debian/0000755000000000000000000000000012064431440007164 5ustar debian/watch0000644000000000000000000000017111701421157010215 0ustar version=3 opts="uversionmangle=s/-/./" \ https://github.com/taoliu/MACS/downloads /downloads/.*/MACS/MACS-(.*)\.tar\.gz debian/copyright0000644000000000000000000000116612061606703011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: MACS Upstream-Contact: Tao Liu , Yong Zhang Source: https://github.com/taoliu/MACS/downloads Files: * Copyright: 2008 Zhang et al. License: Artistic The complete text of the Artistic License can be found in /usr/share/common-licenses/Artistic Files: debian/* Copyright: 2011 Tim Booth , Andreas Tille License: Artistic The complete text of the Artistic License can be found in /usr/share/common-licenses/Artistic debian/changelog0000644000000000000000000000234312064424373011047 0ustar macs (2.0.9.1-1) unstable; urgency=low * Initial upload to Debian (Closes: #696331) * debian/control: - Adaptations to Debian Med team maintenance - X-Python-Version: >=2.7 because build fails for Python 2.6 - Standards-Version: 3.9.4 (no changes needed) - Priority: optional * debian/watch: Removed useless comments * debian/README.*: Removed unused dh-make templates * debian/copyright: Added some missing information * debian/rules: - Removed useless dh-make comment - use dh_python2 - use help2man to create manpages * debhelper 9 (control+compat) -- Andreas Tille Wed, 19 Dec 2012 19:32:44 +0100 macs (2.0.9.1-1ubuntu3) lucid; urgency=low * Fix typo in debian/rules -- Tim Booth Thu, 05 Jan 2012 18:22:46 +0000 macs (2.0.9.1-1ubuntu2) lucid; urgency=low * Package for PPA * Packaged from version 2.0.9-1 * Changed debian/rules to override dh_auto_clean to remove *.c files -- H. Soon Gweon (Key for package building) Thu, 05 Jan 2012 13:10:02 +0000 macs (2.0.9.1-1) unstable; urgency=low * Initial packaging attempt -- H. Soon Gweon (Key for package building) Thu, 05 Jan 2012 10:52:22 +0000 debian/source/0000755000000000000000000000000011701413206010461 5ustar debian/source/format0000644000000000000000000000001411701410232011663 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212064352331010363 0ustar 9 debian/rules0000755000000000000000000000407212064370625010256 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for macs # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- ) mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/ %: dh $@ --with python2 override_dh_auto_clean: dh_auto_clean find -type f -name '*.c' -exec rm -f '{}' ';' override_dh_auto_install: dh_auto_install # try to create man pages whereever possible mkdir -p $(mandir) export PYTHONPATH=$(CURDIR)/build/`ls build | grep ^lib\. | head -n 1` ; \ export PATH=$(CURDIR)/build/`ls build | grep ^scripts- | head -n 1`:$${PATH} ; \ help2man --no-info --name='Fine-tuning script to call broad peaks from a single bedGraph track for scores' \ --version-string="$(version)" \ bdgbroadcall > $(mandir)/bdgbroadcall.1 ; \ help2man --no-info --name='Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias' \ --version-string="$(version)" \ bdgcmp > $(mandir)/bdgcmp.1 ; \ help2man --no-info --name='Naive call differential peaks from 4 bedGraph tracks for scores' \ --version-string="$(version)" \ bdgdiff > $(mandir)/bdgdiff.1 ; \ help2man --no-info --name='Naive call peaks from a single bedGraph track for scores' \ --version-string="$(version)" \ bdgpeakcall > $(mandir)/bdgpeakcall.1 ; \ help2man --no-info --name='Filter duplicate reads depending on sequencing depth' \ --version-string="$(version)" \ filterdup > $(mandir)/filterdup.1 ; \ help2man --no-info --name='Model-based Analysis for ChIP-Sequencing' \ --version-string="$(version)" \ macs2 > $(mandir)/macs2.1 ; \ help2man --no-info --name='Differential Analysis for ChIP-Sequencing' \ --version-string="$(version)" \ macs2diff > $(mandir)/macs2diff.1 ; \ help2man --no-info --name='Random sample certain number/percentage of tags' \ --version-string="$(version)" \ randsample > $(mandir)/randsample.1 debian/control0000644000000000000000000000250112064364713010575 0ustar Source: macs Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Tim Booth , H. Soon Gweon , Andreas Tille Build-Depends: debhelper (>= 9), cython (>= 0.15), python-dev (>= 2.7), help2man, python-numpy Standards-Version: 3.9.4 X-Python-Version: >=2.7 Homepage: https://github.com/taoliu/MACS/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/macs/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/macs/trunk/ Package: macs Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy Description: Model-based Analysis of ChIP-Seq on short reads sequencers MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples. debian/docs0000644000000000000000000000000711701410232010025 0ustar README