[med-svn] [Git][med-team/cmdock][master] Initial packaging
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Sun Jun 6 21:03:10 BST 2021
Steffen Möller pushed to branch master at Debian Med / cmdock
Commits:
e298446b by Steffen Moeller at 2021-06-06T22:03:01+02:00
Initial packaging
- - - - -
14 changed files:
- + debian/changelog
- + debian/cmdock.install
- + debian/control
- + debian/copyright
- + debian/libcmdock0.install
- + debian/patches/installdir.patch
- + debian/patches/noPCGtest.patch
- + debian/patches/pythonVersion.patch
- + debian/patches/series
- + debian/rules
- + debian/salsa-ci.yml
- + debian/source/format
- + debian/upstream/metadata
- + debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+cmdock (0.1.3-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #989535)
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 06 Jun 2021 19:20:43 +0200
=====================================
debian/cmdock.install
=====================================
@@ -0,0 +1,2 @@
+usr/bin
+usr/share
=====================================
debian/control
=====================================
@@ -0,0 +1,37 @@
+Source: cmdock
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper-compat (= 13),
+ meson,
+ libcxxopts-dev,
+ libpcg-cpp-dev,
+ googletest <!nocheck>
+Standards-Version: 4.5.1
+Homepage: https://sidock.si
+Vcs-Browser: https://salsa.debian.org/med-team/cmdock
+Vcs-Git: https://salsa.debian.org/med-team/cmdock.git
+Rules-Requires-Root: no
+
+Package: cmdock
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+Recommends: python3,
+ perl
+Suggests: tcsh
+Description: fit chemical compounds to proteins and nucleotides
+ This tool for molecular docking / in silico drug screening is a
+ derivative of rDock and the core to the SiDock at Home project to
+ find inhibitors of the SARS-CoV-2 virus.
+
+Package: libcmdock0
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: cmdock
+Description: library of cmdock
+ cmdock performs docking / in silico drug screening as a
+ derivative of rDock and is core to the SiDock at Home project to
+ find inhibitors of the SARS-CoV-2 virus.
+ .
+ This package provides its shared library.
=====================================
debian/copyright
=====================================
@@ -0,0 +1,35 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: cmdock
+Source:
+
+Files: *
+Copyright: 1998-2006 RiboTargets (subsequently Vernalis (R&D) Ltd)
+ 2006-2012 University of York
+ 2012-2014 University of Barcelona
+ 2019-2020 RxTx
+License: LGPL-3.0+
+
+Files: include/indicators/termcolor.hpp
+Copyright: 2013 Ihor Kalnytskyi
+License: BSD
+
+Files: debian/*
+Copyright: 2021 Steffen Moeller <moeller at debian.org>
+License: LGPL-3.0+
+
+License: LGPL-3.0+
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in "/usr/share/common-licenses/LGPL-3".
=====================================
debian/libcmdock0.install
=====================================
@@ -0,0 +1 @@
+usr/lib
=====================================
debian/patches/installdir.patch
=====================================
@@ -0,0 +1,82 @@
+Author: Steffen Moeller <moeller at debian.org>
+Description: Adjusting install paths to mostly fit Debian policy
+Forwarding: Not required.
+
+Index: cmdock-0.1.3/meson.build
+===================================================================
+--- cmdock-0.1.3.orig/meson.build
++++ cmdock-0.1.3/meson.build
+@@ -109,7 +109,7 @@ libcmdock = library(
+ version : meson.project_version(),
+ include_directories : incRbt,
+ install : true,
+- install_dir: './build'
++ install_dir: './lib'
+ )
+
+ cxxopts_dep = dependency('cxxopts', fallback : ['cxxopts', 'cxxopts_dep'])
+@@ -118,42 +118,42 @@ cmdock = executable(
+ 'cmdock', 'src/exe/cmdock.cxx', link_with : libcmdock,
+ dependencies : [cxxopts_dep, eigen3_dep, pcg_cpp_dep],
+ include_directories : incRbt, install : true,
+- install_dir: './build'
++ install_dir: './bin'
+ )
+ cmcavity = executable(
+ 'cmcavity', 'src/exe/cmcavity.cxx', link_with : libcmdock,
+ dependencies : [cxxopts_dep, eigen3_dep, pcg_cpp_dep],
+ include_directories : incRbt, install : true,
+- install_dir: './build'
++ install_dir: './bin'
+ )
+ executable(
+ 'cmrms', 'src/exe/cmrms.cxx', link_with : libcmdock,
+ dependencies : eigen3_dep,
+ include_directories : incRbt, install: true,
+- install_dir: './build'
++ install_dir: './bin'
+ )
+ executable(
+ 'cmmoegrid', 'src/exe/cmmoegrid.cxx', link_with : libcmdock,
+ dependencies : [cxxopts_dep, eigen3_dep, pcg_cpp_dep],
+ include_directories : incRbt, install : true,
+- install_dir: './build'
++ install_dir: './bin'
+ )
+ executable(
+ 'cmlist', 'src/exe/cmlist.cxx', link_with : libcmdock,
+ dependencies : eigen3_dep,
+ include_directories : incRbt, install : true,
+- install_dir: './build'
++ install_dir: './bin'
+ )
+ executable(
+ 'cmcalcgrid', 'src/exe/cmcalcgrid.cxx', link_with : libcmdock,
+ dependencies : [eigen3_dep, pcg_cpp_dep], include_directories : incRbt,
+ install : true,
+- install_dir: './build'
++ install_dir: './bin'
+ )
+ executable(
+ 'cmconvgrid', 'src/exe/cmconvgrid.cxx', link_with : libcmdock,
+ dependencies : eigen3_dep, include_directories : incRbt, install : true,
+- install_dir: './build'
++ install_dir: './bin'
+ )
+
+ dt_smarts_dep = dependency('dt_smarts', required : false)
+@@ -178,11 +178,11 @@ endif
+
+ # Copy entire folder with subfolders
+ # Scripts in bin
+-install_subdir('bin', install_dir : './')
++install_subdir('bin', install_dir : '.')
+ # Data and protocols
+-install_subdir('data', install_dir : './')
++install_subdir('data', install_dir : './share/cmdock/')
+ # Perl scripts
+-install_subdir('lib', install_dir : './')
++install_subdir('lib', install_dir : './share/cmdock/')
+
+
+ tests_opt = get_option('tests')
=====================================
debian/patches/noPCGtest.patch
=====================================
@@ -0,0 +1,28 @@
+Author: Steffen Moeller
+Description: Hack to overcome difficulty to spot pcg library
+Forwarding: Not required.
+
+Index: cmdock-0.1.3/meson.build
+===================================================================
+--- cmdock-0.1.3.orig/meson.build
++++ cmdock-0.1.3/meson.build
+@@ -93,12 +93,13 @@ endif
+ # Use standard C++11 RNG on Solaris and Windows/MSVC due to PCG build failure
+ # Solaris issue: https://github.com/imneme/pcg-cpp/issues/42
+ # Windows/MSVC issue: https://github.com/imneme/pcg-cpp/issues/11
+-if (host_machine.system() == 'sunos' or (host_machine.system() == 'windows' and
+- cpp_compiler.get_id() == 'msvc'))
+- pcg_cpp_dep = declare_dependency()
+-else
+- pcg_cpp_dep = dependency('pcg-cpp', fallback : ['pcg', 'pcg_cpp_dep'])
+-endif
++#if (host_machine.system() == 'sunos' or (host_machine.system() == 'windows' and
++# cpp_compiler.get_id() == 'msvc'))
++# pcg_cpp_dep = declare_dependency()
++#else
++# pcg_cpp_dep = dependency('pcg-cpp', fallback : ['pcg', 'pcg_cpp_dep'])
++#endif
++pcg_cpp_dep = dependency('pcg', required : false)
+
+ library_soversion = meson.project_version().split('.')[0]
+ libcmdock = library(
=====================================
debian/patches/pythonVersion.patch
=====================================
@@ -0,0 +1,134 @@
+Author: Steffen Moeller <moeller at debian.org>
+Description: Adjusting paths of interpreters.
+Forwarding: Not required.
+
+Index: cmdock-0.1.3/bin/rbhtfinder
+===================================================================
+--- cmdock-0.1.3.orig/bin/rbhtfinder
++++ cmdock-0.1.3/bin/rbhtfinder
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl -w
++#!/usr/bin/perl -w
+
+ # Script that simulates the result of a high throughput protocol.
+
+Index: cmdock-0.1.3/bin/run_rbdock.pl
+===================================================================
+--- cmdock-0.1.3.orig/bin/run_rbdock.pl
++++ cmdock-0.1.3/bin/run_rbdock.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ use lib "$ENV{'CMDOCK_ROOT'}/lib";
+ require "run_rbfuncs.pl";
+
+Index: cmdock-0.1.3/bin/run_rbscreen.pl
+===================================================================
+--- cmdock-0.1.3.orig/bin/run_rbscreen.pl
++++ cmdock-0.1.3/bin/run_rbscreen.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ use File::stat;
+ use lib "$ENV{'CMDOCK_ROOT'}/lib";
+ use strict;
+Index: cmdock-0.1.3/bin/sdfield
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdfield
++++ cmdock-0.1.3/bin/sdfield
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ # add extra fields to SD records
+ use lib "$ENV{'CMDOCK_ROOT'}/lib";
+ use SDRecord;
+Index: cmdock-0.1.3/bin/sdfilter
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdfilter
++++ cmdock-0.1.3/bin/sdfilter
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ # Filters SD records by given data field *
+ # *
+ # Usage: sdfilter -f'$<DataField> <Operator> <Value>' [sdFiles] *
+Index: cmdock-0.1.3/bin/sdmodify
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdmodify
++++ cmdock-0.1.3/bin/sdmodify
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ # Script to set the first title line equal to a given data field
+ #
+ # Usage: sdmodify -f<DataField> [sdFiles]
+Index: cmdock-0.1.3/bin/sdreport
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdreport
++++ cmdock-0.1.3/bin/sdreport
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ # Produces text summaries of SD records *
+ # *
+ # Usage: sdreport [-l] [-t] [-s<DataField>] [sdFiles] *
+Index: cmdock-0.1.3/bin/sdrmsd
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdrmsd
++++ cmdock-0.1.3/bin/sdrmsd
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+ #
+ # Calculate SMART RMSD with or without molecular superposition (FIT or NOFIT)
+ # Script distributed under GNU LGPL 3.0 along rDock software.
+Index: cmdock-0.1.3/bin/sdsort
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdsort
++++ cmdock-0.1.3/bin/sdsort
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ # Sorts SD records by given data field
+ use lib "$ENV{'CMDOCK_ROOT'}/lib";
+
+Index: cmdock-0.1.3/bin/sdsplit
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdsplit
++++ cmdock-0.1.3/bin/sdsplit
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ # Splits SD records into multiple files of equal no. of records
+ use lib "$ENV{'CMDOCK_ROOT'}/lib";
+
+Index: cmdock-0.1.3/data/pmf/smoothed/m2pmf.awk
+===================================================================
+--- cmdock-0.1.3.orig/data/pmf/smoothed/m2pmf.awk
++++ cmdock-0.1.3/data/pmf/smoothed/m2pmf.awk
+@@ -1,4 +1,4 @@
+-#!/bin/awk -f
++#!/usr/bin/awk -f
+ BEGIN{
+ true = 1;
+ false = !true;
+Index: cmdock-0.1.3/data/pmf/smoothed/pmf2m.awk
+===================================================================
+--- cmdock-0.1.3.orig/data/pmf/smoothed/pmf2m.awk
++++ cmdock-0.1.3/data/pmf/smoothed/pmf2m.awk
+@@ -1,4 +1,4 @@
+-#!/bin/awk -f
++#!/usr/bin/awk -f
+ {
+ a[NR]=$1;
+ b[NR]=$2;
+Index: cmdock-0.1.3/bin/sdtether
+===================================================================
+--- cmdock-0.1.3.orig/bin/sdtether
++++ cmdock-0.1.3/bin/sdtether
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/python3
+ #
+ # Substitute for rbtether of rDock. Will align input molecules to a reference fragment defined by a smarts string,
+ # it will add a TETHERED ATOM property field to the output SDF that is correctly understood by rDock
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,3 @@
+noPCGtest.patch
+installdir.patch
+pythonVersion.patch
=====================================
debian/rules
=====================================
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+export DH_VERBOSE = 1
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+%:
+ dh $@
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,11 @@
+# For more information on what jobs are run see:
+# https://salsa.debian.org/salsa-ci-team/pipeline
+#
+# To enable the jobs, go to your repository (at salsa.debian.org)
+# and click over Settings > CI/CD > Expand (in General pipelines).
+# In "Custom CI config path" write debian/salsa-ci.yml and click
+# in "Save Changes". The CI tests will run after the next commit.
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,37 @@
+---
+References:
+ - Author: Jukič, M., Škrlj, B., Tomšič, G., Pleško, S., Podlipnik Č., Bren, U.
+ Year: 2021
+ Title: >
+ Prioritisation of Compounds for 3CLpro Inhibitor Development on SARS-CoV-2 Variants.
+ Journal: Molecules
+ Volume: 26
+ Numer: 10
+ Pages: 3003
+ DOI: 10.3390/molecules26103003
+ URL: https://www.mdpi.com/1420-3049/26/10/3003
+ - Author: Ruiz-Carmona, S., Alvarez-Garcia, D., Foloppe, N. Garmendia-Doval, A. B., Juhos S., et al.
+ Year: 2014
+ Title: >
+ rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids.
+ Journal: PLoS Comput Biol
+ Volume: 10
+ Number: 4
+ Pages: e1003571
+ DOI: 10.1371/journal.pcbi.1003571
+ Volume: https://doi.org/10.1371/journal.pcbi.1003571
+ - Author: Morley, S. D. and Afshar, M.
+ Year: 2004
+ Title: Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®.
+ Journal: J. Comput. Aided. Mol. Des.
+ Volume: 18
+ Pages: 189-208
+ DOI: 10.1023/B:JCAM.0000035199.48747.1e
+ URL: https://doi.org/10.1023/B:JCAM.0000035199.48747.1e
+Registry:
+ - Name: bio.tools
+ Entry: NA
+ Checked: 2021-06-06
+ - Name: conda:bioconda
+ Entry: NA
+ Checked: 2021-06-06
=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=4
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.bz2%cmdock-$1.tar.bz2%" \
+ https://gitlab.com/Jukic/cmdock/-/releases \
+ (?:.*?/)?cmdock-v(\d[\d.]*)\.tar\.bz2
View it on GitLab: https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256
--
View it on GitLab: https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256
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