Update mummer4 to 4.0.0 (#53477)

* Update mummer4 to 4.0.0 * clean up patches * add m4 * Update build.sh --------- Co-authored-by: mencian <joshua.zhuang@yahoo.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
bioconda · Jan 26, 2025 · 1b0e16c · 1b0e16c
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commit 1b0e16c
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diff --git a/recipes/mummer4/0001-Makefile.am.patch b/recipes/mummer4/0001-Makefile.am.patch
@@ -0,0 +1,32 @@
+diff --git a/Makefile.am b/Makefile.am
+index 9a885ca..22d95e4 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -171,10 +171,10 @@ deltafiltername = $(shell echo delta-filter | sed '$(transform)')
+ repeatmatchname = $(shell echo repeat-match | sed '$(transform)')
+
+
+-script_inst_subst  = sed -e 's,[@]PERL[@],$(PERL),g' \
+-                         -e 's,[@]BIN_DIR[@],$(bindir),g' \
+-                         -e 's,[@]LIB_DIR[@],$(script_libdir),g' \
+-                         -e 's,[@]LIBEXEC_DIR[@],$(pkglibexecdir),g' \
++script_inst_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
++                         -e -e 's,"[@]BIN_DIR[@]",\x27$(bindir)\x27,g' \
++                         -e -e 's,"[@]LIB_DIR[@]",\x27$(script_libdir)\x27,g' \
++                         -e 's,"[@]LIBEXEC_DIR[@]",\x27$(pkglibexecdir)\x27,g' \
+                          -e 's,[@]MUMMER[@],$(mummername),g' \
+                          -e 's,[@]MGAPS[@],$(mgapsname),g' \
+                          -e 's,[@]PRENUC[@],$(prenucname),g' \
+@@ -188,9 +188,9 @@ script_inst_subst  = sed -e 's,[@]PERL[@],$(PERL),g' \
+                          -e 's,[@]DELTAFILTER[@],$(deltafiltername),g' \
+                          -e 's,[@]REPEATMATCH[@],$(repeatmatchname),g'
+ script_local_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
+-                         -e 's,[@]BIN_DIR[@],$(abs_builddir),g' \
+-                         -e 's,[@]LIB_DIR[@],$(abs_srcdir)/scripts,g' \
+-                         -e 's,[@]LIBEXEC_DIR[@],$(abs_builddir),g' \
++                         -e 's,"[@]BIN_DIR[@]",\x27$(abs_builddir)\x27,g' \
++                         -e 's,"[@]LIB_DIR[@]",\x27$(abs_srcdir)/scripts\x27,g' \
++                         -e 's,"[@]LIBEXEC_DIR[@]",\x27$(abs_builddir)\x27,g' \
+                          -e 's,[@]MUMMER[@],mummer,g' \
+                          -e 's,[@]MGAPS[@],mgaps,g' \
+                          -e 's,[@]PRENUC[@],prenuc,g' \
diff --git a/recipes/mummer4/0002-Makefile.in.patch b/recipes/mummer4/0002-Makefile.in.patch
@@ -0,0 +1,30 @@
+diff --git a/Makefile.in b/Makefile.in
+index 2d4c65d..5da668f 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -1048,9 +1048,9 @@ showsnpsname = $(shell echo show-snps | sed '$(transform)')
+ deltafiltername = $(shell echo delta-filter | sed '$(transform)')
+ repeatmatchname = $(shell echo repeat-match | sed '$(transform)')
+ script_inst_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
+-                         -e 's,[@]BIN_DIR[@],$(bindir),g' \
+-                         -e 's,[@]LIB_DIR[@],$(script_libdir),g' \
+-                         -e 's,[@]LIBEXEC_DIR[@],$(pkglibexecdir),g' \
++                         -e 's,"[@]BIN_DIR[@]",\x27$(bindir)\x27,g' \
++                         -e 's,"[@]LIB_DIR[@]",\x27$(script_libdir)\x27,g' \
++                         -e 's,"[@]LIBEXEC_DIR[@]",\x27$(pkglibexecdir)\x27,g' \
+                          -e 's,[@]MUMMER[@],$(mummername),g' \
+                          -e 's,[@]MGAPS[@],$(mgapsname),g' \
+                          -e 's,[@]PRENUC[@],$(prenucname),g' \
+@@ -1065,9 +1065,9 @@ script_inst_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
+                          -e 's,[@]REPEATMATCH[@],$(repeatmatchname),g'
+
+ script_local_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
+-                         -e 's,[@]BIN_DIR[@],$(abs_builddir),g' \
+-                         -e 's,[@]LIB_DIR[@],$(abs_srcdir)/scripts,g' \
+-                         -e 's,[@]LIBEXEC_DIR[@],$(abs_builddir),g' \
++                         -e 's,"[@]BIN_DIR[@]",\x27$(abs_builddir)\x27,g' \
++                         -e 's,"[@]LIB_DIR[@]",\x27$(abs_srcdir)/scripts\x27,g' \
++                         -e 's,"[@]LIBEXEC_DIR[@]",\x27$(abs_builddir)\x27,g' \
+                          -e 's,[@]MUMMER[@],mummer,g' \
+                          -e 's,[@]MGAPS[@],mgaps,g' \
+                          -e 's,[@]PRENUC[@],prenuc,g' \
diff --git a/...efore-postpro.-on-behalf-of-jervied.patch → ...efore-postpro.-on-behalf-of-jervied.patch b/...efore-postpro.-on-behalf-of-jervied.patch → ...efore-postpro.-on-behalf-of-jervied.patch
@@ -1,18 +1,8 @@
-From 32bd3e6d8a35060459319fe244a1d673b4997500 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Hermann=20Schw=C3=A4rzler?= <hermann.schwaerzler@uibk.ac.at>
-Date: Wed, 30 Jan 2019 09:47:17 +0100
-Subject: [PATCH] sort mgaps file before postpro. (on behalf of @jerviedog -
- fixes #55 (and #74 ?))
-
----
- scripts/promer.pl | 66 +++++++++++++++++++++++++++++++++++++++++++++++
- 1 file changed, 66 insertions(+)
-
 diff --git a/scripts/promer.pl b/scripts/promer.pl
-index 8932515..756ecb4 100644
+index 3d5acb4..537e1be 100644
 --- a/scripts/promer.pl
 +++ b/scripts/promer.pl
-@@ -346,6 +346,8 @@ sub main ( )
+@@ -344,6 +344,8 @@ sub main ( )
 
      #-- Run postpro and assert return value is zero
      print (STDERR "4: FINISHING DATA\n");
@@ -21,7 +11,7 @@ index 8932515..756ecb4 100644
      $err[0] = $tigr->runCommand
  	("$postpro_path $psw -x $blsm -b $blen ".
  	 "$ref_file $qry_file $pfx < $pfx.mgaps");
-@@ -379,4 +381,68 @@ sub main ( )
+@@ -377,4 +379,68 @@ sub main ( )
 
  exit ( main ( ) );
 
@@ -90,6 +80,3 @@ index 8932515..756ecb4 100644
 +    close($fh);
 +}
  #-- END OF SCRIPT
--- 
-2.24.0
-
diff --git a/recipes/mummer4/Makefile.am.patch b/recipes/mummer4/Makefile.am.patch
diff --git a/recipes/mummer4/Makefile.in.patch b/recipes/mummer4/Makefile.in.patch
diff --git a/recipes/mummer4/build.sh b/recipes/mummer4/build.sh
@@ -2,6 +2,20 @@
 
 set -xe
 
-./configure --prefix=$PREFIX
-make -j ${CPU_COUNT}
+export M4="${BUILD_PREFIX}/bin/m4"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -Wno-deprecated-declarations"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+autoreconf -if
+./configure --prefix="${PREFIX}" CC="${CC}" CXX="${CXX}" \
+	CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" \
+	CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS}" YAGGO="$(which yaggo)" --enable-swig \
+	--enable-python-binding --disable-option-checking \
+	--enable-silent-rules --disable-dependency-tracking
+
+make -j"${CPU_COUNT}"
 make install