changed tar command to variable TAR_COMMAND so that (optionally) syst…

…ems with a native non-gnu tar could use an alternative; tar is default so that there is no change for other users; for example on Mac the homebrew install of gnu-tar is gtar; see lines 61-65 of vars.sample, and line 11 of makefile.inc

R/Makefile

@@ -7,7 +7,7 @@ R_EXEC = $(PREFIX)/bin/R
 R_FLAGS ?= -O2 -march=native -mtune=native
 
 $(R_SOURCE):
-	curl -f $(R_MIRROR)/src/base/R-3/$@.tar.gz | tar xzf -
+	curl -f $(R_MIRROR)/src/base/R-3/$@.tar.gz | $(TAR_COMMAND) xzf -
 
 build/Makefile: $(R_SOURCE)
 	mkdir -p build && cd build && \

env/Makefile

@@ -2,7 +2,7 @@ REMOTE_FILE_STORAGE = http://files.thehyve.net
 KETTLE_VERSION=4.4.0
 
 UBUNTU_PACKAGES=postgresql make git rsync libcairo-dev php5-cli php5-json curl \
-				tar openjdk-7-jdk gfortran g++ unzip
+				$(TAR_COMMAND) openjdk-7-jdk gfortran g++ unzip
 
 GROOVY_VERSION=2.1.9
 
@@ -31,7 +31,7 @@ $(TRANSMART_LOADER_ARCHIVE):
 	curl -f $(REMOTE_FILE_STORAGE)/$@ > $@
 
 $(TRANSMART_LOADER)-from-file-server: $(TRANSMART_LOADER_ARCHIVE) $(TRANSMART_LOADER)-from-file-server/conf/log4j.properties
-	tar --touch -xf $< -C $@
+	$(TAR_COMMAND) --touch -xf $< -C $@
 
 $(GROOVY_ZIP):
 	curl -f "$(GROOVY_URL)" > $@
@@ -67,7 +67,7 @@ $(KETTLE_ARCHIVE):
 	curl -L -f "http://downloads.sourceforge.net/project/pentaho/Data%20Integration/4.4.0-stable/$@" > $@
 
 data-integration: $(KETTLE_ARCHIVE)
-	tar --touch -xzf $<
+	$(TAR_COMMAND) --touch -xzf $<
 
 /var/lib/postgresql/tablespaces:
 	/bin/bash -c 'mkdir -p $@/{biomart,deapp,indx,search_app,transmart}'

makefile.inc

@@ -8,4 +8,6 @@ PSQL_COMMAND = $(PGSQL_BIN)psql -v ON_ERROR_STOP=1 --single-transaction -X
 PGDUMP_COMMAND = $(PGSQL_BIN)pg_dump
 PGDUMPALL_COMMAND = $(PGSQL_BIN)pg_dumpall
 
+TAR_COMMAND ?= tar
+
 .DELETE_ON_ERROR:

samples/common/Makefile

@@ -2,19 +2,19 @@ DATA_LOCATION := http://files.thehyve.net/sample_data/
 
 
 %/clinical: %/%_clinical.tar.xz
-	tar -C $* -xJf $(subst %,$*,$<)
+	$(TAR_COMMAND) -C $* -xJf $(subst %,$*,$<)
 
 %/annotation: %/%_annotation.tar.xz
-	tar -C $* -xJf $(subst %,$*,$<)
+	$(TAR_COMMAND) -C $* -xJf $(subst %,$*,$<)
 
 %/expression: %/%_expression.tar.xz
-	tar -C $* -xJf $(subst %,$*,$<)
+	$(TAR_COMMAND) -C $* -xJf $(subst %,$*,$<)
 
 %/analysis: %/%_analysis.tar.xz
-	tar -C $* -xJf $(subst %,$*,$<)
+	$(TAR_COMMAND) -C $* -xJf $(subst %,$*,$<)
 
 %/acgh: %/%_acgh.tar.xz
-	tar -C $* -xJf $(subst %,$*,$<)
+	$(TAR_COMMAND) -C $* -xJf $(subst %,$*,$<)
 
 %/%_clinical.tar.xz %/%_annotation.tar.xz %/%_expression.tar.xz %/%_analysis.tar.xz %/%_acgh.tar.xz:
 	curl -f $(DATA_LOCATION)$(notdir $(subst %,$*,$@)) > $(subst %,$*,$@)

solr/Makefile

@@ -22,24 +22,24 @@ EXAMPLE_FILES=etc contexts lib logs resources solr-webapp \
 			  webapps README.txt start.jar
 
 $(ROOT_FILES): solr-$(SOLR_VERSION).tgz
-	tar xzf $< --touch --strip-components=1 solr-$(SOLR_VERSION)/$@
+	$(TAR_COMMAND) xzf $< --touch --strip-components=1 solr-$(SOLR_VERSION)/$@
 
 $(EXAMPLE_FILES): solr-$(SOLR_VERSION).tgz
-	tar xzf $< --touch --strip-components=2 solr-$(SOLR_VERSION)/example/$@
+	$(TAR_COMMAND) xzf $< --touch --strip-components=2 solr-$(SOLR_VERSION)/example/$@
 
 DRIVER=contrib/dataimporthandler/lib/$(JDBC_DRIVER)
 $(DRIVER): $(JDBC_DRIVER_PATH)
 	test -d contrib || $(MAKE) contrib
 	cp "$<" "$@"
 
 solr: solr-$(SOLR_VERSION).tgz
-	tar xzf $< --touch --strip-components=2 \
+	$(TAR_COMMAND) xzf $< --touch --strip-components=2 \
 		--exclude $(SOLR_VERSION)/solr/collection1 \
 		solr-$(SOLR_VERSION)/example/solr
 
 solr/collection1:
 	test -d solr || $(MAKE) solr #don't add dep because solr is touched on each run
-	tar xzf solr-$(SOLR_VERSION).tgz --touch --strip-components=3 \
+	$(TAR_COMMAND) xzf solr-$(SOLR_VERSION).tgz --touch --strip-components=3 \
 		-C solr solr-$(SOLR_VERSION)/example/solr/collection1
 	rm $@/core.properties #so solr doesn't see the dir as core
 

vars.sample

@@ -58,6 +58,12 @@ KITCHEN=/path/to/data-integration/kitchen.sh
 #end with /
 TSUSER_HOME=$HOME/
 
+#optional TAR commend - e.g. tar on Mac does not work; 
+# on Mac homebrew: brew install gnu-tar ; will set command gtar
+# if this is unset, then value defaults to tar (system tar command)
+#TAR_COMMAND=gtar
+#export TAR_COMMAND 
+
 # If your distro uses an old version of groovy, do make -C env groovy,
 # and uncomment this. Version 2.1.9 is known to work, versions before 2
 # are known not to work