ }
++
++ ki = kvm_getprocs(kd, KERN_PROC_PID, getpid(), &nproc);
++ size = ki->ki_size;
++
++ kvm_close(kd);
++
++ return ((double) size)/1e6;
++ }
++#else // __FreeBSD__ > 2
+ double GetMemUseMB()
+ {
+ static char statm[64];
+@@ -83,6 +117,7 @@
+
+ return ((double) Pages * (double) PageSize)/1e6;
+ }
++#endif // __FreeBSD__ > 2
+
+ void SaveCmdLine(int argc, char *argv[])
+ {
+@@ -118,6 +153,28 @@
+ dPeakMemUseMB = dMB;
+ }
+
++#if __FreeBSD__ > 2
++double GetRAMSizeMB()
++ {
++ const double DEFAULT_RAM = 500;
++ unsigned int physmem;
++ size_t len = sizeof physmem;
++ static int mib[2] = { CTL_HW, HW_PHYSMEM };
++
++ if (sysctl(mib, 2, &physmem, &len, NULL, 0))
++ {
++ static bool Warned = false;
++ if (!Warned)
++ {
++ Warned = true;
++ Warning("*Warning* Cannot get hw.physmem");
++ }
++ return DEFAULT_RAM;
++ }
++
++ return ((double) physmem)/1e6;
++ }
++#else // __FreeBSD__ > 2
+ double GetRAMSizeMB()
+ {
+ const double DEFAULT_RAM = 500;
+@@ -168,5 +225,6 @@
+ int Bytes = atoi(pMem+9)*1000;
+ return ((double) Bytes)/1e6;
+ }
++#endif // __FreeBSD__ > 2
+
+ #endif // !WIN32
diff --git a/muscle/patches/patch-mk b/muscle/patches/patch-mk
new file mode 100644
index 0000000000..95fac23f20
--- /dev/null
+++ b/muscle/patches/patch-mk
@@ -0,0 +1,29 @@
+$NetBSD$
+
+--- mk.orig 2010-05-02 08:15:42.000000000 +0900
++++ mk 2014-06-17 23:45:55.000000000 +0900
+@@ -1,4 +1,4 @@
+-#!/bin/bash
++#!/bin/sh
+ CPPNames='aligngivenpath aligngivenpathsw aligntwomsas aligntwoprofs aln alpha anchors bittraceback blosum62 blosumla clust cluster clwwt color cons diaglist diffobjscore diffpaths difftrees difftreese distcalc distfunc distpwkimura domuscle dosp dpreglist drawtree edgelist enumopts enumtostr estring fasta fasta2 fastclust fastdist fastdistjones fastdistkbit fastdistkmer fastdistmafft fastdistnuc fastscorepath2 finddiags finddiagsn glbalign glbalign352 glbaligndiag glbalignle glbalignsimple glbalignsp glbalignspn glbalignss glbalndimer globals globalslinux globalsosx globalsother globalswin32 gonnet henikoffweight henikoffweightpb html hydro intmath local main makerootmsa makerootmsab maketree mhack mpam200 msa msa2 msadistkimura msf muscle muscleout nucmx nwdasimple nwdasimple2 nwdasmall nwrec nwsmall objscore objscore2 objscoreda onexception options outweights pam200mafft params phy phy2 phy3 phy4 phyfromclust phyfromfile physeq phytofile posgap ppscore profdb profile pro
filefrommsa progalign progress progressivealign pwpath readmx realigndiffs realigndiffse refine refinehoriz refinesubfams refinetree refinetreee refinevert refinew savebest scoredist scoregaps scorehistory scorepp seq seqvect setblosumweights setgscweights setnewhandler spfast sptest stabilize subfam subfams sw termgaps textfile threewaywt tomhydro traceback tracebackopt tracebacksw treefrommsa typetostr upgma2 usage validateids vtml2 writescorefile'
+ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o
objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o'
+
+@@ -6,16 +6,15 @@
+ for CPPName in $CPPNames
+ do
+ echo $CPPName >> /dev/tty
+- g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
++ ${CXX} $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
+ done
+
+ LINK_OPTS=
+ if [ `uname -s` == Linux ] ; then
+ LINK_OPTS=-static
+ fi
+-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
++${CXX} $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
+ tail muscle.make.stderr.txt
+
+-strip muscle
+ ls -lh muscle
+ sum muscle
Home |
Main Index |
Thread Index |
Old Index