Correct installation step for mummer (and dependency) (#4293)

* Trailing whitespace cleanup

* Handcraft an install process for mummer (grumble)

Mummer punts on an installation step, they just build in and run from
the same directory.

Mummer also has various hardcoded paths built into it that allow it to
find other executables that it needs as well as its Perl library.

This updates the package to deal with this approach.

It patches the Makefile and scripts/Makefile so that the correct info
is fed to sed when it munges the perl scripts.

The install step is now finer grained and puts things where mummer
relatively wants to find them.

* Add perl dependency

* perl should be build/run dependency

* Fix whitespace

* Delete stray u at top of file

3 files changed, 121 insertions, 11 deletions

diff --git a/var/spack/repos/builtin/packages/mummer/Makefile.patch b/var/spack/repos/builtin/packages/mummer/Makefile.patch
new file mode 100644
index 0000000000..0c96565afb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mummer/Makefile.patch
@@ -0,0 +1,24 @@
+--- a/Makefile	2017-05-15 17:33:05.132803923 -0700
++++ b/Makefile	2017-05-16 16:01:29.264842369 -0700
+@@ -35,6 +35,13 @@
+ TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
+ KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
+ 
++ifndef INSTALL_TOP_DIR
++INSTALL_TOP_DIR     := $(TOP_DIR)
++endif
++INSTALL_BIN_DIR := $(INSTALL_TOP_DIR)/bin
++INSTALL_AUX_BIN_DIR := $(INSTALL_TOP_DIR)/aux_bin
++INSTALL_SCRIPT_DIR    := $(INSTALL_TOP_DIR)/scripts
++
+ CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
+ CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
+ SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
+@@ -52,6 +59,7 @@
+ 
+ #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES
+ export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
++export INSTALL_BIN_DIR INSTALL_AUX_BIN_DIR INSTALL_SCRIPT_DIR
+ 
+ 
+ 
diff --git a/var/spack/repos/builtin/packages/mummer/package.py b/var/spack/repos/builtin/packages/mummer/package.py
index 49533ed95e..222aab54b7 100644
--- a/var/spack/repos/builtin/packages/mummer/package.py
+++ b/var/spack/repos/builtin/packages/mummer/package.py
@@ -34,22 +34,34 @@ class Mummer(Package):
     version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2')
 
     depends_on('gnuplot')
+    depends_on('perl', type=('build', 'run'))
+
+    patch('Makefile.patch')
+    patch('scripts-Makefile.patch')
 
     def install(self, spec, prefix):
         if self.run_tests:
             make('check')
-        make('install')
-        mkdirp(prefix.bin)
+        make('INSTALL_TOP_DIR={0}'.format(prefix))
+        bd = prefix.bin
+        abd = join_path(prefix, 'aux_bin')
+        sd = join_path(prefix, 'scripts')
+        mkdirp(bd)
+        mkdirp(abd)
+        mkdirp(sd)
 
-        bins = ["show-tiling", "show-snps", "show-coords", "show-aligns", 
-                "show-diff", "delta-filter", "combineMUMs", "mummer", 
-                "repeat-match", "annotate", "mgaps", "gaps", "dnadiff", 
-                "nucmer2xfig", "run-mummer3", "mummerplot", "promer", 
+        bins = ["show-tiling", "show-snps", "show-coords", "show-aligns",
+                "show-diff", "delta-filter", "combineMUMs", "mummer",
+                "repeat-match", "annotate", "mgaps", "gaps", "dnadiff",
+                "nucmer2xfig", "run-mummer3", "mummerplot", "promer",
                 "run-mummer1", "nucmer", "mapview", "exact-tandems"]
         aux_bins = ["aux_bin/postnuc", "aux_bin/postpro",
                     "aux_bin/prenuc", "aux_bin/prepro"]
-                  
-        for b in bins:
-            install(b, join_path(prefix.bin, b))
-        for b in aux_bins:
-            install(b, join_path(prefix.bin, b[8:]))
+        scripts = ["scripts/Foundation.pm"]
+
+        for f in bins:
+            install(f, join_path(bd, f))
+        for f in aux_bins:
+            install(f, join_path(abd, f[8:]))
+        for f in scripts:
+            install(f, join_path(sd, f[8:]))
diff --git a/var/spack/repos/builtin/packages/mummer/scripts-Makefile.patch b/var/spack/repos/builtin/packages/mummer/scripts-Makefile.patch
new file mode 100644
index 0000000000..961a4d5463
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mummer/scripts-Makefile.patch
@@ -0,0 +1,74 @@
+--- a/scripts/Makefile	2011-12-16 18:49:26.000000000 -0800
++++ b/scripts/Makefile	2017-05-16 16:05:48.697853000 -0700
+@@ -37,56 +37,56 @@
+ #-- not so PHONY rules --#
+ exact-tandems: exact-tandems.csh
+ 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
++		-e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
++		-e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+ 		exact-tandems.csh > $(BIN_DIR)/exact-tandems
+ 	chmod 755 $(BIN_DIR)/exact-tandems
+ 
+ mapview: mapview.pl
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
++		-e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+                 mapview.pl > $(BIN_DIR)/mapview
+ 	chmod 755 $(BIN_DIR)/mapview
+ 
+ mummerplot: mummerplot.pl Foundation.pm
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++                -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++                -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                 mummerplot.pl > $(BIN_DIR)/mummerplot
+ 	chmod 755 $(BIN_DIR)/mummerplot
+ 
+ dnadiff: dnadiff.pl Foundation.pm
+ 	$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+-               -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-               -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++               -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++               -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                  dnadiff.pl > $(BIN_DIR)/dnadiff
+ 	chmod 755 $(BIN_DIR)/dnadiff
+ 
+ nucmer: nucmer.pl Foundation.pm
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++                -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++                -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
++                -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                  nucmer.pl > $(BIN_DIR)/nucmer
+ 	chmod 755 $(BIN_DIR)/nucmer
+ 
+ promer: promer.pl Foundation.pm
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++                -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++                -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
++                -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                 promer.pl > $(BIN_DIR)/promer
+ 	chmod 755 $(BIN_DIR)/promer
+ 
+ run-mummer1: run-mummer1.csh
+ 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
++		-e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+ 		run-mummer1.csh > $(BIN_DIR)/run-mummer1
+ 	chmod 755 $(BIN_DIR)/run-mummer1
+ 
+ run-mummer3: run-mummer3.csh
+ 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
++		-e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+ 		run-mummer3.csh > $(BIN_DIR)/run-mummer3
+ 	chmod 755 $(BIN_DIR)/run-mummer3
+