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padlock-pipeline/Makefile
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Nov 7, 2014 @buske Adding makefile to get necessary programs
1 trimmomatic_version := 0.32
2 trimmomatic := Trimmomatic-$(trimmomatic_version)
Nov 7, 2014 @buske Added bowtie to makefile
3 trimmomatic_bin := lib/$(trimmomatic)/trimmomatic-$(trimmomatic_version).jar
4
Nov 7, 2014 @buske Adding makefile to get necessary programs
5 bismark_version := v0.12.3
6 bismark := bismark_$(bismark_version)
Nov 7, 2014 @buske Added bowtie to makefile
7 bismark_bin := lib/$(bismark)/bismark
8
9 bowtie_version := 1.1.1
10 bowtie := bowtie-$(bowtie_version)-linux-x86_64
11 bowtie_bin := lib/bowtie-$(bowtie_version)/bowtie
12
13 install: bismark trimmomatic bowtie
14
15 bismark: $(bismark_bin)
16
17 trimmomatic: $(trimmomatic_bin)
18
19 bowtie: $(bowtie_bin)
Nov 7, 2014 @buske Adding makefile to get necessary programs
20
21
22 lib/$(trimmomatic).zip:
Nov 7, 2014 @buske Added bowtie to makefile
23 curl -L -o $@ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/$(trimmomatic).zip
Nov 7, 2014 @buske Adding makefile to get necessary programs
24
Nov 7, 2014 @buske Added bowtie to makefile
25 $(trimmomatic_bin): lib/$(trimmomatic).zip
Nov 7, 2014 @buske Adding makefile to get necessary programs
26 cd lib; unzip $(<F)
Nov 7, 2014 @buske Added bowtie to makefile
27 touch $@
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28
29 lib/$(bismark).tar.gz:
Nov 7, 2014 @buske Added bowtie to makefile
30 curl -L -o $@ http://www.bioinformatics.babraham.ac.uk/projects/bismark/$(bismark).tar.gz
Nov 7, 2014 @buske Adding makefile to get necessary programs
31
Nov 7, 2014 @buske Added bowtie to makefile
32 $(bismark_bin): lib/$(bismark).tar.gz
Nov 7, 2014 @buske Adding makefile to get necessary programs
33 cd lib; tar -xzf $(<F)
Nov 7, 2014 @buske Added bowtie to makefile
34 touch $@
35
36
37 lib/$(bowtie).zip:
38 curl -L -o $@ http://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.1.1/$(bowtie).zip
39
40 $(bowtie_bin): lib/$(bowtie).zip
41 cd lib; unzip $(<F)
42 touch $@