diff options
Diffstat (limited to 'var')
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 + |