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library(limma) | |
library(statmod) | |
library(scatterplot3d) | |
library(made4) | |
library(arrayQualityMetrics) | |
library(Biobase) | |
## We want to read ony Read channels, the way to do it is to pass custom | |
## names to read.maimages() function specifying the green.only=TRUE option | |
## with source="genepix.custom" and G,Gb=Cy5,Cy5b respectively. | |
## Cy5 => RED Channel Forground |
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require "formula" | |
class Methpipe < Formula | |
head "https://github.com/smithlabcode/methpipe.git" | |
homepage "http://smithlabresearch.org/software/methpipe/" | |
url "http://smithlabresearch.org/downloads/methpipe-3.3.1.tar.gz" | |
sha1 "00dea4a51e7b8ed5e7020bba89db63a91d86a70f" | |
depends_on "gsl" => :build |
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from Bio import SeqIO | |
import pickle | |
from pprint import pprint | |
import sys | |
hg19_location = "/usr/local/share/bcbio/genomes/Hsapiens/hg19/hg19.fa" | |
grch37_location = "/usr/local/share/bcbio/genomes/Hsapiens/GRCh37/bowtie/GRCh37.fa" | |
try: | |
pickled = pickle.load(open('comparison_pickled.p', 'rb')) | |
print (pickled) | |
sys.exit(0) |
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*.aux | |
*.glo | |
*.idx | |
*.log | |
*.toc | |
*.ist | |
*.acn | |
*.acr | |
*.alg | |
*.bbl |
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diff --git a/samblaster.cpp b/samblaster.cpp | |
index 14a2a40..2c33508 100644 | |
--- a/samblaster.cpp | |
+++ b/samblaster.cpp | |
@@ -26,6 +26,14 @@ | |
#include <map> | |
#include "sbhash.h" | |
+// Define mempcpy for Mac OS | |
+#ifdef __APPLE__ |
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--- lib/cpp/antlr/CharScanner.hpp 2015-01-07 00:09:51.747913036 -0800 | |
+++ lib/cpp/antlr/CharScanner.hpp 2015-01-07 00:10:31.883913806 -0800 | |
@@ -11,6 +11,8 @@ | |
#include <antlr/config.hpp> | |
#include <map> | |
+#include <cstring> | |
+#include <stdio.h> | |
#ifdef HAS_NOT_CCTYPE_H |
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diff --git libs/kxml/Makefile libs/kxml/Makefile | |
index 3635fa3..ff19f5b 100644 | |
--- libs/kxml/Makefile | |
+++ libs/kxml/Makefile | |
@@ -42,9 +42,7 @@ include $(TOP)/build/Makefile.env | |
# | |
ifeq (1,$(HAVE_XML2)) | |
-ifneq (,$(XML2_INCDIR)) | |
INCDIRS += $(addprefix -I,$(XML2_INCDIR)) |
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