-
Notifications
You must be signed in to change notification settings - Fork 13
/
Makefile
251 lines (222 loc) · 11.7 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
export MKFILE_DIR = $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
CFLAGS_FUSOR_SV=-I /opt/compsci/python/2.7.3/include/python2.7/ -I ~/.local/lib/python2.7/site-packages/numpy/core/include/numpy/
LDFLAGS=
SRC=src
TARGET_BIN=bin
TOOL_PATHS=$(TARGET_BIN)/tools.py
PROGRAM=sve
SVE_DIR=$(shell pwd)
FUSORSV_DIR=$(SVE_DIR)/scripts/FusorSV
R_PACKAGE=$(SVE_DIR)/$(SRC)/R-package
R_INSTALL_DIR=$(R_PACKAGE)/packages
R_PACKAGE_DEPEN = bzip2-1.0.6 curl-7.47.1 pcre-8.40 xz-5.2.2 zlib-1.2.9
PERL_LIB=$(SVE_DIR)/$(SRC)/perl-lib
PERL_LIB_DEPEN = GD-2.52 GDTextUtil-0.86 GDGraph-histogram-1.1 GDGraph-1.54 Statistics-Descriptive-3.0612 List-MoreUtils-0.17
TARBALLS = jre1.8.0_51 picard-tools-2.5.0 svtoolkit_2.00.1736
SUBDIRS = bwa speedseq htslib samtools samtools-0.1.19 bcftools bedtools2 delly lumpy-sv hydra tigra
AUTOCONF = autoconf
AUTOHEADER = autoheader
PYTHON = `which python`
RSCRIPT = `which Rscript`
R = `which R`
# all
all: unzip_tarballs perl-lib htslib bwa_samtools speedseq bcftools bedtools2 delly hydra tigra CNVnator_v0.3.3 breakdancer lumpy R-package
@test -d $(SVE_DIR)/data || tar -zxvf data.tar.gz # unzip data
@test -d $(SVE_DIR)/$(TARGET_BIN) || mkdir $(SVE_DIR)/$(TARGET_BIN)
$(MAKE) tool_paths
@cp $(SVE_DIR)/scripts/$(PROGRAM).py $(SVE_DIR)/$(TARGET_BIN)/$(PROGRAM)
.PHONY: all
FusorSV: $(FUSORSV_DIR)/FusorSV.py $(FUSORSV_DIR)/fusion_utils.c
#$(PYTHON) $(FUSORSV_DIR)FusorSV.py build
$(CC) -rdynamic $(FUSORSV_DIR)/fusion_utils.c -shared -o $(FUSORSV_DIR)/fusion_utils.so -fPIC $(CFLAGS_FUSOR_SV) $(LDFLAGS)
@cd $(FUSORSV_DIR) && tar -zxvf data.tar.gz
unzip_tarballs:
@for module in $(TARBALLS); do \
if [ ! -d $(SVE_DIR)/$(SRC)/$$module ]; then \
echo "- Unzip $$module"; \
cd $(SVE_DIR)/$(SRC) && test -f $$module.tar.gz && tar -zxvf $$module.tar.gz; \
fi; \
done; \
cd $(SVE_DIR)
bwa_samtools:
@cd $(SVE_DIR)/$(SRC) && tar -zxvf samtools-0.1.19.tar.gz
@for dir in bwa samtools samtools-0.1.19; do \
echo "- Building in $$dir"; \
$(MAKE) --no-print-directory -C $(SRC)/$$dir;\
done
speedseq:
@echo "- Building in speedseq"
sed -i 's#CXX = g++ $$(ROOTFLAGS)#CXX = g++ -std=c++11 $$(ROOTFLAGS)#g' $(SRC)/speedseq/src/cnvnator/Makefile
$(MAKE) --no-print-directory -C $(SRC)/speedseq
bcftools: htslib
@echo "- Building in bcftools"
$(MAKE) --no-print-directory -C $(SRC)/bcftools
bedtools2:
@echo "- Building in bedtools2"
$(MAKE) --no-print-directory -C $(SRC)/bedtools2
delly:
@echo "- Building in delly"
$(MAKE) --no-print-directory -C $(SRC)/delly
hydra:
@echo "- Building in hydra"
$(MAKE) --no-print-directory -C $(SRC)/hydra
tigra: bwa_samtools htslib
@echo "- Building in tigra"
@sed -i "/SAMTOOLS=/d" $(SVE_DIR)/$(SRC)/tigra/Makefile
@sed -i "/HTSLIB=/d" $(SVE_DIR)/$(SRC)/tigra/Makefile
@sed -i "/SAMHTSLIB=/d" $(SVE_DIR)/$(SRC)/tigra/Makefile
@sed -i "2 a SAMHTSLIB=$(SVE_DIR)/$(SRC)/htslib/htslib" $(SVE_DIR)/$(SRC)/tigra/Makefile
@sed -i "2 a HTSLIB=$(SVE_DIR)/$(SRC)/htslib" $(SVE_DIR)/$(SRC)/tigra/Makefile
@sed -i "2 a SAMTOOLS=$(SVE_DIR)/$(SRC)/samtools" $(SVE_DIR)/$(SRC)/tigra/Makefile
$(MAKE) --no-print-directory -C $(SRC)/tigra
htslib:
@echo "- Building in htslib"
@rm -f $(SVE_DIR)/$(SRC)/htslib/configure
@rm -rf $(SVE_DIR)/$(SRC)/htslib/autom4te.cache
@cp $(SVE_DIR)/$(SRC)/htslib/configure.ac $(SVE_DIR)/$(SRC)/htslib/configure.ac~
@sed -i 's#m4_esyscmd_s(\[make print-version\]),##g' $(SVE_DIR)/$(SRC)/htslib/configure.ac
@cd $(SVE_DIR)/$(SRC)/htslib && $(AUTOHEADER) && $(AUTOCONF) && ./configure --disable-lzma
$(MAKE) --no-print-directory -C $(SVE_DIR)/$(SRC)/htslib
@test -f $(SVE_DIR)/$(SRC)/htslib/configure.ac~ && mv $(SVE_DIR)/$(SRC)/htslib/configure.ac~ $(SVE_DIR)/$(SRC)/htslib/configure.ac
CNVnator_v0.3.3:
ifeq ($(ROOTSYS),)
@echo "\nERROR: CNVnator_v0.3.3 cannot be compiled because the ROOT package is not installed."
@echo "\tYou may download Root version 6.09/02 from https://root.cern.ch/content/release-60902."
@echo "\tAfter installing Root, please do\n"
@echo "\texport ROOTSYS=<path_to_root>"
@echo "\texport LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:\$ROOTSYS/lib"
else
@echo "- Building in CNVnator_v0.3.3"
@cd $(SVE_DIR)/$(SRC) && tar -zxvf CNVnator_v0.3.3.tar.gz
$(MAKE) --no-print-directory -C $(SRC)/CNVnator_v0.3.3/src/samtools
$(MAKE) --no-print-directory -C $(SRC)/CNVnator_v0.3.3/src
endif
breakdancer:
@echo "- Building in breakdancer"
@cd $(SVE_DIR)/$(SRC) && tar -zxvf breakdancer-1.4.5.tar.gz
@cd $(SVE_DIR)/$(SRC)/breakdancer-1.4.5; \
test -d build && rm -rf build; \
mkdir build; cd build; \
cmake .. -DCMAKE_BUILD_TYPE=release; \
$(MAKE)
breakseq2:
@echo "- Building in breakseq2"
@cd $(SVE_DIR)/$(SRC)/breakseq2 && $(PYTHON) setup.py build
$(MAKE) --no-print-directory -C $(SRC)/breakseq2
lumpy:
@echo "- Building in lumpy"
@rm -f $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/configure
@rm -rf $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/autom4te.cache
@cp $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/configure.ac $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/configure.ac~
@sed -i 's#m4_esyscmd_s(\[make print-version\]),##g' $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/configure.ac
@cd $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib && $(AUTOHEADER) && $(AUTOCONF) && ./configure --disable-lzma
$(MAKE) --no-print-directory -C $(SVE_DIR)/$(SRC)/lumpy-sv
@test -f $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/configure.ac~ && mv $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/configure.ac~ $(SVE_DIR)/$(SRC)/lumpy-sv/lib/htslib/configure.ac
@sed -i "s#SAMBLASTER=\$$#SAMBLASTER=$(SVE_DIR)/$(SRC)/speedseq/bin/samblaster#g" $(SVE_DIR)/$(SRC)/lumpy-sv/bin/lumpyexpress.config
@sed -i "s#SAMBAMBA=\$$#SAMBAMBA=$(SVE_DIR)/$(SRC)/speedseq/bin/sambamba#g" $(SVE_DIR)/$(SRC)/lumpy-sv/bin/lumpyexpress.config
@sed -i "s#SAMTOOLS=\$$#SAMTOOLS=$(SVE_DIR)/$(SRC)/samtools/samtools#g" $(SVE_DIR)/$(SRC)/lumpy-sv/bin/lumpyexpress.config
perl-lib:
@for module in $(PERL_LIB_DEPEN); do \
if [ ! -d $(PERL_LIB)/$$module ]; then \
echo "- Unzip $$module"; \
cd $(PERL_LIB) && tar -zxvf $$module.tar.gz; \
cd $(PERL_LIB)/$$module; \
perl Makefile.PL INSTALL_BASE=$(PERL_LIB); \
$(MAKE) && $(MAKE) install; \
fi; \
done; \
R-install:
@mkdir -p $(R_INSTALL_DIR)
@for module in $(R_PACKAGE_DEPEN); do \
if [ ! -d $(R_PACKAGE)/$$module ]; then \
echo "- Unzip $$module"; \
cd $(R_PACKAGE) && tar -zxvf $$module.tar.gz; \
fi; \
done;
@test -d $(R_PACKAGE)/R-3.3.3 || (cd $(R_PACKAGE) && tar -zxvf R-3.3.3.tar.gz);
@sed -i "/CFLAGS=/d" $(R_PACKAGE)/bzip2-1.0.6/Makefile
@sed -i '23 a CFLAGS=-Wall -Winline -O2 -g -fPIC $$(BIGFILES)' $(R_PACKAGE)/bzip2-1.0.6/Makefile
@cd $(R_PACKAGE)/bzip2-1.0.6 && $(MAKE) clean && $(MAKE) -f Makefile-libbz2_so && $(MAKE) clean && $(MAKE) && $(MAKE) -n install PREFIX=$(R_INSTALL_DIR) && $(MAKE) install PREFIX=$(R_INSTALL_DIR)
@cd $(R_PACKAGE)/curl-7.47.1 && ./configure --prefix=$(R_INSTALL_DIR) && $(MAKE) && $(MAKE) install
@cd $(R_PACKAGE)/pcre-8.40 && ./configure --prefix=$(R_INSTALL_DIR) --enable-utf8 && $(MAKE) && $(MAKE) install
@cd $(R_PACKAGE)/xz-5.2.2 && ./configure --prefix=$(R_INSTALL_DIR) && $(MAKE) -j3 && $(MAKE) install
@cd $(R_PACKAGE)/zlib-1.2.9 && ./configure --prefix=$(R_INSTALL_DIR) && $(MAKE) && $(MAKE) install
@cd $(R_PACKAGE)/R-3.3.3 && ./configure --prefix=$(R_INSTALL_DIR) \
'LDFLAGS=-L$(R_INSTALL_DIR)/lib' CFLAGS='-I$(R_INSTALL_DIR)/include' --with-readline=no --without-recommended-packages
@$(MAKE) -C $(R_PACKAGE)/R-3.3.3
R-package:
@cd $(R_PACKAGE) && $(R) CMD BATCH installPackage.r logInstall
tool_paths:
@echo "TOOLS={}" > $(TOOL_PATHS)
@echo "TOOLS ['SVE_HOME'] = '$(SVE_DIR)'" >> $(TOOL_PATHS)
@echo "TOOLS ['BWA'] = '$(SVE_DIR)/$(SRC)/bwa/bwa'" >> $(TOOL_PATHS)
@echo "TOOLS ['BWA-POSTALT'] = '$(SVE_DIR)/$(SRC)/k8 $(SVE_DIR)/$(SRC)/bwa/bwakit/bwa-postalt.js'" >> $(TOOL_PATHS)
@echo "TOOLS ['SPEEDSEQ'] = '$(SVE_DIR)/$(SRC)/speedseq/bin/speedseq'" >> $(TOOL_PATHS)
@echo "TOOLS ['SAMBAMBA'] = '$(SVE_DIR)/$(SRC)/speedseq/bin/sambamba'" >> $(TOOL_PATHS)
@echo "TOOLS ['SAMTOOLS'] = '$(SVE_DIR)/$(SRC)/samtools/samtools'" >> $(TOOL_PATHS)
@echo "TOOLS ['TABIX'] = '$(SVE_DIR)/$(SRC)/htslib/tabix'" >> $(TOOL_PATHS)
@echo "TOOLS ['JAVA-1.8'] = '$(SVE_DIR)/$(SRC)/jre1.8.0_51/bin/java'" >> $(TOOL_PATHS)
@echo "TOOLS ['PICARD'] = '$(SVE_DIR)/$(SRC)/picard-tools-2.5.0/picard.jar'" >> $(TOOL_PATHS)
@echo "TOOLS ['CNVNATOR'] = '$(SVE_DIR)/$(SRC)/CNVnator_v0.3.3/src/cnvnator'" >> $(TOOL_PATHS)
@echo "TOOLS ['CNVNATOR2VCF'] = '$(SVE_DIR)/$(SRC)/CNVnator_v0.3.3/cnvnator2VCF.pl'" >> $(TOOL_PATHS)
@echo "TOOLS ['DELLY'] = '$(SVE_DIR)/$(SRC)/delly/src/delly'" >> $(TOOL_PATHS)
@echo "TOOLS ['BCFTOOLS'] = '$(SVE_DIR)/$(SRC)/bcftools/bcftools'" >> $(TOOL_PATHS)
@echo "TOOLS ['BEDTOOLS'] = '$(SVE_DIR)/$(SRC)/bedtools2/bin/bcftools'" >> $(TOOL_PATHS)
@echo "TOOLS ['LUMPY-EXPRESS'] = '$(SVE_DIR)/$(SRC)/lumpy-sv/bin/lumpyexpress'" >> $(TOOL_PATHS)
@echo "TOOLS ['BREAKSEQ'] = '$(SVE_DIR)/$(SRC)/breakseq2/scripts/run_breakseq2.py'" >> $(TOOL_PATHS)
@echo "TOOLS ['TIGRA'] = '$(SVE_DIR)/$(SRC)/tigra/tigra-sv'" >> $(TOOL_PATHS)
@echo "TOOLS ['TIGRA-EXT'] = '$(SVE_DIR)/$(SRC)/tigra-ext/TIGRA-ext.pl'" >> $(TOOL_PATHS)
@echo "TOOLS ['FATO2BIT'] = '$(SVE_DIR)/$(SRC)/faToTwoBit/faToTwoBit_linux'" >> $(TOOL_PATHS)
@echo "TOOLS ['RSCRIPT'] = '$(RSCRIPT)'" >> $(TOOL_PATHS)
@echo "TOOLS ['PERL_LIB_PATH'] = '$(PERL_LIB)'" >> $(TOOL_PATHS)
@echo "TOOLS ['HYDRA_PATH'] = '$(SVE_DIR)/$(SRC)/hydra'" >> $(TOOL_PATHS)
@echo "TOOLS ['BREAKDANCER_PATH'] = '$(SVE_DIR)/$(SRC)/breakdancer-1.4.5'" >> $(TOOL_PATHS)
@echo "TOOLS ['TIGRA_PATH'] = '$(SVE_DIR)/$(SRC)/tigra'" >> $(TOOL_PATHS)
@echo "TOOLS ['BWA_PATH'] = '$(SVE_DIR)/$(SRC)/bwa'" >> $(TOOL_PATHS)
@echo "TOOLS ['SAMTOOLS_PATH'] = '$(SVE_DIR)/$(SRC)/samtools'" >> $(TOOL_PATHS)
@echo "TOOLS ['SAMTOOLS-0.1.19_PATH'] = '$(SVE_DIR)/$(SRC)/samtools-0.1.19'" >> $(TOOL_PATHS)
@echo "TOOLS ['BCFTOOLS_PATH'] = '$(SVE_DIR)/$(SRC)/bcftools'" >> $(TOOL_PATHS)
@echo "TOOLS ['HTSLIB_PATH'] = '$(SVE_DIR)/$(SRC)/htslib'" >> $(TOOL_PATHS)
@echo "TOOLS ['JAVA-1.8_PATH'] = '$(SVE_DIR)/$(SRC)/jre1.8.0_51/bin'" >> $(TOOL_PATHS)
@echo "TOOLS ['GENOME_STRIP_PATH'] = '$(SVE_DIR)/$(SRC)/svtoolkit'" >> $(TOOL_PATHS)
@echo "TOOLS ['BREAKSEQ_PATH'] = '$(SVE_DIR)/$(SRC)/breakseq2'" >> $(TOOL_PATHS)
@echo "" >> $(TOOL_PATHS)
@echo "FILES={}" >> $(TOOL_PATHS)
@echo "FILES ['GRCH38-EXTRA'] = '$(SVE_DIR)/data/bwakit-GRCh38/hs38DH-extra.fa'" >> $(TOOL_PATHS)
@echo "FILES ['GRCH38-ALT'] = '$(SVE_DIR)/data/bwakit-GRCh38/hs38DH.fa.alt'" >> $(TOOL_PATHS)
@echo "FILES ['DELLY-HG19'] = '$(SVE_DIR)/$(SRC)/delly/excludeTemplates/human.hg19.excl.tsv'" >> $(TOOL_PATHS)
@echo "FILES ['DELLY-HG38'] = '$(SVE_DIR)/$(SRC)/delly/excludeTemplates/human.hg38.excl.tsv'" >> $(TOOL_PATHS)
@echo "FILES ['BREAKSEQ-HG19'] = '$(SVE_DIR)/data/breakseq_bplib/breakseq2_bplib_20150129.gff'" >> $(TOOL_PATHS)
@echo "FILES ['BREAKSEQ-HG38'] = '$(SVE_DIR)/data/breakseq_bplib/breakseq2_bplib_20150129_hg38.gff'" >> $(TOOL_PATHS)
clean: clean-R-package
@echo "- Clean up"
@for dir in $(SUBDIRS); do \
if [ -d $$dir ]; then \
$(MAKE) -C $(SRC)/$$dir clean; \
fi; \
done
@for module in $(TARBALLS); do \
if [ -d $(SRC)/$$module ]; then \
rm -rf $(SRC)/$$module; \
fi; \
done
@cd $(SVE_DIR)/$(SRC) && rm -rf samtools-0.1.19 CNVnator_v0.3.3 breakdancer-1.4.5
@for module in $(R_PACKAGE_DEPEN); do \
if [ -d $(R_PACKAGE)/$$module ]; then \
rm -rf $(R_PACKAGE)/$$module; \
fi; \
done;
@rm -rf $(R_INSTALL_DIR)
@if [ -d $(SVE_DIR)/data ]; then \
chmod -R 777 $(SVE_DIR)/data; \
rm -rf $(SVE_DIR)/data; \
fi
@rm -rf $(TARGET_BIN)
clean-R-package:
@rm -rf $(R_PACKAGE)/R-3.3.3
@for module in $(PERL_LIB_DEPEN); do \
if [ -d $(PERL_LIB)/$$module ]; then \
rm -rf $(PERL_LIB)/$$module; \
fi; \
done;
.PHONY: clean