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
This commit is contained in:
George Hartzell
Adam J. Stewart
parent
929c45916b
commit
d0a81fda30
24
var/spack/repos/builtin/packages/mummer/Makefile.patch
Normal file
24
var/spack/repos/builtin/packages/mummer/Makefile.patch
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@ -0,0 +1,24 @@
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--- a/Makefile 2017-05-15 17:33:05.132803923 -0700
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+++ b/Makefile 2017-05-16 16:01:29.264842369 -0700
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@@ -35,6 +35,13 @@
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TIGR_SRC_DIR := $(TOP_DIR)/src/tigr
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KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
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+ifndef INSTALL_TOP_DIR
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+INSTALL_TOP_DIR := $(TOP_DIR)
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+endif
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+INSTALL_BIN_DIR := $(INSTALL_TOP_DIR)/bin
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+INSTALL_AUX_BIN_DIR := $(INSTALL_TOP_DIR)/aux_bin
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+INSTALL_SCRIPT_DIR := $(INSTALL_TOP_DIR)/scripts
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+
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CC := $(filter /%,$(shell /bin/sh -c 'type gcc'))
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CXX := $(filter /%,$(shell /bin/sh -c 'type g++'))
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SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
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@@ -52,6 +59,7 @@
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#-- EXPORT THESE VARIABLES TO OTHER MAKEFILES
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export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
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+export INSTALL_BIN_DIR INSTALL_AUX_BIN_DIR INSTALL_SCRIPT_DIR
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@ -34,22 +34,34 @@ class Mummer(Package):
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version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2')
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depends_on('gnuplot')
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depends_on('perl', type=('build', 'run'))
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patch('Makefile.patch')
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patch('scripts-Makefile.patch')
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def install(self, spec, prefix):
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if self.run_tests:
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make('check')
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make('install')
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mkdirp(prefix.bin)
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make('INSTALL_TOP_DIR={0}'.format(prefix))
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bd = prefix.bin
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abd = join_path(prefix, 'aux_bin')
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sd = join_path(prefix, 'scripts')
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mkdirp(bd)
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mkdirp(abd)
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mkdirp(sd)
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bins = ["show-tiling", "show-snps", "show-coords", "show-aligns",
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"show-diff", "delta-filter", "combineMUMs", "mummer",
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"repeat-match", "annotate", "mgaps", "gaps", "dnadiff",
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"nucmer2xfig", "run-mummer3", "mummerplot", "promer",
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bins = ["show-tiling", "show-snps", "show-coords", "show-aligns",
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"show-diff", "delta-filter", "combineMUMs", "mummer",
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"repeat-match", "annotate", "mgaps", "gaps", "dnadiff",
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"nucmer2xfig", "run-mummer3", "mummerplot", "promer",
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"run-mummer1", "nucmer", "mapview", "exact-tandems"]
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aux_bins = ["aux_bin/postnuc", "aux_bin/postpro",
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"aux_bin/prenuc", "aux_bin/prepro"]
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for b in bins:
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install(b, join_path(prefix.bin, b))
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for b in aux_bins:
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install(b, join_path(prefix.bin, b[8:]))
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scripts = ["scripts/Foundation.pm"]
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for f in bins:
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install(f, join_path(bd, f))
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for f in aux_bins:
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install(f, join_path(abd, f[8:]))
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for f in scripts:
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install(f, join_path(sd, f[8:]))
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@ -0,0 +1,74 @@
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--- a/scripts/Makefile 2011-12-16 18:49:26.000000000 -0800
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+++ b/scripts/Makefile 2017-05-16 16:05:48.697853000 -0700
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@@ -37,56 +37,56 @@
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#-- not so PHONY rules --#
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exact-tandems: exact-tandems.csh
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$(SED) -e 's?__CSH_PATH?$(CSH)?g' \
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- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
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- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
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+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
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+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
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exact-tandems.csh > $(BIN_DIR)/exact-tandems
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chmod 755 $(BIN_DIR)/exact-tandems
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mapview: mapview.pl
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$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
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- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
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+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
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mapview.pl > $(BIN_DIR)/mapview
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chmod 755 $(BIN_DIR)/mapview
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mummerplot: mummerplot.pl Foundation.pm
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$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
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- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
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- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
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+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
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+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
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mummerplot.pl > $(BIN_DIR)/mummerplot
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chmod 755 $(BIN_DIR)/mummerplot
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dnadiff: dnadiff.pl Foundation.pm
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$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
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- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
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- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
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+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
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+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
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dnadiff.pl > $(BIN_DIR)/dnadiff
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chmod 755 $(BIN_DIR)/dnadiff
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nucmer: nucmer.pl Foundation.pm
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$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
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- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
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- -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
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- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
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+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
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+ -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
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+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
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nucmer.pl > $(BIN_DIR)/nucmer
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chmod 755 $(BIN_DIR)/nucmer
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promer: promer.pl Foundation.pm
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$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
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- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
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- -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
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- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
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+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
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+ -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
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+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
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promer.pl > $(BIN_DIR)/promer
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chmod 755 $(BIN_DIR)/promer
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run-mummer1: run-mummer1.csh
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$(SED) -e 's?__CSH_PATH?$(CSH)?g' \
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- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
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+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
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run-mummer1.csh > $(BIN_DIR)/run-mummer1
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chmod 755 $(BIN_DIR)/run-mummer1
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run-mummer3: run-mummer3.csh
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$(SED) -e 's?__CSH_PATH?$(CSH)?g' \
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- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
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+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
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run-mummer3.csh > $(BIN_DIR)/run-mummer3
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chmod 755 $(BIN_DIR)/run-mummer3
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