From 91f4887d1b19c44d68a2b19f0abee56de3dbb8ea Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Fri, 11 Jun 2010 11:11:41 -0700 Subject: [PATCH] Imported Debian patch 0.2-1~karmic --- debian/README.source | 9 +++++++ debian/changelog | 5 ++++ debian/compat | 1 + debian/control | 16 +++++++++++ debian/copyright | 48 +++++++++++++++++++++++++++++++++ debian/pycompat | 1 + debian/pysam.debhelper.log | 33 +++++++++++++++++++++++ debian/pysam.postinst.debhelper | 9 +++++++ debian/pysam.preinst.debhelper | 8 ++++++ debian/pysam.prerm.debhelper | 45 +++++++++++++++++++++++++++++++ debian/pysam.substvars | 4 +++ debian/rules | 13 +++++++++ debian/source/format | 1 + debian/watch | 10 +++++++ 14 files changed, 203 insertions(+) create mode 100644 debian/README.source create mode 100644 debian/changelog create mode 100644 debian/compat create mode 100644 debian/control create mode 100644 debian/copyright create mode 100644 debian/pycompat create mode 100644 debian/pysam.debhelper.log create mode 100644 debian/pysam.postinst.debhelper create mode 100644 debian/pysam.preinst.debhelper create mode 100644 debian/pysam.prerm.debhelper create mode 100644 debian/pysam.substvars create mode 100755 debian/rules create mode 100644 debian/source/format create mode 100644 debian/watch diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..575b3db --- /dev/null +++ b/debian/README.source @@ -0,0 +1,9 @@ +pysam for Debian +---------------- + + + + + + diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..daaa8af --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +pysam (0.2-1~karmic) karmic; urgency=low + + * Initial release + + -- Diane Trout Fri, 11 Jun 2010 11:11:41 -0700 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..7f8f011 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +7 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..4128d0f --- /dev/null +++ b/debian/control @@ -0,0 +1,16 @@ +Source: pysam +Section: science +Priority: extra +Maintainer: Diane Trout +Build-Depends: cdbs, debhelper (>= 7), python-all-dev (>= 2.3.5-11), python-central (>= 0.5.6), python-setuptools (>= 0.6b3), python-pyrex (>= 0.9.8), zlib1g-dev (>= 1.2.3) +Standards-Version: 3.8.4 +XS-Python-Version: >=2.5, <<2.7 +Homepage: http://code.google.com/p/pysam/ + +Package: python-pysam +Architecture: any +Depends: ${python:Depends}, ${shlibs:Depends}, ${misc:Depends} +XB-Python-Version: ${python:Versions} +Description: python module for reading and manipulating Samfiles + Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..c0ba128 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,48 @@ +This work was packaged for Debian by: + + Diane Trout on Fri, 11 Jun 2010 11:11:41 -0700 + + It was downloaded from http://code.google.com/p/pysam/ + +Upstream Author(s): + + andreas + Grant Belgard + martingoodson + gerton.lunter + bunbun68 + + +Copyright: + + Copyright (C) 2008-2009 Genome Research Ltd. + +License: + + The MIT License + + Copyright (c) 2008-2009 Genome Research Ltd. + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. + +The Debian packaging is: + + Copyright (C) 2010 Diane Trout + and is licensed under the MIT license + diff --git a/debian/pycompat b/debian/pycompat new file mode 100644 index 0000000..0cfbf08 --- /dev/null +++ b/debian/pycompat @@ -0,0 +1 @@ +2 diff --git a/debian/pysam.debhelper.log b/debian/pysam.debhelper.log new file mode 100644 index 0000000..bd3417d --- /dev/null +++ b/debian/pysam.debhelper.log @@ -0,0 +1,33 @@ +dh_installdirs +dh_installdirs +dh_installdocs +dh_installexamples +dh_installman +dh_installinfo +dh_installmenu +dh_installcron +dh_installinit +dh_installdebconf +dh_installemacsen +dh_installcatalogs +dh_installpam +dh_installlogrotate +dh_installlogcheck +dh_installchangelogs +dh_installudev +dh_lintian +dh_install +dh_link +dh_installmime +dh_pycentral +dh_strip +dh_compress +dh_fixperms +dh_makeshlibs +dh_installdeb +dh_perl +dh_shlibdeps +dh_gencontrol +dh_link +dh_md5sums +dh_builddeb diff --git a/debian/pysam.postinst.debhelper b/debian/pysam.postinst.debhelper new file mode 100644 index 0000000..b775d06 --- /dev/null +++ b/debian/pysam.postinst.debhelper @@ -0,0 +1,9 @@ +# Automatically added by dh_pycentral +rm -f /var/lib/pycentral/pysam.pkgremove +if which pycentral >/dev/null 2>&1; then + pycentral pkginstall pysam + if grep -qs '^pysam$' /var/lib/pycentral/delayed-pkgs; then + sed -i '/^pysam$/d' /var/lib/pycentral/delayed-pkgs + fi +fi +# End automatically added section diff --git a/debian/pysam.preinst.debhelper b/debian/pysam.preinst.debhelper new file mode 100644 index 0000000..a1830f3 --- /dev/null +++ b/debian/pysam.preinst.debhelper @@ -0,0 +1,8 @@ +# Automatically added by dh_pycentral +case "$1" in + install|upgrade) + mkdir -p /var/lib/pycentral + echo '# the presence of this file allows calling pkgremove on upgrade' \ + > /var/lib/pycentral/pysam.pkgremove +esac +# End automatically added section diff --git a/debian/pysam.prerm.debhelper b/debian/pysam.prerm.debhelper new file mode 100644 index 0000000..983e5a8 --- /dev/null +++ b/debian/pysam.prerm.debhelper @@ -0,0 +1,45 @@ +# Automatically added by dh_pycentral +case "$1" in remove|upgrade) + pkgremove=y +esac +if [ -f /var/lib/pycentral/pysam.pkgremove ] || [ -f /var/lib/pycentral/pkgremove ]; then + pkgremove=y +fi +if [ "$pkgremove" = y ]; then +if which python >/dev/null 2>&1 && which pycentral >/dev/null 2>&1; then + pycentral pkgremove pysam +else + flist=$(tempfile) + slist=$(tempfile) + dpkg -L pysam | tee $flist | \ + while read n; do + case "$n" in + /usr/share/pyshared/*) + n2=${n#/usr/share/pyshared/*} + case "$n" in + *.py) echo "p $n";; + *) [ -d "$n" ] && echo "d $n2" || echo "f $n2" + esac + ;; + *) continue + esac + done > $slist + if [ -s $slist ]; then + for d in /usr/lib/python[0-9].[0-9]/????-packages; do + case "$d" in */python2.1/*|*/python2.2/*) continue; esac + while read t n; do + case "$t" in + p) rm -f $d/$n $d/${n}[co];; + d) rmdir $d/$n 2>/dev/null || true;; + *) rm -f $d/$n + esac + done < $slist + done + fi + awk '/\/usr\/share\/pyshared/ {next} /\.py$/ {print $0"c\n" $0"o"}' $flist \ + | xargs -r rm -f >&2 + rm -f $flist $slist +fi +rm -f /var/lib/pycentral/pysam.pkgremove +fi +# End automatically added section diff --git a/debian/pysam.substvars b/debian/pysam.substvars new file mode 100644 index 0000000..0fb862c --- /dev/null +++ b/debian/pysam.substvars @@ -0,0 +1,4 @@ +python:Versions=2.6 +python:Depends=python (<< 2.7), python (>= 2.6), python-central (>= 0.6.11) +shlibs:Depends=libc6 (>= 2.7), zlib1g (>= 1:1.2.2) +misc:Depends= diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..2f0cc12 --- /dev/null +++ b/debian/rules @@ -0,0 +1,13 @@ +#!/usr/bin/make -f + +DEB_PYTHON_SYSTEM=pycentral + +clean:: + rm -f pysam/csamtools.c + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/python-distutils.mk + + +# Add here any variable or target overrides you need. +DEB_COMPRESS_EXCLUDE := .py diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +1.0 diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..704500f --- /dev/null +++ b/debian/watch @@ -0,0 +1,10 @@ +# Example watch control file for uscan +# Rename this file to "watch" and then you can run the "uscan" command +# to check for upstream updates and more. +# See uscan(1) for format + +# Compulsory line, this is a version 3 file +version=3 + +http://code.google.com/p/pysam/downloads/list pysam-(.*)\.tar\.gz + -- 2.30.2