[med-svn] [qtltools] 01/01: Initial debian/
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Thu Nov 24 21:07:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository qtltools.
commit 0874ca7617c5c494c42b4e884832b120252e8e0c
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Thu Nov 24 22:04:58 2016 +0100
Initial debian/
---
debian/QTLtools.1 | 100 +++++++++++++++++++++
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 42 +++++++++
debian/copyright | 34 +++++++
debian/patches/Correct_Eigen_include.patch | 53 +++++++++++
debian/patches/Makefile_config.patch | 38 ++++++++
debian/patches/Spelling_error.patch | 25 ++++++
debian/patches/series | 3 +
debian/qtltools-example.install | 3 +
debian/qtltools.install | 1 +
debian/qtltools.manpages | 1 +
debian/rules | 16 ++++
debian/source/format | 1 +
debian/source/include-binaries | 7 ++
debian/tests/control | 2 +
debian/tests/run-sample-analysis | 57 ++++++++++++
debian/upstream.docs/README | 24 +++++
debian/upstream.docs/genes.50percent.chr22.bed.gz | Bin 0 -> 1230243 bytes
.../upstream.docs/genes.50percent.chr22.bed.gz.tbi | Bin 0 -> 4634 bytes
debian/upstream.docs/genes.covariates.pc50.txt.gz | Bin 0 -> 73826 bytes
debian/upstream.docs/genes.simulated.chr22.bed.gz | Bin 0 -> 1910444 bytes
.../upstream.docs/genes.simulated.chr22.bed.gz.tbi | Bin 0 -> 4719 bytes
debian/upstream.docs/genotypes.chr22.vcf.gz | Bin 0 -> 10541195 bytes
debian/upstream.docs/genotypes.chr22.vcf.gz.tbi | Bin 0 -> 27269 bytes
debian/upstream/metadata | 9 ++
debian/watch | 3 +
27 files changed, 425 insertions(+)
diff --git a/debian/QTLtools.1 b/debian/QTLtools.1
new file mode 100644
index 0000000..d1f0d61
--- /dev/null
+++ b/debian/QTLtools.1
@@ -0,0 +1,100 @@
+.\"
+.TH QTLtools "1" "November 2016" "1.0"
+.SH NAME
+QTLtools \- Tool set for molecular QTL discovery and analysis
+.SH SYNOPSIS
+.B QTLtools [\fImode\fR] [\fIoptions\fR]
+.SH DESCRIPTION
+QTLtools is a tool set for molecular QTL discovery and analysis.
+It allows user to go from the raw sequence data to collection of molecular
+Quantitative Trait Loci (QTLs) in few easy-to-perform steps.
+.SH MODE
+.TP
+\fBbamstat\fR
+Calculate basic QC metrics for BAM/SAM.
+.br
+To check the quality of some sequence data by counting the number of reads mapped to the reference genome and falling within a reference annotation.
+.TP
+\fBmatch\fR
+Match VCF genotypes to BAM/SAM file.
+.br
+To ensure good match between the sequence and genotype data.
+This is useful to detect sample mislabeling, contamination or PCR amplification biases.
+.TP
+\fBquan\fR
+Quantification mode.
+.br
+To quantify exon and gene expression levels given a reference annotation such as GENCODE.
+.TP
+\fBpca\fR
+Calculate principal components for a BED/VCF/BCF file.
+.br
+To perform Principal Component Analysis (PCA) on genotype or molecular phenotype data.
+.TP
+\fBcis\fR
+cis QTL analysis.
+.br
+To map molecular Quantitative Trait Loci (mQTLs) in cis (i.e. proximal to the phenotype).
+This mode extends FastQTL by including two additional options: (i) to study groups of phenotypes such as genes containing multiple exons or (ii) to perform conditional analysis in order to discover multiple mQTLs per phenotype.
+.TP
+\fBtrans\fR
+trans QTL analysis.
+.br
+To map QTLs in trans.
+This can be done either using a full permutation scheme or with a much quicker approximation.
+.TP
+\fBfdensity\fR
+Functional density around QTLs.
+.br
+To measure the density of functional annotations around the QTL locations.
+Useful to look at the degree of overlap between QTLs and functional annotations.
+.TP
+\fBfenrich\fR
+Functional enrichment for QTLs.
+.br
+To measure how QTLs are enriched in any given functional annotations.
+.TP
+\fBrtc\fR
+Regulatory Trait Concordance analysis.
+.br
+To co-localize collections of QTLs with collection of GWAS hits.
+
+.SH OPTIONS
+.TP
+\fB\-\-help\fR
+.br
+Print help about options for the selected mode.
+
+.SH EXAMPLE
+
+\fBQTLtools\fR \fBbamstat\fR --help
+
+\fBQTLtools\fR \fBbamstat\fR --bam HG00381.chr22.bam --bed gencode.v19.exon.chr22.bed.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt
+.br
+\fBQTLtools\fR \fBmatch\fR --bam HG00381.chr22.bam --vcf genotypes.chr22.vcf.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt
+.br
+\fBQTLtools\fR \fBquan\fR --bam HG00381.chr22.bam --gtf gencode.v19.annotation.chr22.gtf.gz --samples HG00381 --out-prefix HG00381 --filter-mapping-quality 150 --filter-mismatch 5 --filter-mismatch-total 5 --rpkm --no-merge
+.br
+\fBQTLtools\fR \fBpca\fR --bed genes.50percent.chr22.bed.gz --scale --center --out genes.50percent.chr22
+.br
+\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --nominal 0.01 --region chr22:17000000-18000000 --out nominals.txt
+.br
+\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --permute 1000 --region chr22:17000000-18000000 --out permutations.txt
+.br
+\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --mapping permutations_all.thresholds.txt --chunk 12 16 --out conditional_12_16.txt
+.br
+\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --nominal --threshold 1e-5 --out trans.nominal
+.br
+\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --sample 1000 --normal --out trans.sample
+.br
+\fBQTLtools\fR \fBfdensity\fR --qtl results.genes.significant.bed --bed TFs.encode.bed.gz --out density.TF.around.QTL.txt
+.br
+\fBQTLtools\fR \fBfenrich\fR --qtl results.genes.significant.bed --tss results.genes.quantified.bed --bed TFs.encode.bed.gz --out enrichement.QTL.in.TF.txt
+.br
+\fBQTLtools\fR \fBrtc\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --hotspot hotspots_b37_hg19.bed --gwas-cis GWAS.b37.txt permutations_all.significant.txt --normal --out rtc_results.txt
+.br
+
+.SH SEE ALSO
+.BR https://qtltools.github.io/qtltools/
+.SH AUTHOR
+QTLtools was written by Olivier Delaneau, Halit Ongen and Manolis Dermitzakis.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..8fe8668
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+qtltools (1.0+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release. (Closes: #XXXXXX)
+
+ -- Dylan Aïssi <bob.dybian at gmail.com> Mon, 17 Oct 2016 23:22:20 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..f5da60f
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,42 @@
+Source: qtltools
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
+Build-Depends: debhelper (>= 10),
+ libblas-dev,
+ libboost-iostreams-dev,
+ libboost-program-options-dev,
+ libbz2-dev,
+ libeigen3-dev,
+ libgsl-dev,
+ libhts-dev,
+ r-mathlib,
+ zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/git/debian-med/qtltools.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/qtltools.git
+Homepage: https://qtltools.github.io/qtltools/
+
+Package: qtltools
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: qtltools-example
+Description: Tool set for molecular QTL discovery and analysis
+ QTLtools is a tool set for molecular QTL discovery and analysis.
+ It allows user to go from the raw sequence data to collection of molecular
+ Quantitative Trait Loci (QTLs) in few easy-to-perform steps.
+
+Package: qtltools-example
+Section: doc
+Architecture: all
+Multi-Arch: foreign
+Depends: ${misc:Depends}
+Enhances: qtltools
+Description: Tool set for molecular QTL discovery and analysis - example
+ QTLtools is a tool set for molecular QTL discovery and analysis.
+ It allows user to go from the raw sequence data to collection of molecular
+ Quantitative Trait Loci (QTLs) in few easy-to-perform steps.
+ .
+ This package provides example data to work with QTLtools.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..fd5b8e6
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,34 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: QTLtools
+Upstream-Contact: Olivier Delaneau <olivier.delaneau at gmail.com>
+Source: https://qtltools.github.io/qtltools/
+Comment: Exclude embedded Eigen and some other stuff.
+Files-Excluded: bin
+ lib/Eigen
+ obj
+
+Files: *
+Copyright: 2016 Olivier Delaneau, Halit Ongen and Emmanouil T. Dermitzakis
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2016 Dylan Aïssi <bob.dybian at gmail.com>
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 3 can be found in `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/patches/Correct_Eigen_include.patch b/debian/patches/Correct_Eigen_include.patch
new file mode 100644
index 0000000..383e8b3
--- /dev/null
+++ b/debian/patches/Correct_Eigen_include.patch
@@ -0,0 +1,53 @@
+Author: Dylan Aïssi
+Description: Correct include in order to use eigen from Debian repository.
+Last-Update: 2016-11-07
+Forwarded: not-needed
+
+--- a/lib/OTools/residualizer.h
++++ b/lib/OTools/residualizer.h
+@@ -33,8 +33,8 @@
+ #include <string>
+
+ //EIGEN INCLUDES
+-#include <Eigen/Dense>
+-#include <Eigen/LU>
++#include <eigen3/Eigen/Dense>
++#include <eigen3/Eigen/LU>
+
+ //EIGEN NAMESPACE
+ using namespace Eigen;
+--- a/lib/OTools/pca.h
++++ b/lib/OTools/pca.h
+@@ -21,8 +21,8 @@
+ #include <string>
+
+ //EIGEN INCLUDES
+-#include <Eigen/Dense>
+-#include <Eigen/SVD>
++#include <eigen3/Eigen/Dense>
++#include <eigen3/Eigen/SVD>
+ #include <iterator>
+
+ //EIGEN NAMESPACE
+--- a/src/mode_pca/pca_pca.h
++++ b/src/mode_pca/pca_pca.h
+@@ -18,7 +18,7 @@
+
+ #include <vector>
+ #include <string>
+-#include "Eigen/Dense"
++#include <eigen3/Eigen/Dense>
+ #include "../common/data.h"
+
+ class Pca {
+--- a/src/mode_pca/pca_pca.cpp
++++ b/src/mode_pca/pca_pca.cpp
+@@ -16,7 +16,7 @@
+ #include "pca_pca.h"
+ #include <iostream>
+ #include <iterator>
+-#include "Eigen/SVD"
++#include <eigen3/Eigen/SVD>
+
+
+ using namespace std;
diff --git a/debian/patches/Makefile_config.patch b/debian/patches/Makefile_config.patch
new file mode 100644
index 0000000..8b49aaa
--- /dev/null
+++ b/debian/patches/Makefile_config.patch
@@ -0,0 +1,38 @@
+Author: Dylan Aïssi
+Description: Configure the makefile for Debian packaging.
+Last-Update: 2016-11-02
+Forwarded: not-needed
+
+--- a/Makefile
++++ b/Makefile
+@@ -32,7 +32,7 @@
+ VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
+
+ #DEFAULT VERSION (I.E. UNIGE DESKTOP RELEASE VERSION)
+-all: default
++all: debian
+
+ #DEFAULT RELEASE VERSION
+ default: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)
+@@ -145,6 +145,14 @@
+ mac-dbg: LDFLAG=$(LDFLAG_DBG) -L /opt/local/lib
+ mac-dbg: $(BFILE)
+
++#DEBIAN PACKAGE VERSION
++debian: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN) $(CXXFLAGS) $(CPPFLAGS)
++debian: IFLAG=-Ilib/OTools -Ilib
++debian: LIB_FILES=-lRmath -lhts -lboost_iostreams -lboost_program_options
++debian: LDFLAG=$(LDFLAG_REL) $(LDFLAGS)
++debian: LIB_FLAGS=-lz -lgsl -lblas -lbz2 -lm -lpthread
++debian: $(BFILE)
++
+ #COMPILATION RULES
+ $(BFILE): $(OFILE)
+ $(CXX) $^ $(LIB_FILES) -o $@ $(LIB_FLAGS) $(LDFLAG)
+@@ -242,4 +250,4 @@
+ clean-fdensity:
+ rm -f obj/fdensity_*.o $(BFILE)
+
+-
+\ No newline at end of file
++
diff --git a/debian/patches/Spelling_error.patch b/debian/patches/Spelling_error.patch
new file mode 100644
index 0000000..535de25
--- /dev/null
+++ b/debian/patches/Spelling_error.patch
@@ -0,0 +1,25 @@
+Author: Dylan Aïssi
+Description: Fix spelling error.
+Last-Update: 2016-11-16
+Forwarded: https://github.com/qtltools/qtltools/pull/3
+
+--- a/src/mode_fdensity/fdensity_main.cpp
++++ b/src/mode_fdensity/fdensity_main.cpp
+@@ -30,7 +30,7 @@
+
+ boost::program_options::options_description opt_parameters ("\x1B[32mParameters\33[0m");
+ opt_parameters.add_options()
+- ("window", boost::program_options::value< int >()->default_value(1000000), "Window size arround TSS in bp.")
++ ("window", boost::program_options::value< int >()->default_value(1000000), "Window size around TSS in bp.")
+ ("bin", boost::program_options::value< int >()->default_value(1000), "Bin size in bp.");
+
+ D.option_descriptions.add(opt_files).add(opt_parameters);
+@@ -49,7 +49,7 @@
+ //---------------------
+ // 3. PRINT HELP/HEADER
+ //---------------------
+- vrb.ctitle("ANNOTATION DENSITY ARROUND QTLs");
++ vrb.ctitle("ANNOTATION DENSITY AROUND QTLs");
+ if (D.options.count("help")) {
+ cout << D.option_descriptions << endl;
+ exit(EXIT_SUCCESS);
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..21f5429
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+Makefile_config.patch
+Correct_Eigen_include.patch
+Spelling_error.patch
diff --git a/debian/qtltools-example.install b/debian/qtltools-example.install
new file mode 100644
index 0000000..014bbda
--- /dev/null
+++ b/debian/qtltools-example.install
@@ -0,0 +1,3 @@
+debian/tests/run-sample-analysis /usr/share/doc/qtltools/examples/
+debian/upstream.docs/examples.tar.xz /usr/share/doc/qtltools/examples/
+script/* /usr/share/doc/qtltools/examples/
diff --git a/debian/qtltools.install b/debian/qtltools.install
new file mode 100644
index 0000000..2c63906
--- /dev/null
+++ b/debian/qtltools.install
@@ -0,0 +1 @@
+bin/QTLtools usr/bin/
diff --git a/debian/qtltools.manpages b/debian/qtltools.manpages
new file mode 100644
index 0000000..bade48c
--- /dev/null
+++ b/debian/qtltools.manpages
@@ -0,0 +1 @@
+debian/QTLtools.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..36a8c96
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ mkdir -p $(CURDIR)/obj/
+ mkdir -p $(CURDIR)/bin/
+ dh_auto_build
+
+override_dh_install:
+ cd debian/upstream.docs && find -type f | LC_ALL=C sort | tar -T - --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner -Jcvf examples.tar.xz
+ dh_install
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..46ebe02
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
\ No newline at end of file
diff --git a/debian/source/include-binaries b/debian/source/include-binaries
new file mode 100644
index 0000000..f671e9e
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1,7 @@
+debian/upstream.docs/genes.50percent.chr22.bed.gz
+debian/upstream.docs/genes.50percent.chr22.bed.gz.tbi
+debian/upstream.docs/genes.covariates.pc50.txt.gz
+debian/upstream.docs/genes.simulated.chr22.bed.gz
+debian/upstream.docs/genes.simulated.chr22.bed.gz.tbi
+debian/upstream.docs/genotypes.chr22.vcf.gz
+debian/upstream.docs/genotypes.chr22.vcf.gz.tbi
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..3403f8a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: run-sample-analysis
+Depends: @
diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
new file mode 100644
index 0000000..a522749
--- /dev/null
+++ b/debian/tests/run-sample-analysis
@@ -0,0 +1,57 @@
+#!/bin/sh -e
+# http://dep.debian.net/deps/dep8/
+# Autopkgtest: Test if QTLtools run analysis correctly
+# Author: Dylan Aïssi <bob.dybian at gmail.com>
+# Last-Update: 2016-11-16
+
+pkg=qtltools
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
+
+tar Jxvf $ADTTMP/examples.tar.xz
+
+# Mode PCA
+QTLtools pca \
+ --bed genes.50percent.chr22.bed.gz \
+ --scale \
+ --center \
+ --out genes.50percent.chr22
+
+# Mode cis - nominal pass
+QTLtools cis \
+ --vcf genotypes.chr22.vcf.gz \
+ --bed genes.50percent.chr22.bed.gz \
+ --cov genes.covariates.pc50.txt.gz \
+ --nominal 0.01 \
+ --region chr22:17000000-18000000 \
+ --out nominals.txt
+
+# Mode cis - permutations pass
+QTLtools cis \
+ --vcf genotypes.chr22.vcf.gz \
+ --bed genes.50percent.chr22.bed.gz \
+ --cov genes.covariates.pc50.txt.gz \
+ --permute 1000 \
+ --region chr22:17000000-18000000 \
+ --out permutations.txt
+
+# Mode trans - full pass
+QTLtools trans \
+ --vcf genotypes.chr22.vcf.gz \
+ --bed genes.simulated.chr22.bed.gz \
+ --nominal \
+ --threshold 1e-5 \
+ --out trans.nominal
+
+# Mode trans - approximate pass
+QTLtools trans \
+ --vcf genotypes.chr22.vcf.gz \
+ --bed genes.simulated.chr22.bed.gz \
+ --sample 1000 \
+ --normal \
+ --out trans.sample
+
+rm -f $ADTTMP/*
diff --git a/debian/upstream.docs/README b/debian/upstream.docs/README
new file mode 100644
index 0000000..ef76ae3
--- /dev/null
+++ b/debian/upstream.docs/README
@@ -0,0 +1,24 @@
+# Author: Dylan Aïssi <bob.dybian at gmail.com>
+# Last-Update: 2016-11-16
+# These files were downloaded from http://jungle.unige.ch/QTLtools_examples/
+
+# Needed for autopkgtest
+ wget http://jungle.unige.ch/QTLtools_examples/genes.50percent.chr22.bed.gz
+ wget http://jungle.unige.ch/QTLtools_examples/genes.50percent.chr22.bed.gz.tbi
+ wget http://jungle.unige.ch/QTLtools_examples/genotypes.chr22.vcf.gz
+ wget http://jungle.unige.ch/QTLtools_examples/genotypes.chr22.vcf.gz.tbi
+ wget http://jungle.unige.ch/QTLtools_examples/genes.covariates.pc50.txt.gz
+ wget http://jungle.unige.ch/QTLtools_examples/genes.simulated.chr22.bed.gz
+ wget http://jungle.unige.ch/QTLtools_examples/genes.simulated.chr22.bed.gz.tbi
+
+## Not needed for autopkgtest
+# wget http://jungle.unige.ch/QTLtools_examples/GWAS.b37.txt
+# wget http://jungle.unige.ch/QTLtools_examples/HG00381.chr22.bam # ~ 45Mo
+# wget http://jungle.unige.ch/QTLtools_examples/HG00381.chr22.bam.bai
+# wget http://jungle.unige.ch/QTLtools_examples/TFs.encode.bed.gz
+# wget http://jungle.unige.ch/QTLtools_examples/exons.50percent.chr22.bed.gz # ~ 7Mo
+# wget http://jungle.unige.ch/QTLtools_examples/exons.50percent.chr22.bed.gz.tbi
+# wget http://jungle.unige.ch/QTLtools_examples/gencode.v19.annotation.chr22.gtf.gz
+# wget http://jungle.unige.ch/QTLtools_examples/gencode.v19.exon.chr22.bed.gz
+# wget http://jungle.unige.ch/QTLtools_examples/hotspots_b37_hg19.bed
+# wget http://jungle.unige.ch/QTLtools_examples/results.genes.full.txt.gz
diff --git a/debian/upstream.docs/genes.50percent.chr22.bed.gz b/debian/upstream.docs/genes.50percent.chr22.bed.gz
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diff --git a/debian/upstream.docs/genes.covariates.pc50.txt.gz b/debian/upstream.docs/genes.covariates.pc50.txt.gz
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diff --git a/debian/upstream.docs/genes.simulated.chr22.bed.gz b/debian/upstream.docs/genes.simulated.chr22.bed.gz
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diff --git a/debian/upstream/metadata b/debian/upstream/metadata
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+++ b/debian/upstream/metadata
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+Contact: Olivier Delaneau <olivier.delaneau at gmail.com>
+Name: QTLtools
+Reference:
+ - Author: Olivier Delaneau and Halit Ongen and Andrew Anand Brown and Alexandre Fort and Nikolaos Panousis and Emmanouil Dermitzakis
+ Title: "A complete tool set for molecular QTL discovery and analysis"
+ Year: 2016
+ DOI: 10.1101/068635
+ URL: http://biorxiv.org/content/early/2016/08/10/068635
+ eprint: http://biorxiv.org/content/early/2016/08/10/068635.full.pdf
diff --git a/debian/watch b/debian/watch
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+version=3
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://qtltools.github.io/qtltools/pages/basic_install.html https://qtltools.github.io/qtltools/binaries/QTLtools_(\d\S*)_source\.tar\.gz
--
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