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commit c022089861aa497568811e9d13df6bf1e8ea6f26 Author: Jorge Soares <[email protected]> Date: Tue Nov 18 11:14:06 2014 +0000 Imported Upstream version 0.10.0 --- .gitignore | 54 +++++++++++++++++++++++++++++++++++++++++++ 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 -- 12 files changed, 54 insertions(+), 188 deletions(-) diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..51cbe85 --- /dev/null +++ b/.gitignore @@ -0,0 +1,54 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +bin/ +build/ +develop-eggs/ +dist/ +eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.cache +nosetests.xml +coverage.xml + +# Translations +*.mo + +# Mr Developer +.mr.developer.cfg +.project +.pydevproject + +# Rope +.ropeproject + +# Django stuff: +*.log +*.pot + +# Sphinx documentation +docs/_build/ + diff --git a/debian/changelog b/debian/changelog deleted file mode 100644 index 0406b49..0000000 --- a/debian/changelog +++ /dev/null @@ -1,5 +0,0 @@ -iva (0.10.0-1) 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 deleted file mode 100644 index ec63514..0000000 --- a/debian/compat +++ /dev/null @@ -1 +0,0 @@ -9 diff --git a/debian/control b/debian/control deleted file mode 100644 index 742e253..0000000 --- a/debian/control +++ /dev/null @@ -1,34 +0,0 @@ -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 deleted file mode 100644 index c76e73d..0000000 --- a/debian/copyright +++ /dev/null @@ -1,11 +0,0 @@ -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 deleted file mode 100755 index febcd91..0000000 --- a/debian/createmanpages +++ /dev/null @@ -1,16 +0,0 @@ -#!/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 deleted file mode 100755 index e486809..0000000 --- a/debian/get-orig-source +++ /dev/null @@ -1,45 +0,0 @@ -#!/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 deleted file mode 100755 index 02c2222..0000000 --- a/debian/inject-into-alioth-git +++ /dev/null @@ -1,18 +0,0 @@ -#!/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 deleted file mode 100755 index cdfc675..0000000 --- a/debian/rules +++ /dev/null @@ -1,43 +0,0 @@ -#!/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 deleted file mode 100644 index 163aaf8..0000000 --- a/debian/source/format +++ /dev/null @@ -1 +0,0 @@ -3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata deleted file mode 100644 index d8b5812..0000000 --- a/debian/upstream/metadata +++ /dev/null @@ -1,12 +0,0 @@ -Reference: - Author: - Title: - Journal: - Year: - Volume: - Number: - Pages: - DOI: - PMID: - URL: - eprint: diff --git a/debian/watch b/debian/watch deleted file mode 100644 index 922a950..0000000 --- a/debian/watch +++ /dev/null @@ -1,2 +0,0 @@ -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
