mpiblast: new package (#5106)
This commit is contained in:
Audrey Thoma
Adam J. Stewart
parent
3a0e9f29e6
commit
ad8c60239f
@ -0,0 +1,182 @@
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diff -rwu mpiblast-1.6.0/ncbi/corelib/ncbienv.c mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c
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--- mpiblast-1.6.0/ncbi/corelib/ncbienv.c 2009-11-22 01:17:48.000000000 -0500
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+++ mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c 2011-08-06 17:10:08.000000000 -0400
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@@ -1932,7 +1932,7 @@
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static char **targv = NULL;
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-#if defined(WIN_MAC)
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+#if defined(WIN_MAC) || defined(OS_UNIX_DARWIN)
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static FSSpec apFileSpec;
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static Str255 apName;
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static Handle apParam;
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@@ -2047,7 +2047,7 @@
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}
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}
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#endif /* defined(OS_UNIX_DARWIN) */
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-#endif /* defined(WIN_MAC) */
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+#endif /* defined(WIN_MAC) || defined(OS_UNIX_DARWIN) */
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#if defined(OS_MSWIN) || defined(OS_VMS)
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diff -rwu mpiblast-1.6.0/ncbi/make/makedis.csh mpiblast-1.6.0-patched/ncbi/make/makedis.csh
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--- mpiblast-1.6.0/ncbi/make/makedis.csh 2010-06-28 21:04:36.000000000 -0400
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+++ mpiblast-1.6.0-patched/ncbi/make/makedis.csh 2011-08-06 17:06:42.000000000 -0400
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@@ -1,6 +1,6 @@
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#!/bin/csh -f
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#
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-# $Id: makedis.csh 148594 2008-12-30 15:11:36Z ucko $
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+# $Id: makedis.csh 179886 2010-01-04 17:28:02Z ucko $
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#
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## PUBLIC DOMAIN NOTICE
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# National Center for Biotechnology Information
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@@ -54,7 +54,7 @@
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endif
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ls -l $tar_file
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- tar xvf $tar_file
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+ tar xf $tar_file
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else
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# make sure that ncbi/build directory exists
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if ( ! -d "ncbi/build" ) then
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@@ -74,6 +74,7 @@
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set HAVE_MAC=0
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#we will try to build OpenGL version of vibrant
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set HAVE_OGL=1
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+set MPBL_HAVE_MAC=0
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switch ($os)
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case SunOS:
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@@ -164,7 +165,7 @@
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gcc -v
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switch (`uname -m`)
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case "ia64":
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- if (-e `which ecc`) then
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+ if (-e `which icc`) then
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set platform=linux_ecc
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else
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set platform=linux
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@@ -253,7 +254,11 @@
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endif
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endif
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set HAVE_MOTIF=0
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- set HAVE_MAC=1
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+#MPIBLAST <<<
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+# set HAVE_MAC=1
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+ set MPBL_HAVE_MAC=1
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+ set HAVE_MAC=0
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+#MPIBLAST
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breaksw
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case NetBSD:
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set platform=netbsd
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@@ -319,6 +324,7 @@
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goto BADPLATFORM
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endif
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+
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set noglob
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# take the file $NCBI_DOT_MK and convert it to be suitable for csh eval:
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# (1) remove comments at the beginning of the lines
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@@ -328,6 +334,7 @@
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eval `sed -e 's/^ *#.*//g' -e 's/\$(\([a-zA-Z_]*\))/\${\1}/g' -e 's/ *= */=/g' -e 's/^\([^=]*\)=\(.*\)$/setenv \1 "\2";/' < $NCBI_DOT_MK`
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unset noglob
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+
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# disable assert() unless ENABLE_ASSERT is set
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if ("$?ENABLE_ASSERT" == 0) then
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set NCBI_OPTFLAG="-DNDEBUG $NCBI_OPTFLAG"
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@@ -441,13 +448,23 @@
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set NET_VIB=(VIB=\"blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn gene2xml $NONVIBWWWBLAST \")
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endif
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+# MPIBLAST <<<<<
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+if ("$MPBL_HAVE_MAC" == 1) then
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+set CMD='make $MFLG \
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+ CFLAGS1=\"-I/Developer/Headers/FlatCarbon $NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \
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+ LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
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+ SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \
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+ RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all'
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+else
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set CMD='make $MFLG \
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CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \
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LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
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SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \
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RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all'
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+endif
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eval echo $CMD
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eval echo $CMD | sh
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+# MPIBLAST >>>>>
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set make_stat = $status
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@@ -463,12 +480,18 @@
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endif
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# MPIBLAST <<<<<
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-
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+if ("$MPBL_HAVE_MAC" == 1) then
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set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
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LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
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LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"'
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+else
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+set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
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+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
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+ LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"'
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+endif
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eval echo $CMD
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eval echo $CMD | sh
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+if ($status != 0) exit $status
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if( "$platform" == "bluegenel" || "$platform" == "bluegenep" ) then
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exit 0
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@@ -476,7 +499,7 @@
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# MPIBLAST >>>>>
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set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
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- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
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+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
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LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $DEMO_VIB'
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eval echo $CMD
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eval echo $CMD | sh
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@@ -495,7 +518,7 @@
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set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
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- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
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+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
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LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" \
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THREAD_OBJ=$NCBI_THREAD_OBJ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
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$DEMO_VIB $mtapps'
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diff -rwu mpiblast-1.6.0/src/Makefile.am mpiblast-1.6.0-patched/src/Makefile.am
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--- mpiblast-1.6.0/src/Makefile.am 2009-11-22 01:17:48.000000000 -0500
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+++ mpiblast-1.6.0-patched/src/Makefile.am 2011-08-06 17:06:42.000000000 -0400
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@@ -2,7 +2,7 @@
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-D_LARGEFILE64_SOURCE -DMPIBLAST_PIO \
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-I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \
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-I@CONFIG_NCBIDIR@/corelib/
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-AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DINSTALL_PREFIX="\"@prefix@\"" \
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+AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX -DINSTALL_PREFIX="\"@prefix@\"" \
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@COMPILE_FLAGS@ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE \
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-I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \
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-I@CONFIG_NCBIDIR@/corelib/
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@@ -31,7 +31,7 @@
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@CONFIG_NCBIDIR@/build/blast_hooks.o -lmyncbitool -lblastcompadj -lmyncbiobj \
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-lmyncbi -L. -L@CONFIG_NCBIDIR@/lib/ $(MPE_LIBS) -lm @LINK_FLAGS@
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mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@
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-mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK
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+mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX
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mpiformatdb_SOURCES = mpiformatdb.cpp mpiblast_config.cpp mpiblast_config.hpp \
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file_util.cpp file_util.hpp mpiblast_util.cpp mpiblast_util.hpp \
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diff -rwu mpiblast-1.6.0/src/pio_intercept.h mpiblast-1.6.0-patched/src/pio_intercept.h
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--- mpiblast-1.6.0/src/pio_intercept.h 2009-11-22 01:17:48.000000000 -0500
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+++ mpiblast-1.6.0-patched/src/pio_intercept.h 2011-08-06 17:06:42.000000000 -0400
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@@ -60,7 +60,7 @@
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#include <txalign.h>
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/* marcros are duplicated in ncbi files to avoid header file conflict */
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-#define CHECK_NULPTR(x) if(x==NULL) fprintf(stderr, "%s, line%d: cannot allocate enough memory\n", __FILE__, __LINE__);
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+#define CHECK_NULPTR(x) if(x==NULL) { perror("Cannot allocate enough memory:"); exit(-1); }
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#ifndef NO_MPI
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typedef struct _output_record {
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51
var/spack/repos/builtin/packages/mpiblast/package.py
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51
var/spack/repos/builtin/packages/mpiblast/package.py
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@ -0,0 +1,51 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Mpiblast(AutotoolsPackage):
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"""mpiBLAST is a freely available, open-source, parallel implementation of
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NCBI BLAST"""
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homepage = "http://www.mpiblast.org/"
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url = "http://www.mpiblast.org/downloads/files/mpiBLAST-1.6.0.tgz"
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version('1.6.0', '707105ccd56825db776b50bfd81cecd5')
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patch('mpiBLAST-1.6.0-patch-110806')
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depends_on('mpi')
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def configure_args(self):
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args = ['--with-mpi=%s' % self.spec['mpi'].prefix]
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return args
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def build(self, spec, prefix):
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make('ncbi')
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make()
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def setup_environment(self, spack_env, run_env):
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spack_env.set('ac_cv_path_CC', self.spec['mpi'].mpicc)
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spack_env.set('ac_cv_path_CXX', self.spec['mpi'].mpicxx)
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