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====== make ======

===== Introduction =====

While commonly associated with application development //[[http://www.wikipedia.org/wiki/Make_(software)|make]]// is commonly to produce pipelines and workflows using existing command-line tools as components, since //make// can handle dependencies between individual targets.

Some examples in bioinformatics:
  * [[http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile|A pipeline is a makefile]]
  * [[http://swc.scipy.org/lec/build.html|Automated Builds]]
  * [[http://www.slideshare.net/giovanni/makefiles-bioinfo|Makefiles Bioinfo]]

Many implementations of //make// exist, but probably the most popular is [[http://www.gnu.org/software/make/|GNU make]] due to its inclusion on Linux systems.

===== Documentation =====

==== GNU make ====

[[http://www.gnu.org/software/make/|GNU make]] provides a number of additional features over many //make// implementations, see the [[http://www.gnu.org/software/make/manual/|GNU make manual]] for details.

===== Chain of Dependencies =====

A common task in sequence analysis to is obtain a phylogenetic tree on homologues given a sequence:
  - Get query sequence (e.g. using [[:services:dbfetch|WSDbfetch]])
  - Perform a sequence similarity search to find homologues (e.g. SSEARCH against UniProtKB/SwissProt using [[:services:fasta|WSFasta]])
  - Get the sequences for a selection of hits (e.g. using [[:services:dbfetch|WSDbfetch]])
  - Align the homologues sequences using multiple sequence alignment (e.g. using [[:services:clustalw2|WSClustalW2]])
  - Generate a phylogenetic tree from the alignment (e.g. using [[:services:clustalw2|WSClustalW2]])

This can be implemented using //make// and the sample clients provided for the services. For example, using the SOAP::Lite based Perl clients for [[:services:dbfetch|WSDbfetch]], [[:services:fasta|WSFasta]] and [[:services:clustalw2|WSClustalW2]], a sample makefile would look like:
<code make>
# Directory containing Perl clients
WSDIR = ../../perl/soaplite
# Perl installation to use
WSPREFIX = perl
# User e-mail address for jobs
EMAIL = your@email

# First target in makefile is run by default
all: clustalw2-tree.ph

# Get the entry to find homologues for
query_seq.fasta:
	$(WSPREFIX) $(WSDIR)/dbfetch.pl fetchData 'uniprot:wap_rat' fasta raw > $@

# Perform a S&W search using SSEARCH to find homologues
ssearch.idlist: query_seq.fasta
	$(WSPREFIX) $(WSDIR)/fasta.pl --email $(EMAIL) --program ssearch --database swissprot --sequence query_seq.fasta --eupper 0.001 --quiet --async > $@.jobid
	$(WSPREFIX) $(WSDIR)/fasta.pl --jobid `cat $@.jobid` --poll --outfile ssearch
	$(WSPREFIX) $(WSDIR)/fasta.pl --jobid `cat $@.jobid` --ids --quiet > $@

# Get sequences of 20 most significant homologues
homologue_seqs.fasta: ssearch.idlist
	head -20 $^ | $(WSPREFIX) $(WSDIR)/dbfetch.pl fetchBatch uniprot - fasta raw > $@

# Align homologue sequences using ClustalW2
clustalw2-align.aln: homologue_seqs.fasta
	$(WSPREFIX) $(WSDIR)/clustalw2.pl --email $(EMAIL) --align $^ --quiet --async > $@.jobid
	$(WSPREFIX) $(WSDIR)/clustalw2.pl --jobid `cat $@.jobid` --poll --outfile clustalw2-align

# Create a tree from the alignment using ClustalW2.
clustalw2-tree.ph: clustalw2-align.aln
	$(WSPREFIX) $(WSDIR)/clustalw2.pl --email $(EMAIL) --tree --outputtree phylip --kimura $^ --quiet --async > $@.jobid
	$(WSPREFIX) $(WSDIR)/clustalw2.pl --jobid `cat $@.jobid` --poll --outfile clustalw2-tree

# Target to delete working files.
clean:
	rm -f *.fasta ssearch.* clustalw2-align.* clustalw2-tree.*
</code>

If using ''makefile'' or ''Makefile'' for the file name, then //make// will pick up the file automatically:
<code csh>make</code>
Alternatively using a name such as ''clustal.makefile'', the ''-f'' option is used to specify the file:
<code csh>make -f clustal.makefile</code>

===== Examples =====

  * Sequence to phylogentic tree ([[:services:dbfetch|WSDbfetch]], [[:services:fasta|WSFasta]], [[:services:clustalw2|WSClustalW2]]): [[http://www.ebi.ac.uk/Tools/webservices/downloads/workflows/make/clustal.makefile|clustal.makefile]]
  * Protein transmembrane domain prediction ([[:services:dbfetch|WSDbfetch]], [[:services:emboss|WSEmboss]], [[:services:interproscan|WSInterProScan]], [[:services:phobius|WSPhobius]]): [[http://www.ebi.ac.uk/Tools/webservices/downloads/workflows/make/tm.makefile|tm.makefile]]

More examples can be found on [[http://www.myexperiment.org/|myExperiment]].

\\
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