Makefile.tmpl

# these are variables that are defined in the config file. they can be over-
# written at run time by setting an environment variable with the SUPERSMART
# prefix, e.g. conf.MYSQL_BIN becomes SUPERSMART_MYSQL_BIN
MYSQL=[% conf.MYSQL_BIN %]
PERL=[% conf.PERL_BIN %]
CURL=[% conf.CURL_BIN %]
WGET=[% conf.WGET_BIN %]
GUNZIP=[% conf.GUNZIP_BIN %]
FORMATDB=[% conf.FORMATDB_BIN %]

# this file is just used to check whether the InParanoid SQL tables were
# downloaded
INPARANOID_DL=[% conf.INPARANOID_SQL_DIR %]/robots.txt

# these are targets that have names, so that we can do things such as 'make
# tnrs'. They need to be listed here as 'phony' targets because the name of the
# target doesn't imply the creation of a file by that name. In other words,
# 'make tnrs' doesn't result in a file called tnrs, and we need to tell the make
# program about this so that it doesn't think files need to be re-generated.
.PHONY : setup database download inparanoid_blast

# eventually this target should result in all the pre-work being done, so that
# users can do "perl Makefile.PL && make && make setup && make test"
setup :
	@echo "Configured for genbank release number [% conf.currentGBRelease %]"

# downloads and concatenates the phylota database dump chunks
[% conf.DUMP_IN_FILE %] :
	$(CURL) [% conf.DUMP_IN_URL %][% conf.DUMP_IN_CHUNKS %] > $@

# download the concatenated FASTA file for InParanoid
[% conf.INPARANOID_SEQ_FILE %] :
	$(CURL) [% conf.INPARANOID_SEQ_URL %] -o $@

# download the InParanoid pairwise comparison tables
$(INPARANOID_DL) :
	cd [% conf.INPARANOID_SQL_DIR %] && $(WGET) --recursive --no-directories --no-parent --accept sqltable.* --level=1 [% conf.INPARANOID_SQL_URL %] && cd -

# does all the download targets
download : [% conf.DUMP_IN_FILE %] [% conf.INPARANOID_SEQ_FILE %] $(INPARANOID_DL)

# initializes the database:
# - creates the user
# - creates the empty database
# - grants newly created user all privileges on database
# - creates inparanoid database table
# - loads phylota database dump
# - applies a patch to the phylota schema (index on cigi.ti_of_gi)
database : [% conf.DUMP_IN_FILE %]
	$(MYSQL) -e "create user '[% conf.USER %]'@'localhost' identified by '[% conf.PASS %]';"
	$(MYSQL) -e "create database [% conf.DATABASE %];"
	$(MYSQL) -e "grant all privileges on [% conf.DATABASE %].* to '[% conf.USER %]'@'localhost';"
	$(MYSQL) -u [% conf.USER %] -p[% conf.PASS %] [% conf.DATABASE %] < [% conf.INPARANOID_SQL_FILE %]		
	$(GUNZIP) -c $< | mysql -u [% conf.USER %] -p[% conf.PASS %] [% conf.DATABASE %]
	$(MYSQL) -u [% conf.USER %] -p[% conf.PASS %] [% conf.DATABASE %] -e "alter table ci_gi_[% conf.currentGBRelease %] add index(ti_of_gi);"
	@echo "Database initialized succesfully"

# index the InParanoid BLAST database
[% conf.INPARANOID_LOG_FILE %] : [% conf.INPARANOID_SEQ_FILE %]
	$(FORMATDB) -i $< -l [% conf.INPARANOID_LOG_FILE %] -p T -o T

inparanoid_blast : [% conf.INPARANOID_LOG_FILE %]