debian/README.Source

+Mothur for Debian
+=================
+
 Hints for using ccache with mothur build
 -----------------------------------------
 
@@ -18,3 +21,20 @@ but note MPICXX which is hooking into the MPI compiler,
 which is not replaced by ccache.
 
  -- Tomasz Buchert <toma@buchert.pl>, Fri,  4 Sep 2015 10:28:58 +0200
+
+
+
+The MPI version was droped upstream
+-----------------------------------
+
+commit 1e5f8e2927fca338e659621ac24cd9166705c3a2 refs/tags/v1.37.0
+Author: Sarah Westcott <mothur.westcott@gmail.com>
+Date:   Wed Aug 19 12:16:49 2015 -0400
+
+    Removes MPI source code
+    
+    Issue #144
+    
+    The MPI version is slower and requires dual maintenance. No advantage to keeping it.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 14 Sep 2018 10:01:35 +0200

debian/changelog

+mothur (1.40.5-2) UNRELEASED; urgency=medium
+
+  * Upstream droped MPI support since it is slower and requires dual
+    maintenance (see README.Debian)  Thus droping MPI support from
+    Debian package
+    CLoses: #908786
+  * Remove Tim Booth from Uploaders (Tim, thanks for your work on this
+    package)
+  * Drop unneeded get-orig-source target
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Fri, 14 Sep 2018 10:01:35 +0200
+
 mothur (1.40.5-1) unstable; urgency=medium
 
   * New upstream version 1.40.5

debian/control

@@ -2,7 +2,6 @@ Source: mothur
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>,
-           Tim Booth <tbooth@ceh.ac.uk>,
            Tomasz Buchert <tomasz@debian.org>
 Section: science
 Priority: optional
@@ -12,14 +11,15 @@ Build-Depends: debhelper (>= 11),
                libopenmpi-dev,
                libreadline-dev,
                zlib1g-dev
-Standards-Version: 3.9.8
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/mothur
 Vcs-Git: https://salsa.debian.org/med-team/mothur.git
 Homepage: http://www.mothur.org
 
 Package: mothur
 Architecture: any
-Depends: ${misc:Depends}, ${shlibs:Depends}
+Depends: ${misc:Depends},
+         ${shlibs:Depends}
 Conflicts: uchime
 Provides: uchime
 Description: sequence analysis suite for research on microbiota
@@ -29,18 +29,3 @@ Description: sequence analysis suite for research on microbiota
  treeclimber, s-libshuff, unifrac, and much more. In addition to improving
  the flexibility of these algorithms, a number of other features including
  calculators and visualization tools were added.
-
-Package: mothur-mpi
-Architecture: any
-Depends: mothur, openmpi-bin, ${misc:Depends}, ${shlibs:Depends}
-Description: mpi-enabled binary for mothur
- Mothur seeks to develop a single piece of open-source, expandable
- software to fill the bioinformatics needs of the microbial ecology
- community. It has incorporated the functionality of dotur, sons,
- treeclimber, s-libshuff, unifrac, and much more. In addition to improving
- the flexibility of these algorithms, a number of other features including
- calculators and visualization tools were added.
- .
- Provides the MPI-enabled binary for Mothur
- This is recommended for operations like shhh.flows which will be
- very slow on a single processor.

debian/mothur-mpi.install

-mothur-mpi /usr/bin

debian/mothur-mpi.links

-usr/share/man/man1/mothur.1.gz usr/share/man/man1/mothur-mpi.1.gz

debian/rules

@@ -19,20 +19,13 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 	dh $@
 
 override_dh_auto_build:
-	dh_auto_build -- 64BIT_VERSION=$(64BIT_VERSION) USEMPI=yes
-	mv mothur mothur-mpi
-	make clean
-	dh_auto_build -- 64BIT_VERSION=$(64BIT_VERSION) USEMPI=no
-	# cp mothur mothur-mpi # XXX: debug
+	dh_auto_build -- 64BIT_VERSION=$(64BIT_VERSION)
 
 override_dh_auto_install:
 	true
 
 #Cleaning needs help right now
 override_dh_auto_clean:
-	rm -f mothur mothur-mpi
+	rm -f mothur
 	make clean
 	( cd source/uchime_src && rm -f *.o mk.stdout mk.stderr tmp.stderr )
-
-get-orig-source:
-	uscan --verbose --force-download