... | ... |
@@ -27,7 +27,6 @@ DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \ |
27 | 27 |
-Dabort=_samtools_abort |
28 | 28 |
|
29 | 29 |
PKG_CPPFLAGS += -I$(INCLUDE_DIR) |
30 |
-PKG_CFLAGS += -g -O3 $(DFLAGS) |
|
31 | 30 |
PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz |
32 | 31 |
|
33 | 32 |
SHLIB = gmapR.so |
... | ... |
@@ -39,6 +38,9 @@ $(SHLIB): $(OBJECTS) $(GSTRUCT_LIB) |
39 | 38 |
|
40 | 39 |
$(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c) |
41 | 40 |
|
41 |
+samtools/%.o: samtools/%.c |
|
42 |
+ $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(DFLAGS) -c $< -o $@ |
|
43 |
+ |
|
42 | 44 |
$(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct |
43 | 45 |
|
44 | 46 |
$(SAMTOOLS_LIB): $(BAMOBJ) |
... | ... |
@@ -69,6 +71,5 @@ clean: |
69 | 71 |
for dir in $(SUBDIRS); do \ |
70 | 72 |
$(MAKE) -C $$dir distclean; \ |
71 | 73 |
done |
72 |
- rm -rf samtools $(PREFIX) |
|
73 | 74 |
rm -f *.o *.so *.dll |
74 | 75 |
|
... | ... |
@@ -13,8 +13,21 @@ GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct |
13 | 13 |
|
14 | 14 |
SAMTOOLS_LIB = samtools/libbam.a |
15 | 15 |
|
16 |
+PATCH_O = samtools_patch.o |
|
17 |
+KNETFILE_O = knetfile.o |
|
18 |
+BAMOBJ_0 = \ |
|
19 |
+ bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ |
|
20 |
+ bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \ |
|
21 |
+ $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o $(PATCH_O) |
|
22 |
+BAMOBJ=$(BAMOBJ_0:%=samtools/%) |
|
23 |
+DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \ |
|
24 |
+ -U_FORTIFY_SOURCE -DBGZF_CACHE \ |
|
25 |
+ -Dfprintf=_samtools_fprintf \ |
|
26 |
+ -Dexit=_samtools_exit \ |
|
27 |
+ -Dabort=_samtools_abort |
|
28 |
+ |
|
16 | 29 |
PKG_CPPFLAGS += -I$(INCLUDE_DIR) |
17 |
-PKG_CFLAGS += -g -O3 |
|
30 |
+PKG_CFLAGS += -g -O3 $(DFLAGS) |
|
18 | 31 |
PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz |
19 | 32 |
|
20 | 33 |
SHLIB = gmapR.so |
... | ... |
@@ -28,22 +41,14 @@ $(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c) |
28 | 41 |
|
29 | 42 |
$(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct |
30 | 43 |
|
31 |
-RSAMTOOLS_PATH := $(shell R_LIBS=$(R_LIBRARY_DIR) $(R_HOME)/bin/Rscript \ |
|
32 |
- --vanilla -e 'cat(system.file(package="Rsamtools"))') |
|
33 |
-${R_SRC_DIR}/samtools: $(RSAMTOOLS_PATH) |
|
34 |
-## gmap/gstruct assume samtools headers and libs are in one directory, |
|
35 |
-## so we need to create one and populate it with links to Rsamtools. |
|
36 |
- rm -rf samtools; mkdir samtools |
|
37 |
- ln -sf $(RSAMTOOLS_PATH)/usrlib/$(R_ARCH)/libbam.a samtools/libbam.a |
|
38 |
- for header in $(RSAMTOOLS_PATH)/include/samtools/*.h; do \ |
|
39 |
- ln -sf $$header samtools/$(notdir $(header)); \ |
|
40 |
- done |
|
44 |
+$(SAMTOOLS_LIB): $(BAMOBJ) |
|
45 |
+ $(AR) -crus $@ $(BAMOBJ) |
|
41 | 46 |
|
42 |
-$(SUBDIRS): %: %/Makefile |
|
47 |
+$(SUBDIRS): %: %/Makefile $(SAMTOOLS_LIB) |
|
43 | 48 |
cd $@; \ |
44 | 49 |
$(MAKE) install |
45 | 50 |
|
46 |
-gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
|
51 |
+gstruct/Makefile: gstruct/configure |
|
47 | 52 |
cd $(dir $@); \ |
48 | 53 |
CFLAGS="-g -O3" \ |
49 | 54 |
./configure --enable-static --disable-shared \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@123973 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -50,6 +50,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
50 | 50 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
51 | 51 |
--libdir=${PREFIX}/${LIBnn} \ |
52 | 52 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
53 |
+ --disable-maintainer-mode \ |
|
53 | 54 |
--disable-binaries |
54 | 55 |
## does not appear to be a true dependency yet |
55 | 56 |
## --with-gmap=${PREFIX}/bin |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@123972 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -50,8 +50,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
50 | 50 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
51 | 51 |
--libdir=${PREFIX}/${LIBnn} \ |
52 | 52 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
53 |
- --disable-binaries \ |
|
54 |
- --disable-maintainer-mode |
|
53 |
+ --disable-binaries |
|
55 | 54 |
## does not appear to be a true dependency yet |
56 | 55 |
## --with-gmap=${PREFIX}/bin |
57 | 56 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111237 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -58,7 +58,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
58 | 58 |
gmap/Makefile: gmap/configure |
59 | 59 |
cd $(dir $@); \ |
60 | 60 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
61 |
- --libdir=${PREFIX}/${LIBnn} # \ # \ # \ # \ # --disable-maintainer-mode;;;; |
|
61 |
+ --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode |
|
62 | 62 |
|
63 | 63 |
clean: |
64 | 64 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110045 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -45,13 +45,13 @@ $(SUBDIRS): %: %/Makefile |
45 | 45 |
|
46 | 46 |
gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
47 | 47 |
cd $(dir $@); \ |
48 |
+ CFLAGS="-g -O3" \ |
|
48 | 49 |
./configure --enable-static --disable-shared \ |
49 | 50 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 51 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 52 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
52 | 53 |
--disable-binaries \ |
53 |
- CFLAGS="-g -O3" |
|
54 |
-# \ # \ # \ # \ # --disable-maintainer-mode \;;;; |
|
54 |
+ --disable-maintainer-mode |
|
55 | 55 |
## does not appear to be a true dependency yet |
56 | 56 |
## --with-gmap=${PREFIX}/bin |
57 | 57 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110039 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -50,14 +50,15 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
52 | 52 |
--disable-binaries \ |
53 |
- --disable-maintainer-mode \ |
|
53 |
+ CFLAGS="-g -O3" |
|
54 |
+# \ # \ # \ # \ # --disable-maintainer-mode \;;;; |
|
54 | 55 |
## does not appear to be a true dependency yet |
55 | 56 |
## --with-gmap=${PREFIX}/bin |
56 | 57 |
|
57 | 58 |
gmap/Makefile: gmap/configure |
58 | 59 |
cd $(dir $@); \ |
59 | 60 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
60 |
- --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode |
|
61 |
+ --libdir=${PREFIX}/${LIBnn} # \ # \ # \ # \ # --disable-maintainer-mode;;;; |
|
61 | 62 |
|
62 | 63 |
clean: |
63 | 64 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102487 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -50,15 +50,14 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
52 | 52 |
--disable-binaries \ |
53 |
- CFLAGS="-g -O3" |
|
54 |
-# \ # \ # \ # \ # --disable-maintainer-mode \;;;; |
|
53 |
+ --disable-maintainer-mode \ |
|
55 | 54 |
## does not appear to be a true dependency yet |
56 | 55 |
## --with-gmap=${PREFIX}/bin |
57 | 56 |
|
58 | 57 |
gmap/Makefile: gmap/configure |
59 | 58 |
cd $(dir $@); \ |
60 | 59 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
61 |
- --libdir=${PREFIX}/${LIBnn} # \ # \ # \ # \ # --disable-maintainer-mode;;;; |
|
60 |
+ --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode |
|
62 | 61 |
|
63 | 62 |
clean: |
64 | 63 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102485 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -50,14 +50,15 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
52 | 52 |
--disable-binaries \ |
53 |
-# --disable-maintainer-mode \ |
|
53 |
+ CFLAGS="-g -O3" |
|
54 |
+# \ # \ # \ # \ # --disable-maintainer-mode \;;;; |
|
54 | 55 |
## does not appear to be a true dependency yet |
55 | 56 |
## --with-gmap=${PREFIX}/bin |
56 | 57 |
|
57 | 58 |
gmap/Makefile: gmap/configure |
58 | 59 |
cd $(dir $@); \ |
59 | 60 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
60 |
- --libdir=${PREFIX}/${LIBnn} # --disable-maintainer-mode |
|
61 |
+ --libdir=${PREFIX}/${LIBnn} # \ # \ # \ # \ # --disable-maintainer-mode;;;; |
|
61 | 62 |
|
62 | 63 |
clean: |
63 | 64 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@101176 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -50,14 +50,14 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
52 | 52 |
--disable-binaries \ |
53 |
- --disable-maintainer-mode \ |
|
53 |
+# --disable-maintainer-mode \ |
|
54 | 54 |
## does not appear to be a true dependency yet |
55 | 55 |
## --with-gmap=${PREFIX}/bin |
56 | 56 |
|
57 | 57 |
gmap/Makefile: gmap/configure |
58 | 58 |
cd $(dir $@); \ |
59 | 59 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
60 |
- --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode |
|
60 |
+ --libdir=${PREFIX}/${LIBnn} # --disable-maintainer-mode |
|
61 | 61 |
|
62 | 62 |
clean: |
63 | 63 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@99427 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -13,7 +13,7 @@ GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct |
13 | 13 |
|
14 | 14 |
SAMTOOLS_LIB = samtools/libbam.a |
15 | 15 |
|
16 |
-PKG_CPPFLAGS += -I$(INCLUDE_DIR) -g -O3 |
|
16 |
+PKG_CPPFLAGS += -I$(INCLUDE_DIR) |
|
17 | 17 |
PKG_CFLAGS += -g -O3 |
18 | 18 |
PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz |
19 | 19 |
|
... | ... |
@@ -28,8 +28,8 @@ $(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c) |
28 | 28 |
|
29 | 29 |
$(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct |
30 | 30 |
|
31 |
-RSAMTOOLS_PATH := $(shell R_LIBS_USER=$(R_LIBRARY_DIR) $(R_HOME)/bin/Rscript --vanilla -e \ |
|
32 |
- 'cat(system.file(package="Rsamtools"))') |
|
31 |
+RSAMTOOLS_PATH := $(shell R_LIBS=$(R_LIBRARY_DIR) $(R_HOME)/bin/Rscript \ |
|
32 |
+ --vanilla -e 'cat(system.file(package="Rsamtools"))') |
|
33 | 33 |
${R_SRC_DIR}/samtools: $(RSAMTOOLS_PATH) |
34 | 34 |
## gmap/gstruct assume samtools headers and libs are in one directory, |
35 | 35 |
## so we need to create one and populate it with links to Rsamtools. |
... | ... |
@@ -45,7 +45,7 @@ $(SUBDIRS): %: %/Makefile |
45 | 45 |
|
46 | 46 |
gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
47 | 47 |
cd $(dir $@); \ |
48 |
- CFLAGS="-g" ./configure --enable-static --disable-shared \ |
|
48 |
+ ./configure --enable-static --disable-shared \ |
|
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
... | ... |
@@ -57,8 +57,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
57 | 57 |
gmap/Makefile: gmap/configure |
58 | 58 |
cd $(dir $@); \ |
59 | 59 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
60 |
- --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode \ |
|
61 |
- CFLAGS=-g #added by gabe 5/14/14 |
|
60 |
+ --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode |
|
62 | 61 |
|
63 | 62 |
clean: |
64 | 63 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93390 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -45,13 +45,12 @@ $(SUBDIRS): %: %/Makefile |
45 | 45 |
|
46 | 46 |
gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
47 | 47 |
cd $(dir $@); \ |
48 |
- CFLAGS="-g -O0" ./configure --enable-static --disable-shared \ |
|
48 |
+ CFLAGS="-g" ./configure --enable-static --disable-shared \ |
|
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools-lib=${R_SRC_DIR}/samtools \ |
52 | 52 |
--disable-binaries \ |
53 |
-# --disable-maintainer-mode \ |
|
54 |
- #\ added by gabe 5/14/14 |
|
53 |
+ --disable-maintainer-mode \ |
|
55 | 54 |
## does not appear to be a true dependency yet |
56 | 55 |
## --with-gmap=${PREFIX}/bin |
57 | 56 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93386 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -13,8 +13,8 @@ GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct |
13 | 13 |
|
14 | 14 |
SAMTOOLS_LIB = samtools/libbam.a |
15 | 15 |
|
16 |
-PKG_CPPFLAGS += -I$(INCLUDE_DIR) -g -O0 |
|
17 |
-PKG_CFLAGS += -g -O0 |
|
16 |
+PKG_CPPFLAGS += -I$(INCLUDE_DIR) -g -O3 |
|
17 |
+PKG_CFLAGS += -g -O3 |
|
18 | 18 |
PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz |
19 | 19 |
|
20 | 20 |
SHLIB = gmapR.so |
... | ... |
@@ -28,7 +28,7 @@ $(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c) |
28 | 28 |
|
29 | 29 |
$(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct |
30 | 30 |
|
31 |
-RSAMTOOLS_PATH := $(shell $(R_HOME)/bin/Rscript --vanilla -e \ |
|
31 |
+RSAMTOOLS_PATH := $(shell R_LIBS_USER=$(R_LIBRARY_DIR) $(R_HOME)/bin/Rscript --vanilla -e \ |
|
32 | 32 |
'cat(system.file(package="Rsamtools"))') |
33 | 33 |
${R_SRC_DIR}/samtools: $(RSAMTOOLS_PATH) |
34 | 34 |
## gmap/gstruct assume samtools headers and libs are in one directory, |
... | ... |
@@ -45,11 +45,12 @@ $(SUBDIRS): %: %/Makefile |
45 | 45 |
|
46 | 46 |
gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
47 | 47 |
cd $(dir $@); \ |
48 |
- ./configure --enable-static --disable-shared \ |
|
48 |
+ CFLAGS="-g -O0" ./configure --enable-static --disable-shared \ |
|
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 |
- --with-samtools=${R_SRC_DIR}/samtools \ |
|
52 |
- --disable-binaries --disable-maintainer-mode \ |
|
51 |
+ --with-samtools-lib=${R_SRC_DIR}/samtools \ |
|
52 |
+ --disable-binaries \ |
|
53 |
+# --disable-maintainer-mode \ |
|
53 | 54 |
#\ added by gabe 5/14/14 |
54 | 55 |
## does not appear to be a true dependency yet |
55 | 56 |
## --with-gmap=${PREFIX}/bin |
... | ... |
@@ -58,7 +59,7 @@ gmap/Makefile: gmap/configure |
58 | 59 |
cd $(dir $@); \ |
59 | 60 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
60 | 61 |
--libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode \ |
61 |
- CFLAGS=-g0 #added by gabe 5/14/14 |
|
62 |
+ CFLAGS=-g #added by gabe 5/14/14 |
|
62 | 63 |
|
63 | 64 |
clean: |
64 | 65 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93316 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -13,8 +13,8 @@ GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct |
13 | 13 |
|
14 | 14 |
SAMTOOLS_LIB = samtools/libbam.a |
15 | 15 |
|
16 |
-PKG_CPPFLAGS += -I$(INCLUDE_DIR) |
|
17 |
-PKG_CFLAGS += -g |
|
16 |
+PKG_CPPFLAGS += -I$(INCLUDE_DIR) -g -O0 |
|
17 |
+PKG_CFLAGS += -g -O0 |
|
18 | 18 |
PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz |
19 | 19 |
|
20 | 20 |
SHLIB = gmapR.so |
... | ... |
@@ -49,14 +49,16 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools=${R_SRC_DIR}/samtools \ |
52 |
- --disable-binaries --disable-maintainer-mode #\ |
|
52 |
+ --disable-binaries --disable-maintainer-mode \ |
|
53 |
+ #\ added by gabe 5/14/14 |
|
53 | 54 |
## does not appear to be a true dependency yet |
54 | 55 |
## --with-gmap=${PREFIX}/bin |
55 | 56 |
|
56 | 57 |
gmap/Makefile: gmap/configure |
57 | 58 |
cd $(dir $@); \ |
58 |
- ./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
|
59 |
- --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode |
|
59 |
+ ./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
|
60 |
+ --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode \ |
|
61 |
+ CFLAGS=-g0 #added by gabe 5/14/14 |
|
60 | 62 |
|
61 | 63 |
clean: |
62 | 64 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@85525 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -49,7 +49,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools=${R_SRC_DIR}/samtools \ |
52 |
- --disable-maintainer-mode #\ |
|
52 |
+ --disable-binaries --disable-maintainer-mode #\ |
|
53 | 53 |
## does not appear to be a true dependency yet |
54 | 54 |
## --with-gmap=${PREFIX}/bin |
55 | 55 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@85521 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -49,7 +49,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools=${R_SRC_DIR}/samtools \ |
52 |
- --disable-binaries --disable-maintainer-mode #\ |
|
52 |
+ --disable-maintainer-mode #\ |
|
53 | 53 |
## does not appear to be a true dependency yet |
54 | 54 |
## --with-gmap=${PREFIX}/bin |
55 | 55 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@82202 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -49,7 +49,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools=${R_SRC_DIR}/samtools \ |
52 |
- --disable-binaries #--disable-maintainer-mode #\ |
|
52 |
+ --disable-binaries --disable-maintainer-mode #\ |
|
53 | 53 |
## does not appear to be a true dependency yet |
54 | 54 |
## --with-gmap=${PREFIX}/bin |
55 | 55 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80611 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -49,7 +49,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools=${R_SRC_DIR}/samtools \ |
52 |
- --disable-binaries --disable-maintainer-mode #\ |
|
52 |
+ --disable-binaries #--disable-maintainer-mode #\ |
|
53 | 53 |
## does not appear to be a true dependency yet |
54 | 54 |
## --with-gmap=${PREFIX}/bin |
55 | 55 |
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@79207 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -49,14 +49,14 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 | 50 |
--libdir=${PREFIX}/${LIBnn} \ |
51 | 51 |
--with-samtools=${R_SRC_DIR}/samtools \ |
52 |
- --disable-binaries #\ |
|
52 |
+ --disable-binaries --disable-maintainer-mode #\ |
|
53 | 53 |
## does not appear to be a true dependency yet |
54 | 54 |
## --with-gmap=${PREFIX}/bin |
55 | 55 |
|
56 | 56 |
gmap/Makefile: gmap/configure |
57 | 57 |
cd $(dir $@); \ |
58 | 58 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
59 |
- --libdir=${PREFIX}/${LIBnn} |
|
59 |
+ --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode |
|
60 | 60 |
|
61 | 61 |
clean: |
62 | 62 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@74871 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -2,7 +2,7 @@ SUBDIRS = gmap gstruct |
2 | 2 |
|
3 | 3 |
.PHONY: all clean $(SUBDIRS) |
4 | 4 |
|
5 |
-OBJECTS = bamreader.o bamtally.o iit.o variantsummary.o R_init_gmapR.o |
|
5 |
+OBJECTS = bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o |
|
6 | 6 |
|
7 | 7 |
R_SRC_DIR = ${CURDIR} |
8 | 8 |
PREFIX = ${R_SRC_DIR}/../inst/usr |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@71466 bc3139a8-67e5-0310-9ffc-ced21a209358
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69806 bc3139a8-67e5-0310-9ffc-ced21a209358
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68277 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -47,6 +47,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
47 | 47 |
cd $(dir $@); \ |
48 | 48 |
./configure --enable-static --disable-shared \ |
49 | 49 |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
50 |
+ --libdir=${PREFIX}/${LIBnn} \ |
|
50 | 51 |
--with-samtools=${R_SRC_DIR}/samtools \ |
51 | 52 |
--disable-binaries #\ |
52 | 53 |
## does not appear to be a true dependency yet |
... | ... |
@@ -54,7 +55,8 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
54 | 55 |
|
55 | 56 |
gmap/Makefile: gmap/configure |
56 | 57 |
cd $(dir $@); \ |
57 |
- ./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} |
|
58 |
+ ./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \ |
|
59 |
+ --libdir=${PREFIX}/${LIBnn} |
|
58 | 60 |
|
59 | 61 |
clean: |
60 | 62 |
for dir in $(SUBDIRS); do \ |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68219 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -8,7 +8,7 @@ R_SRC_DIR = ${CURDIR} |
8 | 8 |
PREFIX = ${R_SRC_DIR}/../inst/usr |
9 | 9 |
INCLUDE_DIR = $(PREFIX)/include |
10 | 10 |
|
11 |
-GSTRUCT_LIB = $(PREFIX)/lib/libgstruct-1.0.a |
|
11 |
+GSTRUCT_LIB = $(PREFIX)/$(LIBnn)/libgstruct-1.0.a |
|
12 | 12 |
GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct |
13 | 13 |
|
14 | 14 |
SAMTOOLS_LIB = samtools/libbam.a |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358
1 | 1 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,65 @@ |
1 |
+SUBDIRS = gmap gstruct |
|
2 |
+ |
|
3 |
+.PHONY: all clean $(SUBDIRS) |
|
4 |
+ |
|
5 |
+OBJECTS = bamreader.o bamtally.o R_init_gmapR.o |
|
6 |
+ |
|
7 |
+R_SRC_DIR = ${CURDIR} |
|
8 |
+PREFIX = ${R_SRC_DIR}/../inst/usr |
|
9 |
+INCLUDE_DIR = $(PREFIX)/include |
|
10 |
+ |
|
11 |
+GSTRUCT_LIB = $(PREFIX)/lib/libgstruct-1.0.a |
|
12 |
+GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct |
|
13 |
+ |
|
14 |
+SAMTOOLS_LIB = samtools/libbam.a |
|
15 |
+ |
|
16 |
+PKG_CPPFLAGS += -I$(INCLUDE_DIR) |
|
17 |
+PKG_CFLAGS += -g |
|
18 |
+PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz |
|
19 |
+ |
|
20 |
+SHLIB = gmapR.so |
|
21 |
+ |
|
22 |
+all: $(SHLIB) gmap |
|
23 |
+ |
|
24 |
+$(SHLIB): $(OBJECTS) $(GSTRUCT_LIB) |
|
25 |
+ $(SHLIB_LINK) -o $@ $(OBJECTS) $(ALL_LIBS) |
|
26 |
+ |
|
27 |
+$(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c) |
|
28 |
+ |
|
29 |
+$(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct |
|
30 |
+ |
|
31 |
+RSAMTOOLS_PATH := $(shell $(R_HOME)/bin/Rscript --vanilla -e \ |
|
32 |
+ 'cat(system.file(package="Rsamtools"))') |
|
33 |
+${R_SRC_DIR}/samtools: $(RSAMTOOLS_PATH) |
|
34 |
+## gmap/gstruct assume samtools headers and libs are in one directory, |
|
35 |
+## so we need to create one and populate it with links to Rsamtools. |
|
36 |
+ rm -rf samtools; mkdir samtools |
|
37 |
+ ln -sf $(RSAMTOOLS_PATH)/usrlib/$(R_ARCH)/libbam.a samtools/libbam.a |
|
38 |
+ for header in $(RSAMTOOLS_PATH)/include/samtools/*.h; do \ |
|
39 |
+ ln -sf $$header samtools/$(notdir $(header)); \ |
|
40 |
+ done |
|
41 |
+ |
|
42 |
+$(SUBDIRS): %: %/Makefile |
|
43 |
+ cd $@; \ |
|
44 |
+ $(MAKE) -j install |
|
45 |
+ |
|
46 |
+gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools |
|
47 |
+ cd $(dir $@); \ |
|
48 |
+ ./configure --enable-static --disable-shared \ |
|
49 |
+ --prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \ |
|
50 |
+ --with-samtools=${R_SRC_DIR}/samtools \ |
|
51 |
+ --disable-binaries #\ |
|
52 |
+## does not appear to be a true dependency yet |
|
53 |
+## --with-gmap=${PREFIX}/bin |
|
54 |
+ |
|
55 |
+gmap/Makefile: gmap/configure |
|
56 |
+ cd $(dir $@); \ |
|
57 |
+ ./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} |
|
58 |
+ |
|
59 |
+clean: |
|
60 |
+ for dir in $(SUBDIRS); do \ |
|
61 |
+ $(MAKE) -C $$dir distclean; \ |
|
62 |
+ done |
|
63 |
+ rm -rf samtools $(PREFIX) |
|
64 |
+ rm -f *.o *.so *.dll |
|
65 |
+ |