.gitignore

+*.pyc

debian/changelog

-metabit (0.0+20170220-1) UNRELEASED; urgency=medium
+metabit (0.0+git20170725.24cb3ee+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
 
- -- Andreas Tille <tille@debian.org>  Mon, 25 Jul 2016 14:09:29 +0200
+ -- Andreas Tille <tille@debian.org>  Wed, 11 Sep 2019 10:44:49 +0200

debian/compat

-9

debian/control

@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper-compat (= 12),
                python-all,
                dh-python,
-               python-markdown,
+               markdown,
                bowtie2
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/metabit.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/metabit.git
+Standards-Version: 4.4.0
+Vcs-Browser: https://salsa.debian.org/med-team/metabit
+Vcs-Git: https://salsa.debian.org/med-team/metabit.git
 Homepage: https://bitbucket.org/Glouvel/metabit/wiki/
 
 Package: metabit
@@ -21,7 +21,7 @@ Depends: ${python:Depends},
          r-base-core,
          metaphlan2,
          python-pysam,
-         libpicard-java (>= 1.138+dfsg.1),
+         libpicard-java,
          samtools,
          radiant,
          bedtools,
@@ -43,7 +43,7 @@ Description: analysing microbial profiles from high-throughput sequencing shotgu
 
 Package: metabit-examples
 Architecture: all
-Depends: ${misc:Depends},
+Depends: ${misc:Depends}
 Recommends: metabit
 Description: example data for MetaBIT pipeline for high-throughput sequencing data
  MetaBIT is an integrative and automated metagenomic pipeline for

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: metaBIT
 Source: https://bitbucket.org/Glouvel/metabit/downloads
 Files-Excluded: */pypeline/yaml

debian/get-orig-source

-#!/bin/sh -e
-
-COMPRESS=xz
-
-NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'`
-
-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 *
-git clone --quiet https://bitbucket.org/Glouvel/metabit.git
-cd $NAME
-VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d`
-# for esthetical reasons set file timestamps (if git-restore-mtime is installed)
-git restore-mtime || true
-cd ..
-TARDIR=${NAME}-${VERSION}
-mv ${NAME} ${TARDIR}
-rm -rf ${TARDIR}/.git*
-find ${TARDIR} -path */pypeline/yaml | xargs rm -rf
-
-GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
-rm -rf ${TARDIR}

debian/rules

@@ -3,19 +3,19 @@
 # DH_VERBOSE := 1
 export LC_ALL=C.UTF-8
 
-DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-RDIR := debian/$(DEBPKGNAME)/usr/lib/R/site-library/metabit
+include /usr/share/dpkg/default.mk
+RDIR := debian/$(DEB_SOURCE)/usr/lib/R/site-library/metabit
 
 %:
 	dh $@  --with python2
 
 override_dh_auto_build:
 	dh_auto_build
-	markdown_py -f README.html README.md
+	markdown README.md > README.html
 
 override_dh_link:
 	dh_link
 	mkdir -p $(RDIR)
-	for r in debian/$(DEBPKGNAME)/usr/share/metabit/nodes/tools/statax_Rmodule/*.R ; do \
+	for r in debian/$(DEB_SOURCE)/usr/share/metabit/nodes/tools/statax_Rmodule/*.R ; do \
 		ln -s `echo $$r | sed 's:.*/usr:../../../..:'` $(RDIR) ; \
 	done

debian/watch

-# version=3
-# upstream has not proper versioning
+version=4
 
+opts="mode=git,pretty=0.0+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+    https://bitbucket.org/Glouvel/metabit.git HEAD

metaBIT.py

@@ -36,7 +36,8 @@ _tools = {"filterMetaphlan":  ["nodes", "tools", "filterMetaphlan.py"],
           "doPcoa":           ["nodes", "tools", "statax_Rmodule", "doPcoa.R"],
           "doClust":          ["nodes", "tools", "statax_Rmodule", "doClust.R"],
           "doDiv":            ["nodes", "tools", "statax_Rmodule", "doDiv.R"],
-          "doHeatmap":        ["nodes", "tools", "statax_Rmodule", "doHeatmap.R"]}
+          "doHeatmap":        ["nodes", "tools", "statax_Rmodule", "doHeatmap.R"],
+          "doBarplot":        ["nodes", "tools", "statax_Rmodule", "doBarplot.R"]}
 
 
 def run(config, args):