This is an automated email from the git hooks/post-receive script. jssoares-guest pushed a commit to branch master in repository iva.
commit 7ea672c7758cac44f441057ca135c39faac6c315 Author: Jorge Soares <[email protected]> Date: Tue Nov 18 11:15:35 2014 +0000 now commited debian folder --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 34 ++++++++++++++++++++++++++++++++ debian/copyright | 11 +++++++++++ debian/createmanpages | 16 +++++++++++++++ debian/get-orig-source | 45 +++++++++++++++++++++++++++++++++++++++++++ debian/inject-into-alioth-git | 18 +++++++++++++++++ debian/rules | 43 +++++++++++++++++++++++++++++++++++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++++ debian/watch | 2 ++ 11 files changed, 188 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..81bd10d --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +iva (0.10-1) UNRELEASED; urgency=low + + * Initial release (Closes: #1234) + + -- Jorge Soares <[email protected]> Tue, 18 Nov 2014 08:56:54 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..742e253 --- /dev/null +++ b/debian/control @@ -0,0 +1,34 @@ +Source: iva +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]>, + Jorge Soares <[email protected]> +Build-Depends: debhelper (>= 9), + python3, + python3-setuptools, + python3-numpy, + python3-nose, + python3-networkx, + python-pysam, + fastaq, + samtools, + mummer, + smalt, + trimmomatic, + help2man +Standards-Version: 3.9.6 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/iva.git +Homepage: https://github.com/sanger-pathogens/iva + +Package: iva +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Assemble virus genomes that have no repeat sequences, using Illumina read pairs + IVA is a de novo assembler designed to assemble virus genomes that have no + repeat sequences, using Illumina read pairs sequenced from mixed populations + at extremely high depth. + . + IVA's main algorithm works by iteratively extending contigs using aligned read pairs. + Its input can be just read pairs, or additionally you can provide an existing set of + contigs to be extended. Alternatively, it can take reads together with a reference sequence. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..c76e73d --- /dev/null +++ b/debian/copyright @@ -0,0 +1,11 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: <pkg> +Source: <path_to_download> + +Files: * +Copyright: © 20xx-20yy <upstream> +License: <license> + +Files: debian/* +Copyright: © 2014 maintainername <[email protected]> +License: <license> diff --git a/debian/createmanpages b/debian/createmanpages new file mode 100755 index 0000000..febcd91 --- /dev/null +++ b/debian/createmanpages @@ -0,0 +1,16 @@ +#!/bin/sh +MANDIR=debian +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` + +help2man --no-info --no-discard-stderr --help-option=" " \ + --name='<optional description of the program>' \ + --version-string="$VERSION" <programname> > $MANDIR/<programname>.1 + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT + diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..e486809 --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,45 @@ +#!/bin/sh +# if you need to repack for whatever reason you can +# use this script via uscan or directly +# +# FIXME: currently the code is not conform to Debian Policy +# http://www.debian.org/doc/debian-policy/ch-source.html +# "get-orig-source (optional)" +# This target may be invoked in any directory, ... +# --> currently it is assumed the script is called in the +# source directory featuring the debian/ dir + +COMPRESS=xz + +set -e +NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` + +if ! echo $@ | grep -q upstream-version ; then + VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` + uscan --force-download +else + VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"` + if echo "$VERSION" | grep -q "upstream-version" ; then + echo "Unable to parse version number" + exit + fi +fi + +TARDIR=${NAME}-${VERSION} +mkdir -p ../tarballs +cd ../tarballs +# need to clean up the tarballs dir first because upstream tarball might +# contain a directory with unpredictable name +rm -rf * +tar -xaf ../${TARDIR}.tar.gz + +UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d` +if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then + mv "${UPSTREAMTARDIR}" "${TARDIR}" +fi + +# Remove useless binaries +# ... do something which needs to be done ... + +GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}" +rm -rf ${TARDIR} diff --git a/debian/inject-into-alioth-git b/debian/inject-into-alioth-git new file mode 100755 index 0000000..02c2222 --- /dev/null +++ b/debian/inject-into-alioth-git @@ -0,0 +1,18 @@ +#!/bin/sh -e + +echo "Please verify whether this script is obsoleted by gbp-create-remote-repo !" + +# This script implements the "Git tips" given here +# http://debian-med.alioth.debian.org/docs/policy.html#git-tips +# Use it with caution since it is less testet + +DEBPKGNAME=`dpkg-parsechangelog | awk '/^Source:/ {print $2}'` +SHORTDESC=`grep "^Description: " debian/control | head -n 1 | sed 's/^Description: //'` +VCSGIT=`grep "^Vcs-Git: " debian/control | sed -e 's/^Vcs-Git: //' -e 's#git://anonscm.debian.org/#ssh://git.debian.org/git/#'` +DIRatALIOTH=`echo $VCSGIT | sed -e 's#ssh://git.debian.org/git/#/git/#' -e 's#/[^/]\+\.git##'` + +ssh git.debian.org "cd $DIRatALIOTH; ./setup-repository $DEBPKGNAME '$SHORTDESC'" +git remote add origin $VCSGIT +git push origin master +git push --all --set-upstream +git push --tags diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..cdfc675 --- /dev/null +++ b/debian/rules @@ -0,0 +1,43 @@ +#!/usr/bin/make -f + +export DH_VERBOSE := 1 +export PYBUILD_NAME=fastaq + +# some helpful variables - uncomment them if needed +# shamelessly stolen from http://jmtd.net/log/awk/ +#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') +#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') +#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}') +#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') +#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf) +#GIT_TAG := $(subst ~,_,$(VERSION)) + +# alternatively to manually set those variables you can +# include /usr/share/cdbs/1/rules/buildvars.mk +# and use what is set there. Any hint whether dh might set variables in +# a similar manner are welcome. + +mandir := $(CURDIR)/debian/man +debfolder := $(CURDIR)/debian + +%: + dh $@ --with python3 --buildsystem=pybuild + +override_dh_auto_build: + dh_python3 + dh_auto_build + mkdir $(CURDIR)/doc + cd $(CURDIR)/doc + +override_dh_auto_clean: + rm -rf build .pybuild + rm -rf $(mandir) + +# override_dh_installman: +# mkdir -p $(mandir) +# $(debfolder)/usage_to_man +# dh_installman -- + + +#get-orig-source: +# . debian/get-orig-source diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..d8b5812 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: + Title: + Journal: + Year: + Volume: + Number: + Pages: + DOI: + PMID: + URL: + eprint: diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..922a950 --- /dev/null +++ b/debian/watch @@ -0,0 +1,2 @@ +version=3 +https://github.com/sanger-pathogens/iva/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) \ No newline at end of file -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/iva.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
