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Commit 421cb0f5 authored by sauloal's avatar sauloal
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running in node command line

parent 01400151
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.gitignore
View file @ 421cb0f5
*.o
*.tar.gz
bed/
data/
bedToBigBed2/
inc/
jksrc.zip
kent/
old/
bedTools/.gitignore
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old/
libs/old
*.o
*.tar.gz
bedGraphToBigWig
bedToBigBed
wigToBedGraph
wigToBed
wigToBigWig
bedGraphToBigWig_static
bedToBigBed_static
wigToBedGraph_static
wigToBed_static
wigToBigWig_static
bedTools/bedGraphToBigWig_static.js
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bedTools/bedGraphToBigWig_static.js.html
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......@@ -1297,22 +1297,22 @@
</script>
<script>
(function() {
var memoryInitializer = 'bedGraphToBigWig_static.js.html.mem';
if (typeof Module['locateFile'] === 'function') {
memoryInitializer = Module['locateFile'](memoryInitializer);
} else if (Module['memoryInitializerPrefixURL']) {
memoryInitializer = Module['memoryInitializerPrefixURL'] + memoryInitializer;
}
var xhr = Module['memoryInitializerRequest'] = new XMLHttpRequest();
xhr.open('GET', memoryInitializer, true);
xhr.responseType = 'arraybuffer';
xhr.send(null);
})();
(function() {
var memoryInitializer = 'bedGraphToBigWig_static.js.html.mem';
if (typeof Module['locateFile'] === 'function') {
memoryInitializer = Module['locateFile'](memoryInitializer);
} else if (Module['memoryInitializerPrefixURL']) {
memoryInitializer = Module['memoryInitializerPrefixURL'] + memoryInitializer;
}
var xhr = Module['memoryInitializerRequest'] = new XMLHttpRequest();
xhr.open('GET', memoryInitializer, true);
xhr.responseType = 'arraybuffer';
xhr.send(null);
})();
var script = document.createElement('script');
script.src = "bedGraphToBigWig_static.js.js";
document.body.appendChild(script);
var script = document.createElement('script');
script.src = "bedGraphToBigWig_static.js.js";
document.body.appendChild(script);
</script>
</body>
......
bedTools/bedGraphToBigWig_static.js.js
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bedTools/bedToBigBed_static.js
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bedTools/bedToBigBed_static.js.html
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......@@ -1297,22 +1297,22 @@
</script>
<script>
(function() {
var memoryInitializer = 'bedToBigBed_static.js.html.mem';
if (typeof Module['locateFile'] === 'function') {
memoryInitializer = Module['locateFile'](memoryInitializer);
} else if (Module['memoryInitializerPrefixURL']) {
memoryInitializer = Module['memoryInitializerPrefixURL'] + memoryInitializer;
}
var xhr = Module['memoryInitializerRequest'] = new XMLHttpRequest();
xhr.open('GET', memoryInitializer, true);
xhr.responseType = 'arraybuffer';
xhr.send(null);
})();
(function() {
var memoryInitializer = 'bedToBigBed_static.js.html.mem';
if (typeof Module['locateFile'] === 'function') {
memoryInitializer = Module['locateFile'](memoryInitializer);
} else if (Module['memoryInitializerPrefixURL']) {
memoryInitializer = Module['memoryInitializerPrefixURL'] + memoryInitializer;
}
var xhr = Module['memoryInitializerRequest'] = new XMLHttpRequest();
xhr.open('GET', memoryInitializer, true);
xhr.responseType = 'arraybuffer';
xhr.send(null);
})();
var script = document.createElement('script');
script.src = "bedToBigBed_static.js.js";
document.body.appendChild(script);
var script = document.createElement('script');
script.src = "bedToBigBed_static.js.js";
document.body.appendChild(script);
</script>
</body>
......
bedTools/bedToBigBed_static.js.js
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bedTools/makefile
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......@@ -2,7 +2,7 @@ GCC?=gcc
EXT?=
LIBS?=-lz -lpthread -lm
OPTS?=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64
OPTS?=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64
#LINKS?=-L./libs -L./global -L./extra -L/lib -L/usr/lib/x86_64-linux-gnu
#INCLUDES?=-I./libs -I./global -I./extra -I/lib -I/usr/lib/x86_64-linux-gnu
......@@ -13,7 +13,33 @@ INCLUDES?=-I./libs -I/lib -I/usr/include/ -I/usr/lib/x86_64-linux-gnu
WARNINGS?=-Wall -Wformat -Wimplicit -Wreturn-type
ZLIB=zlib-1.2.8/
PREJS=
POSJS=
ifneq ("$(wildcard pre.js)","")
PREJS=--pre-js pre.js
endif
ifneq ("$(wildcard post.js)","")
POSJS=--post-js post.js
endif
#ZLIB=zlib-1.2.8/
#https://github.com/kripken/emscripten/blob/master/src/settings.js
EMCCOPTS=-s USE_ZLIB=1 -s NO_EXIT_RUNTIME=1 -s INVOKE_RUN=1 -s FORCE_FILESYSTEM=1
# --separate-asm
#-s MODULARIZE=1
#-s USE_PTHREADS=1
#-s USE_ZLIB=1
......@@ -72,7 +98,7 @@ print:
#$(GCC) -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
#$(GCC) -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
ZLIBCS=$(ZLIB)adler32.c $(ZLIB)crc32.c $(ZLIB)deflate.c $(ZLIB)infback.c $(ZLIB)inffast.c $(ZLIB)inflate.c $(ZLIB)inftrees.c $(ZLIB)trees.c $(ZLIB)zutil.c $(ZLIB)compress.c $(ZLIB)uncompr.c $(ZLIB)gzclose.c $(ZLIB)gzlib.c $(ZLIB)gzread.c $(ZLIB)gzwrite.c
#ZLIBCS=$(ZLIB)adler32.c $(ZLIB)crc32.c $(ZLIB)deflate.c $(ZLIB)infback.c $(ZLIB)inffast.c $(ZLIB)inflate.c $(ZLIB)inftrees.c $(ZLIB)trees.c $(ZLIB)zutil.c $(ZLIB)compress.c $(ZLIB)uncompr.c $(ZLIB)gzclose.c $(ZLIB)gzlib.c $(ZLIB)gzread.c $(ZLIB)gzwrite.c
......@@ -91,13 +117,18 @@ $(EXE): %$(EXT) : %.o $(OS)
ifeq ($(EXT),.js)
$(STA): %_static$(EXT) : %.c $(CS) $(ZLIBCS)
$(GCC) $(OPTS) -O -g -static $(WARNINGS) $(LINKS) $(INCLUDES) -I$(ZLIB) -o $@ $^ $(LIBS) $(ZLIBCS)
$(GCC) $(OPTS) -O -g -static $(WARNINGS) $(LINKS) $(INCLUDES) -I$(ZLIB) -o $@.html $^ $(LIBS) $(ZLIBCS)
$(STA): %_static$(EXT) : %.c $(CS)
$(GCC) $(EMCCOPTS) $(OPTS) -O -Oz -static $(WARNINGS) $(LINKS) $(INCLUDES) -o $@ $^ $(LIBS) $(PREJS) $(POSJS)
$(GCC) $(EMCCOPTS) $(OPTS) -O -Oz -static $(WARNINGS) $(LINKS) $(INCLUDES) -o $@.html $^ $(LIBS)
# $(GCC) $(EMCCOPTS) $(OPTS) -O -Oz -static $(WARNINGS) $(LINKS) $(INCLUDES) -I$(ZLIB) -o $@ $^ $(LIBS)
# $(GCC) $(EMCCOPTS) $(OPTS) -O -Oz -static $(WARNINGS) $(LINKS) $(INCLUDES) -I$(ZLIB) -o $@.html $^ $(LIBS)
# $(ZLIBCS)
#-s EXPORT_NAME="$(subst _static$(EXT),,$@)"
else
$(STA): %_static$(EXT) : %.c $(CS)
$(GCC) $(OPTS) -O -g -static $(WARNINGS) $(LINKS) $(INCLUDES) -o $@ $^ $(LIBS)
$(GCC) $(OPTS) -O -g -static $(WARNINGS) $(LINKS) $(INCLUDES) -o $@.html $^ $(LIBS)
$(GCC) $(OPTS) -O3 -O -g -static $(WARNINGS) $(LINKS) $(INCLUDES) -o $@ $^ $(LIBS)
endif
......
bedTools/pre.js 0 → 100644
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var Module = {
'preRun': function() {
if (ENVIRONMENT_IS_NODE) {
console.log("preRun");
FS.mkdir('/PWD');
FS.mount(NODEFS,{root:'.'},'/PWD');
console.log("PREFIX YOUR FILE NAMES WITH /PWD");
}
}
};
bedTools/wigToBedGraph_static.js
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bedTools/wigToBedGraph_static.js.html
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......@@ -1297,22 +1297,22 @@
</script>
<script>
(function() {
var memoryInitializer = 'wigToBedGraph_static.js.html.mem';
if (typeof Module['locateFile'] === 'function') {
memoryInitializer = Module['locateFile'](memoryInitializer);
} else if (Module['memoryInitializerPrefixURL']) {
memoryInitializer = Module['memoryInitializerPrefixURL'] + memoryInitializer;
}
var xhr = Module['memoryInitializerRequest'] = new XMLHttpRequest();
xhr.open('GET', memoryInitializer, true);
xhr.responseType = 'arraybuffer';
xhr.send(null);
})();
(function() {
var memoryInitializer = 'wigToBedGraph_static.js.html.mem';
if (typeof Module['locateFile'] === 'function') {
memoryInitializer = Module['locateFile'](memoryInitializer);
} else if (Module['memoryInitializerPrefixURL']) {
memoryInitializer = Module['memoryInitializerPrefixURL'] + memoryInitializer;
}
var xhr = Module['memoryInitializerRequest'] = new XMLHttpRequest();
xhr.open('GET', memoryInitializer, true);
xhr.responseType = 'arraybuffer';
xhr.send(null);
})();
var script = document.createElement('script');
script.src = "wigToBedGraph_static.js.js";
document.body.appendChild(script);
var script = document.createElement('script');
script.src = "wigToBedGraph_static.js.js";
document.body.appendChild(script);
</script>
</body>
......
bedTools/wigToBedGraph_static.js.js
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bedTools/wigToBed_static.js
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