<pre style='margin:0'>
Renee Otten (reneeotten) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/b0ba9280eab572558a893dd27e17f1ceade9ab38">https://github.com/macports/macports-ports/commit/b0ba9280eab572558a893dd27e17f1ceade9ab38</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new b0ba928 theseus: new port, version 3.3.0
</span>b0ba928 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit b0ba9280eab572558a893dd27e17f1ceade9ab38
</span>Author: Renee Otten <reneeotten@macports.org>
AuthorDate: Tue Mar 3 21:46:51 2020 -0500
<span style='display:block; white-space:pre;color:#404040;'> theseus: new port, version 3.3.0
</span>---
science/theseus/Portfile | 87 ++++++++++++++
science/theseus/files/patch-make.inc.diff | 126 +++++++++++++++++++++
.../theseus/files/patch-theseus_align-mafft.diff | 31 +++++
.../theseus/files/patch-theseus_align-muscle.diff | 18 +++
4 files changed, 262 insertions(+)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/theseus/Portfile b/science/theseus/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..f7cdae7
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/theseus/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,87 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortSystem 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+name theseus
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version 3.3.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories science
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+platforms darwin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license GPL-2+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers {reneeotten @reneeotten} openmaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description A program for maximum likelihood superpositioning and analysis of macromolecular structures
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description ${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://theobald.brandeis.edu/theseus
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+master_sites ${homepage}/src/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+distname theseus_${version}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 33c23525cbc0dc1ae805766492d29e16844d311b \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 3cfd4f906717f9cb8e77f689fc97059b32df355c0696077034ea99a485e3f2fe \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 22548124
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build port:cctools
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib port:gsl
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-make.inc.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant muscle description {Use MUSCLE for multiple sequence alignment} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ depends_run-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:muscle
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patchfiles-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-theseus_align-muscle.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ notes-append "**\tMUSCLE will be used as alignment program by 'theseus_align' \t**"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant mafft description {Use MAFFT for multiple sequence alignment} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ depends_run-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:mafft
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patchfiles-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-theseus_align-mafft.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ notes-append "**\tMAFFT will be used as alignment program by 'theseus_align' \t**"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+if {![variant_isset mafft]} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ default_variants +muscle
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-patch {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/make.inc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/theseus_align
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace "s|error.h|Error.h|g" ${worksrcpath}/NWfill.c
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+use_configure no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+build.env CC=${configure.cc} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CFLAGS=${configure.cflags} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LDFLAGS=${configure.ldflags}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-destroot {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 0755 -W ${worksrcpath} theseus theseus_align ${destroot}${prefix}/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 0644 -W ${worksrcpath} theseus.1 ${destroot}${prefix}/share/man/man1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set docdir ${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -d ${destroot}${docdir}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 0644 -W ${worksrcpath} AUTHORS COPYING \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ INSTALL.txt LICENSE README theseus_man.pdf ${destroot}${docdir}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+livecheck.type regex
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+livecheck.url ${homepage}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+livecheck.regex Version (\[0-9.\]+)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+notes "The provided wrapper script 'theseus_align', runs THESEUS on multiple PDB files.\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ This script transparently extracts the proper sequences from the PDB files, aligns\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ them, and then performs the ML superposition based on that alignment.\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ \n\nIt can use different alignment programs: MUSCLE and MAFFT are currently present\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ in MacPorts; others (PROBCONS, CLUSTALW, CLUSTAL-OMEGA, T_COFFEE, KALIGN, DIALIGN2)\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ can be utilized as well, but will require editing of the script located in:\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ${prefix}/bin/theseus_align"
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/theseus/files/patch-make.inc.diff b/science/theseus/files/patch-make.inc.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..ea0f274
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/theseus/files/patch-make.inc.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,126 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- make.inc.orig 2020-03-02 13:43:23.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ make.inc 2020-03-02 13:43:28.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,116 +1,18 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# The archiver and the flag(s) to use when building archive (library)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# If you system has no ranlib, set RANLIB = echo.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-ARCH = libtool
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ARCH = @@PREFIX@@/bin/libtool
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ARCHFLAGS = -o
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#ARCH = ar
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#ARCHFLAGS = -rvs
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-RANLIB = ranlib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#MACOSX_DEPLOYMENT_TARGET=10.4
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#export MACOSX_DEPLOYMENT_TARGET
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LOCALLIBDIR = /usr/local/lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# SYSLIBS = -lpthread -lgsl -lgslcblas -lm -lc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LIBDIR = -L./lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# INSTALLDIR = /usr/local/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# #OPT = -O0 -ggdb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# WARN = -Werror -Wno-error=unused-result -Wall -pedantic -std=c99
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CFLAGS += $(WARN) #-force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch x86_64 -arch i386 #-DNDEBUG
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# # CPPFLAGS are ignored by the rest of the build system but necessary for hardening flags.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CFLAGS += $(CPPFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# # Filter out -O2 which overwrites the default -O3 because OPT is used before CFLAGS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CFLAGS := $(filter-out -O2,$(CFLAGS))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CC = gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++RANLIB = @@PREFIX@@/bin/ranlib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#Mac OSX
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++# macOS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-LOCALLIBDIR = /usr/local/lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++LOCALLIBDIR = @@PREFIX@@/lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LIBS = -lgsl -lgslcblas -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SYSLIBS = -lpthread -lgsl -lgslcblas -lm -lc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LIBDIR = -L./lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-INSTALLDIR = /usr/local/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#OPT = -O0 -ggdb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-OPT = -ggdb -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -mtune=native
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++INSTALLDIR = $(DESTDIR)@@PREFIX@@/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++OPT = -ggdb -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ WARN = -Wall -pedantic -std=c99
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CFLAGS += $(WARN)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++CFLAGS += $(WARN)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # CPPFLAGS are ignored by the rest of the build system but necessary for hardening flags
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CFLAGS += $(CPPFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # Filter out -O2 which overwrites the default -O3 because OPT is used before CFLAGS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CFLAGS := $(filter-out -O2,$(CFLAGS))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CC = /usr/bin/gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#CC = /usr/local/bin/gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# Mac OSX Universal
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#LOCALLIBDIR = /usr/local/lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#LIBS = -lgsl -lgslcblas -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#SYSLIBS = -lpthread -lgsl -lgslcblas -lm -lc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#LIBDIR = -L./lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#INSTALLDIR = /usr/local/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-##OPT = -O0 -ggdb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#OPT = -s -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-##WARN = -Werror -Wno-error=unused-result -Wall -pedantic -std=c99
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#WARN = -Werror -Wall -pedantic -std=c99 # for APPLE MACOSX
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#CFLAGS += $(WARN) -force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch x86_64 -arch i386 #-DNDEBUG
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-##CFLAGS += $(WARN)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-## CPPFLAGS are ignored by the rest of the build system but necessary for hardening flags
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#CFLAGS += $(CPPFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-## Filter out -O2 which overwrites the default -O3 because OPT is used before CFLAGS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#CFLAGS := $(filter-out -O2,$(CFLAGS))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#CC = /usr/bin/gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# Ubuntu LINUX Dual processor Core2 x86_32, gulon (2010-09-07)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#LOCALLIBDIR = /usr/local/lib/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#SYSLIBS = -lpthread -lgsl -lgslcblas -lm -lc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-##SYSLIBS = -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lgsl -lgslcblas -lm -lc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-## --whole-archive is needed for pthread lib, due to static linking -- screwed but true
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-## see http://gcc.gnu.org/bugzilla/show_bug.cgi?id=44927
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#LIBDIR = -L./lib/ -L/usr/lib/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#INCDIR = -I/usr/local/include/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#INSTALLDIR = /usr/local/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-##OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -mtune=native
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-## OPT = -m64 -O3 -march=native -funroll-loops -ffast-math -mfpmath=sse
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#OPT = -O0 -ggdb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#WARN = -Wall -Werror -pedantic -std=c99 -Wno-unused-result
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#CFLAGS = $(WARN) -pthread
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#CC = /usr/local/bin/gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LINUX CentOS 5 after "yum install blas-devel lapack-devel atlas-devel gsl-devel" and dependencies
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LOCALLIBDIR = /usr/local/lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# SYSLIBS = -lm -lc -lgsl -lgslcblas
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LIBDIR = -L./lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# BLASLIB = -lblas
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LAPACKLIB = -llapack
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# INSTALLDIR = /usr/local/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# OPT = -O3 -funroll-loops -ffast-math
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# WARN = -Wall -pedantic -std=c99
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CFLAGS = $(WARN) -pthread
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CC = gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# BROKEN
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# Win32 using mingw -- requires win32 pthread library
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# SYSLIBS = -static -lpthreadGC2 -lg2c -lm
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LIBDIR = -L./lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# BLASLIB = -lblas
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# LAPACKLIB = -llapack
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# INSTALLDIR = /usr/local/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# WARN = -Wall -pedantic -std=c99
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CFLAGS = $(WARN) -DNDEBUG
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# CC = /usr/local/cross-tools/i386-mingw32msvc/bin/cc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/theseus/files/patch-theseus_align-mafft.diff b/science/theseus/files/patch-theseus_align-mafft.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..47d77ed
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/theseus/files/patch-theseus_align-mafft.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,31 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- theseus_align.orig 2020-03-03 21:42:45.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ theseus_align 2020-03-03 21:44:29.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -44,14 +44,14 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CAT="/bin/cat";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SED="/usr/bin/sed";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ TEE="/usr/bin/tee";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++theseus="@@PREFIX@@/bin/theseus"; # where to find the THESEUS binary executable
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ fastafile="theseus.fasta";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ filemapfile="theseus.filemap";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ alignmentfile="theseus.aln";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # for MUSCLE -- http://www.drive5.com/muscle/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-alignprog="/usr/local/bin/muscle";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++# alignprog="/usr/local/bin/muscle";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++# align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # for PROBCONS -- http://probcons.stanford.edu/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # alignprog="/usr/local/bin/probcons";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -68,8 +68,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #align_cmd="${alignprog} -outorder=input -infile=${fastafile} -outfile=${alignmentfile}";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# alignprog="/usr/local/bin/mafft";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++alignprog="@@PREFIX@@/bin/mafft";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # for T_COFFEE -- http://igs-server.cnrs-mrs.fr/%7Ecnotred/Projects_home_page/t_coffee_home_page.html
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #alignprog="/usr/local/bin/t_coffee";
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/theseus/files/patch-theseus_align-muscle.diff b/science/theseus/files/patch-theseus_align-muscle.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..3c3cef6
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/theseus/files/patch-theseus_align-muscle.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,18 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- theseus_align.orig 2020-03-03 21:42:45.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ theseus_align 2020-03-03 21:43:11.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -44,13 +44,13 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CAT="/bin/cat";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SED="/usr/bin/sed";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ TEE="/usr/bin/tee";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++theseus="@@PREFIX@@/bin/theseus"; # where to find the THESEUS binary executable
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ fastafile="theseus.fasta";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ filemapfile="theseus.filemap";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ alignmentfile="theseus.aln";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # for MUSCLE -- http://www.drive5.com/muscle/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-alignprog="/usr/local/bin/muscle";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++alignprog="@@PREFIX@@/bin/muscle";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # for PROBCONS -- http://probcons.stanford.edu/
</span></pre><pre style='margin:0'>
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