diff -Nru relion-1.4+dfsg/debian/changelog relion-1.4+dfsg/debian/changelog --- relion-1.4+dfsg/debian/changelog 2018-05-13 21:55:16.000000000 +0000 +++ relion-1.4+dfsg/debian/changelog 2018-06-14 12:10:42.000000000 +0000 @@ -1,15 +1,16 @@ -relion (1.4+dfsg-3ubuntu2) cosmic; urgency=medium +relion (1.4+dfsg-4) unstable; urgency=medium - * No-change rebuild for dune openmpi soname change. + * Team upload. + * Add watch file (and delete README.source that explains why there is no + watch file) + * New upstream version + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.1.4 + * Restrict architectures to amd64 and i386 + Closes: #897239 - -- Matthias Klose Sun, 13 May 2018 21:55:16 +0000 - -relion (1.4+dfsg-3ubuntu1) bionic; urgency=medium - - * Drop librelion+mpi+gui-dev on architectures that don't have - librelion+mpi+gui-1.4-1. - - -- Steve Langasek Sat, 10 Feb 2018 00:57:21 -0800 + -- Andreas Tille Thu, 14 Jun 2018 14:10:42 +0200 relion (1.4+dfsg-3) unstable; urgency=medium diff -Nru relion-1.4+dfsg/debian/compat relion-1.4+dfsg/debian/compat --- relion-1.4+dfsg/debian/compat 2017-12-07 09:27:59.000000000 +0000 +++ relion-1.4+dfsg/debian/compat 2018-06-14 12:10:42.000000000 +0000 @@ -1 +1 @@ -9 +11 diff -Nru relion-1.4+dfsg/debian/control relion-1.4+dfsg/debian/control --- relion-1.4+dfsg/debian/control 2018-02-10 08:57:21.000000000 +0000 +++ relion-1.4+dfsg/debian/control 2018-06-14 12:10:42.000000000 +0000 @@ -1,28 +1,28 @@ Source: relion -Maintainer: Ubuntu Developers -XSBC-Original-Maintainer: Debian Med Packaging Team +Maintainer: Debian Med Packaging Team Uploaders: Roland Fehrenbacher , Navid Fehrenbacher , Goswin von Brederlow , Andreas Tille Section: science Priority: optional -Build-Depends: debhelper (>= 9), - dh-autoreconf, - dh-exec (>=0.3), +Build-Depends: debhelper (>= 11~), + dh-exec, libfltk1.3-dev, libfftw3-dev, libopenmpi-dev -Standards-Version: 4.1.1 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/relion.git -Vcs-Git: git://anonscm.debian.org/debian-med/relion.git +Standards-Version: 4.1.4 +Vcs-Browser: https://salsa.debian.org/med-team/relion +Vcs-Git: https://salsa.debian.org/med-team/relion.git Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Package: relion-bin -Architecture: any +Architecture: amd64 i386 Depends: ${shlibs:Depends}, ${misc:Depends} -Conflicts: relion-bin+mpi, relion-bin+gui, relion-bin+mpi+gui +Conflicts: relion-bin+mpi, + relion-bin+gui, + relion-bin+mpi+gui Description: toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -34,11 +34,13 @@ relion-bin provides the serial command-line tools Package: relion-bin+mpi -Architecture: any +Architecture: amd64 i386 Depends: ${shlibs:Depends}, ${misc:Depends}, openmpi-gcc | openmpi-bin -Conflicts: relion-bin, relion-bin+gui, relion-bin+mpi+gui +Conflicts: relion-bin, + relion-bin+gui, + relion-bin+mpi+gui Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -51,10 +53,12 @@ OpenMPI. Package: relion-bin+gui -Architecture: any +Architecture: amd64 i386 Depends: ${shlibs:Depends}, ${misc:Depends} -Conflicts: relion-bin, relion-bin+mpi, relion-bin+mpi+gui +Conflicts: relion-bin, + relion-bin+mpi, + relion-bin+mpi+gui Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -67,11 +71,13 @@ interface. Package: relion-bin+mpi+gui -Architecture: any +Architecture: amd64 i386 Depends: ${shlibs:Depends}, ${misc:Depends}, openmpi-gcc | openmpi-bin -Conflicts: relion-bin, relion-bin+mpi, relion-bin+gui +Conflicts: relion-bin, + relion-bin+mpi, + relion-bin+gui Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -98,12 +104,14 @@ This is the developers API package including only the common header files. Package: librelion-dev -Architecture: any +Architecture: amd64 i386 Section: libdevel Depends: librelion-1.4-1 (= ${binary:Version}), librelion-dev-common, ${misc:Depends} -Conflicts: librelion+mpi-dev, librelion+gui-dev, librelion+mpi+gui-dev +Conflicts: librelion+mpi-dev, + librelion+gui-dev, + librelion+mpi+gui-dev Description: C++ API for RELION (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -115,12 +123,14 @@ This is the developers API package for use without GUI and MPI. Package: librelion+mpi-dev -Architecture: any +Architecture: amd64 i386 Section: libdevel Depends: librelion+mpi-1.4-1 (= ${binary:Version}), librelion-dev-common, ${misc:Depends} -Conflicts: librelion-dev, librelion+gui-dev, librelion+mpi+gui-dev +Conflicts: librelion-dev, + librelion+gui-dev, + librelion+mpi+gui-dev Description: C++ API for RELION (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -132,12 +142,14 @@ This is the developers API package for use with MPI but without GUI. Package: librelion+gui-dev -Architecture: any +Architecture: amd64 i386 Section: libdevel Depends: librelion+gui-1.4-1 (= ${binary:Version}), librelion-dev-common, ${misc:Depends} -Conflicts: librelion-dev, librelion+mpi-dev, librelion+mpi+gui-dev +Conflicts: librelion-dev, + librelion+mpi-dev, + librelion+mpi+gui-dev Description: C++ API for RELION (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -149,12 +161,14 @@ This is the developers API package for use with GUI but without MPI. Package: librelion+mpi+gui-dev -Architecture: i386 amd64 +Architecture: amd64 i386 Section: libdevel Depends: librelion+mpi+gui-1.4-1 (= ${binary:Version}), librelion-dev-common, ${misc:Depends} -Conflicts: librelion-dev, librelion+mpi-dev, librelion+gui-dev +Conflicts: librelion-dev, + librelion+mpi-dev, + librelion+gui-dev Description: C++ API for RELION (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -166,17 +180,25 @@ This is the developers API package for use with MPI and GUI. Package: librelion-1.4-1 -Architecture: any -Section: libs -Pre-Depends: ${misc:Pre-Depends} +Architecture: amd64 i386 Multi-Arch: same +Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} -Conflicts: librelion+mpi-1.4-1, librelion+gui-1.4-1, librelion+mpi+gui-1.4-1, - librelion-1.3-1v5, librelion+mpi-1.3-1v5, librelion+gui-1.3-1v5, - librelion+mpi+gui-1.3-1v5, - librelion-1.3-1, librelion+mpi-1.3-1, librelion+gui-1.3-1, librelion+mpi+gui-1.3-1 -Replaces: librelion-1.3-1v5, librelion-1.3-1 +Pre-Depends: ${misc:Pre-Depends} +Conflicts: librelion+mpi-1.4-1, + librelion+gui-1.4-1, + librelion+mpi+gui-1.4-1, + librelion-1.3-1v5, + librelion+mpi-1.3-1v5, + librelion+gui-1.3-1v5, + librelion+mpi+gui-1.3-1v5, + librelion-1.3-1, + librelion+mpi-1.3-1, + librelion+gui-1.3-1, + librelion+mpi+gui-1.3-1 +Replaces: librelion-1.3-1v5, + librelion-1.3-1 Description: RELION dynnamic library (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -188,17 +210,25 @@ This is the runtime library. Package: librelion+mpi-1.4-1 -Architecture: any -Section: libs -Pre-Depends: ${misc:Pre-Depends} +Architecture: amd64 i386 Multi-Arch: same +Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} -Conflicts: librelion-1.4-1, librelion+gui-1.4-1, librelion+mpi+gui-1.4-1, - librelion-1.3-1v5, librelion+mpi-1.3-1v5, librelion+gui-1.3-1v5, - librelion+mpi+gui-1.3-1v5, - librelion-1.3-1, librelion+mpi-1.3-1, librelion+gui-1.3-1, librelion+mpi+gui-1.3-1 -Replaces: librelion+mpi-1.3-1v5, librelion+mpi-1.3-1 +Pre-Depends: ${misc:Pre-Depends} +Conflicts: librelion-1.4-1, + librelion+gui-1.4-1, + librelion+mpi+gui-1.4-1, + librelion-1.3-1v5, + librelion+mpi-1.3-1v5, + librelion+gui-1.3-1v5, + librelion+mpi+gui-1.3-1v5, + librelion-1.3-1, + librelion+mpi-1.3-1, + librelion+gui-1.3-1, + librelion+mpi+gui-1.3-1 +Replaces: librelion+mpi-1.3-1v5, + librelion+mpi-1.3-1 Description: RELION dynnamic library (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -210,17 +240,25 @@ This is the runtime library for use with MPI but without GUI. Package: librelion+gui-1.4-1 -Architecture: any -Section: libs -Pre-Depends: ${misc:Pre-Depends} +Architecture: amd64 i386 Multi-Arch: same +Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} -Conflicts: librelion-1.4-1, librelion+mpi-1.4-1, librelion+mpi+gui-1.4-1, - librelion-1.3-1v5, librelion+mpi-1.3-1v5, librelion+gui-1.3-1v5, - librelion+mpi+gui-1.3-1v5, - librelion-1.3-1, librelion+mpi-1.3-1, librelion+gui-1.3-1, librelion+mpi+gui-1.3-1 -Replaces: librelion+gui-1.3-1v5, librelion+gui-1.3-1 +Pre-Depends: ${misc:Pre-Depends} +Conflicts: librelion-1.4-1, + librelion+mpi-1.4-1, + librelion+mpi+gui-1.4-1, + librelion-1.3-1v5, + librelion+mpi-1.3-1v5, + librelion+gui-1.3-1v5, + librelion+mpi+gui-1.3-1v5, + librelion-1.3-1, + librelion+mpi-1.3-1, + librelion+gui-1.3-1, + librelion+mpi+gui-1.3-1 +Replaces: librelion+gui-1.3-1v5, + librelion+gui-1.3-1 Description: RELION dynnamic library (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -233,16 +271,24 @@ Package: librelion+mpi+gui-1.4-1 Architecture: i386 amd64 -Section: libs -Pre-Depends: ${misc:Pre-Depends} Multi-Arch: same +Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} -Conflicts: librelion-1.4-1, librelion+mpi-1.4-1, librelion+gui-1.4-1, - librelion-1.3-1v5, librelion+mpi-1.3-1v5, librelion+gui-1.3-1v5, - librelion+mpi+gui-1.3-1v5, - librelion-1.3-1, librelion+mpi-1.3-1, librelion+gui-1.3-1, librelion+mpi+gui-1.3-1 -Replaces: librelion+mpi+gui-1.3-1v5, librelion+mpi+gui-1.3-1 +Pre-Depends: ${misc:Pre-Depends} +Conflicts: librelion-1.4-1, + librelion+mpi-1.4-1, + librelion+gui-1.4-1, + librelion-1.3-1v5, + librelion+mpi-1.3-1v5, + librelion+gui-1.3-1v5, + librelion+mpi+gui-1.3-1v5, + librelion-1.3-1, + librelion+mpi-1.3-1, + librelion+gui-1.3-1, + librelion+mpi+gui-1.3-1 +Replaces: librelion+mpi+gui-1.3-1v5, + librelion+mpi+gui-1.3-1 Description: RELION dynnamic library (3D reconstructions in cryo-electron microscopy) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D @@ -252,4 +298,3 @@ versions as well as a C++ API. . This is the runtime library for use with MPI and GUI. - diff -Nru relion-1.4+dfsg/debian/README.source relion-1.4+dfsg/debian/README.source --- relion-1.4+dfsg/debian/README.source 2017-12-07 09:27:59.000000000 +0000 +++ relion-1.4+dfsg/debian/README.source 1970-01-01 00:00:00.000000000 +0000 @@ -1,9 +0,0 @@ -The source for RELION is downloadable from the following URL: - -http://www2.mrc-lmb.cam.ac.uk/groups/scheres/download_relion.html - -Note, that the download requires registration, which is why a watch file is not -provided with this package. - -Upstream has been contacted on the DedMed list and was informed about -our packaging effort. They are fine with this. diff -Nru relion-1.4+dfsg/debian/rules relion-1.4+dfsg/debian/rules --- relion-1.4+dfsg/debian/rules 2017-12-07 09:27:59.000000000 +0000 +++ relion-1.4+dfsg/debian/rules 2018-06-14 12:10:42.000000000 +0000 @@ -34,7 +34,7 @@ --libdir=\$${prefix}/lib/$(DEB_HOST_MULTIARCH) %: - dh $@ --parallel --with autoreconf + dh $@ override_dh_auto_configure: diff -Nru relion-1.4+dfsg/debian/upstream/metadata relion-1.4+dfsg/debian/upstream/metadata --- relion-1.4+dfsg/debian/upstream/metadata 2017-12-07 09:27:59.000000000 +0000 +++ relion-1.4+dfsg/debian/upstream/metadata 2018-06-14 12:10:42.000000000 +0000 @@ -1,11 +1,20 @@ Reference: - Author: Sjors H. W. Scheres - Title: "RELION: implementation of a Bayesian approach to cryo-EM structure determination" - Journal: J Struct Biol. - Year: 2012 - Year: 180 - Number: 3 - Pages: 519-30 - DOI: 10.1016/j.jsb.2012.09.006 - PMID: 23000701 - URL: http://www.sciencedirect.com/science/article/pii/S1047847712002481 + Author: Sjors H. W. Scheres + Title: > + RELION: implementation of a Bayesian approach to + cryo-EM structure determination + Journal: J Struct Biol. + Year: 2012 + Year: 180 + Number: 3 + Pages: 519-30 + DOI: 10.1016/j.jsb.2012.09.006 + PMID: 23000701 + URL: http://www.sciencedirect.com/science/article/pii/S1047847712002481 +Registry: + - Name: OMICtools + Entry: OMICS_15597 + - Name: bio.tools + Entry: NA + - Name: SciCrunch + Entry: NA diff -Nru relion-1.4+dfsg/debian/watch relion-1.4+dfsg/debian/watch --- relion-1.4+dfsg/debian/watch 1970-01-01 00:00:00.000000000 +0000 +++ relion-1.4+dfsg/debian/watch 2018-06-14 12:10:42.000000000 +0000 @@ -0,0 +1,3 @@ +version=4 + +https://github.com/3dem/relion/releases .*/archive/(\d[\d.]+)@ARCHIVE_EXT@