Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>
 Build-Depends: debhelper-compat (= 12),
               libfftw3-dev,
-               libopenmpi-dev
+               libopenmpi-dev,
+               nvidia-cuda-toolkit,
+               help2man
 Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/megadock
 Vcs-Git: https://salsa.debian.org/med-team/megadock.git
@@ -14,14 +16,23 @@ Homepage: http://www.bi.cs.titech.ac.jp/megadock/
 Package: megadock
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
-Recommends: opnempi-bin
-Description: ultra-high-performance protein-protein docking for heterogeneous supercomputers
- MEGADOCK is an ultra-high-performance protein-protein prediction software for heterogeneous supercomputers using FFT-grid-based docking with MPI/OpenMP/GPU parallelization
+Recommends: openmpi-bin
+Description: ultra-high-performance protein-protein docking
+ MEGADOCK is an ultra-high-performance protein-protein prediction software for
+ heterogeneous supercomputers using FFT-grid-based docking with MPI/OpenMP/GPU
+ parallelization
+ .
+ This package contains the non-GPU variants.

-# Package: megadock-gpu
-# Section: contrib/science
-# Architecture: any
-# Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
-# Recommends: opnempi-bin
-# Description: ultra-high-performance protein-protein docking for heterogeneous supercomputers
-#  MEGADOCK is an ultra-high-performance protein-protein prediction software for heterogeneous supercomputers using FFT-grid-based docking with MPI/OpenMP/GPU parallelization
+Package: megadock-gpu
+Section: contrib/science
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
+Recommends: openmpi-bin, megadock
+Enhances: megadock
+Description: ultra-high-performance protein-protein docking, CUDA version
+ MEGADOCK is an ultra-high-performance protein-protein prediction software for
+ heterogeneous supercomputers using FFT-grid-based docking with MPI/OpenMP/GPU
+ parallelization
+ .
+ This package contains the GPU variants.
--- a/debian/copyright
+++ b/debian/copyright
@@ -10,6 +10,33 @@ Files: debian/*
 Copyright: 2019 Michael R. Crusoe <michael.crusoe@gmail.com>
 License: GPL-3+

+Files: debian/patches/add-missing-headers
+Copyright: (c) 2019, NVIDIA CORPORATION. All rights reserved.
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+  * Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+  * Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+  * Neither the name of NVIDIA CORPORATION nor the names of its
+    contributors may be used to endorse or promote products derived
+    from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+ EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+ OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 License: GPL-3+
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

--- a/debian/patches/add-missing-headers
+++ b/debian/patches/add-missing-headers
--- a/debian/patches/correct-format
+++ b/debian/patches/correct-format
+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Accept 2 suggestions from gcc-9 about format codes
+--- megadock.orig/src/control.cpp
+++ megadock/src/control.cpp
+@@ -56,7 +56,7 @@
+     if(_parallel->num_gpu() > gpu_limit || _parallel->num_gpu() > _parallel->nproc2()) {
+         _parallel->num_gpu( min(gpu_limit, (int)_parallel->nproc2()) );
+     }
+-    printf("# Using %3d CPU cores, %d GPUs\n", _parallel->nproc2(), _parallel->num_gpu());
+    printf("# Using %3ld CPU cores, %d GPUs\n", _parallel->nproc2(), _parallel->num_gpu());
+ 
+     // Receptor
+     _receptor = new Receptor(_parameter->_RecPDB_file);
+--- megadock.orig/src/docking.cpp
+++ megadock/src/docking.cpp
+@@ -983,7 +983,7 @@
+     if( !Output_detail ) {
+         printf("cannot open calc-log file\n");
+     } else {
+-        sprintf(buff,"%s,%d,%d,%s,%s,%d,%d,%d,%d,%d,%d,%d,%d,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f"
+        sprintf(buff,"%s,%ld,%d,%s,%s,%d,%d,%d,%d,%d,%d,%d,%d,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f"
+                 , calc_id.c_str()
+                 , _parallel->nproc2(), _parallel->num_gpu()
+                 , rfile.c_str(), lfile.c_str()
--- a/debian/patches/series
+++ b/debian/patches/series
+add-missing-headers
 hardening
 not_static
 spelling
+correct-format
--- a/debian/rules
+++ b/debian/rules
@@ -4,26 +4,48 @@
 export LC_ALL=C.UTF-8

 export DEB_CXXFLAGS_MAINT_APPEND="-Wno-error=format-security"
-#include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all

+include /usr/share/dpkg/default.mk
+mandir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/
+bindir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
+gpumandir=$(CURDIR)/debian/$(DEB_SOURCE)-gpu/usr/share/man/man1/
+
 %:
 	dh $@

 override_dh_auto_build:
 	dh_auto_build -- USE_GPU=0 USE_MPI=0
 	dh_auto_build -- USE_GPU=0 USE_MPI=1
+	dh_auto_build -- USE_GPU=1 USE_MPI=0 CUDA_INSTALL_PATH=/usr/lib/nvidia-cuda-toolkit
+	dh_auto_build -- USE_GPU=1 USE_MPI=1 CUDA_INSTALL_PATH=/usr/lib/nvidia-cuda-toolkit

 override_dh_auto_clean:
 	dh_auto_clean
 	make allclean
+
+override_dh_installman:
+	dh_installman
+	mkdir -p $(mandir)
+	mkdir -p $(gpumandir)
+	help2man \
+		--version-string="$(DEB_VERSION_UPSTREAM)" \
+		--no-info \
+		--name "structural bioinformatics software for FFT-grid-based protein-protein docking" \
+		--output $(mandir)/megadock.1 \
+		$(bindir)/megadock
+	cp $(mandir)/megadock.1 $(gpumandir)/megadock-gpu.1
+	cp $(mandir)/megadock.1 $(mandir)/megadock-dp.1
+	cp $(mandir)/megadock.1 $(gpumandir)/megadock-gpu-dp.1
+	help2man \
+		--version-string="$(DEB_VERSION_UPSTREAM)" \
+		--no-info \
+		--name "generate decoy (candidate protein complexes) pdbfiles" \
+		--output $(mandir)/decoygen.1 \
+		$(bindir)/decoygen
+	help2man \
+		--version-string="$(DEB_VERSION_UPSTREAM)" \
+		--no-info \
+		--name "calculate center points of ligand" \
+		--output $(mandir)/calcrg.1 \
+		$(bindir)/calcrg
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
 Reference:
-  Author: 
-  Title: 
-  Journal: 
-  Year: 
-  Volume: 
-  Number: 
-  Pages: 
-  DOI: 
-  PMID:
-  URL: 
-  eprint: 
+ - Author: Ohue, Masahito and Shimoda, Takehiro and Suzuki, Shuji and Matsuzaki, Yuri and Ishida, Takashi and Akiyama, Yutaka
+   Title: "MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers"
+   Journal: Bioinformatics
+   Year: 2014
+   Volume: 30
+   Number: 22
+   Pages: 3281-3283
+   DOI: 10.1093/bioinformatics/btu532
+   ISSN: 1367-4803
+   URL: https://doi.org/10.1093/bioinformatics/btu532
+   eprint: https://academic.oup.com/bioinformatics/article-pdf/30/22/3281/17146412/btu532.pdf
+ - Author: Ohue, Masahito and Matsuzaki, Yuri and Uchikoga, Nobuyuki and Ishida, Takashi and Akiyama, Yutaka
+   Title: "MEGADOCK: An All-to-All Protein-Protein Interaction Prediction System Using Tertiary Structure Data"
+   Journal: Protein & Peptide Letters
+   Year: 2014
+   Volume: 21
+   Number: 8
+   Pages: 766-778
+   DOI: 10.2174/09298665113209990050
+   ISSN: 0929-8665/1875-5305
+   URL: http://www.eurekaselect.com/node/112757/article
+Registry:
+ - Name: bio.tools
+   Entry: megadock
+ - Name: OMICtools
+   Entry: OMICS_05456