[med-svn] [iva] 01/03: Imported Upstream version 0.10.0
Jorge Soares
jssoares-guest at moszumanska.debian.org
Tue Nov 18 11:15:54 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a commit to branch master
in repository iva.
commit c022089861aa497568811e9d13df6bf1e8ea6f26
Author: Jorge Soares <j.s.soares at gmail.com>
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 <j.s.soares at gmail.com> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Jorge Soares <j.s.soares at gmail.com>
-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 <maintainer at e.mail>
-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
--
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