[med-svn] [libpsortb] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Mon Apr 24 13:18:30 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libpsortb.
commit 089a1072f06851bbe7695303c4912d81733c231e
Author: Andreas Tille <tille at debian.org>
Date: Mon Apr 24 15:11:44 2017 +0200
Add initial packaging
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 107 ++++++++++++++++++++++++
debian/copyright | 43 ++++++++++
debian/patches/series | 2 +
debian/patches/use_debian_packaged_libs.patch | 27 ++++++
debian/patches/use_debian_packaged_libsvm.patch | 76 +++++++++++++++++
debian/rules | 21 +++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++
debian/watch | 4 +
11 files changed, 299 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..7bb9046
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+libpsortb (1.0+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 17 Mar 2017 10:23:15 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..3b9f8c2
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,107 @@
+Source: libpsortb
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10),
+ d-shlibs,
+ libsvm-dev,
+ libsquid-dev (>= 1.9g+cvs20050121-9~),
+ libhmmer2-dev (>= 2.3.2+dfsg-2~),
+ pkg-config
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libpsortb.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libpsortb.git
+Homepage: http://www.psort.org/
+
+Package: libmodhmm0
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: library for constructing, training and scoring hidden Markov models
+ Library for constructing, training and scoring hidden Markov models. It
+ is provided with PSORTb but might be used separately.
+ .
+ PSORTb enables prediction of bacterial protein subcellular localization
+ (SCL) and provides a quick and inexpensive means for gaining insight
+ into protein function, verifying experimental results, annotating newly
+ sequenced bacterial genomes, detecting potential cell surface/secreted
+ drug targets, as well as identifying biomarkers for microbes.
+ .
+ This library needed by PSORTb is distributed separately by upstream.
+ .
+ This package contains the shared library which is needed to run PSORTb.
+
+Package: libmodhmm-dev
+Section: libdevel
+Architecture: any
+Depends: libmodhmm0 (= ${binary:Version}),
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: library for constructing, training and scoring hidden Markov models (dev)
+ Library for constructing, training and scoring hidden Markov models. It
+ is provided with PSORTb but might be used separately.
+ .
+ PSORTb enables prediction of bacterial protein subcellular localization
+ (SCL) and provides a quick and inexpensive means for gaining insight
+ into protein function, verifying experimental results, annotating newly
+ sequenced bacterial genomes, detecting potential cell surface/secreted
+ drug targets, as well as identifying biomarkers for microbes.
+ .
+ This library needed by PSORTb is distributed separately by upstream.
+ .
+ This package contains the static library which is needed to link PSORTb.
+
+Package: libsvmloc0
+Section: libs
+Architecture: any
+Depends: libsvm3,
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: PSORTb adapted library for svm machine-learning library
+ Libsvm is a machine-learning library which is an easy-to-use package
+ for support vector classification, regression and one-class SVM. It
+ supports multi-class classification, probability outputs, and
+ parameter selection.
+ .
+ PSORTb was featuring a code copy plus some local additions. This
+ library is linked against the Debian packaged libsvn and just contains
+ the PSORTb extensions.
+ .
+ PSORTb enables prediction of bacterial protein subcellular localization
+ (SCL) and provides a quick and inexpensive means for gaining insight
+ into protein function, verifying experimental results, annotating newly
+ sequenced bacterial genomes, detecting potential cell surface/secreted
+ drug targets, as well as identifying biomarkers for microbes.
+ .
+ This library needed by PSORTb is distributed separately by upstream.
+ .
+ This package contains the shared library which is needed to run PSORb.
+
+Package: libsvmloc-dev
+Section: libdevel
+Architecture: any
+Depends: libsvmloc0 (= ${binary:Version}),
+ libsvm-dev,
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: PSORTb adapted library for svm machine-learning library (dev)
+ Libsvm is a machine-learning library which is an easy-to-use package
+ for support vector classification, regression and one-class SVM. It
+ supports multi-class classification, probability outputs, and
+ parameter selection.
+ .
+ PSORTb was featuring a code copy plus some local additions. This
+ library is linked against the Debian packaged libsvn and just contains
+ the PSORTb extensions.
+ .
+ PSORTb enables prediction of bacterial protein subcellular localization
+ (SCL) and provides a quick and inexpensive means for gaining insight
+ into protein function, verifying experimental results, annotating newly
+ sequenced bacterial genomes, detecting potential cell surface/secreted
+ drug targets, as well as identifying biomarkers for microbes.
+ .
+ This library needed by PSORTb is distributed separately by upstream.
+ .
+ This package contains the static library which is needed to link PSORTb.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5ad65f2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,43 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: libpsortb
+Source: http://www.psort.org/download/libpsortb-1.0.tar.gz
+Files-Excluded: hmmer/
+ squid/
+ include/
+ svmloc/libsvm.*
+ svmloc/COPYRIGHT
+ */Makefile.in
+ aclocal.m4
+ compile
+ *config.*
+ configure
+ depcomp
+ install-sh
+ ltmain.sh
+ missing
+
+Files: *
+Copyright: 2008, the Brinkman Laboratory, Simon Fraser Univserity
+License: GPL-2+
+
+Files: modhmm0.92b/*
+Copyright: 2008-2012 Hakan Viklund
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille
+License: GPL-2+
+
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program 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 General Public License for more details.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL-2.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..69778ba
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+use_debian_packaged_libs.patch
+use_debian_packaged_libsvm.patch
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
new file mode 100644
index 0000000..6dfbecf
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -0,0 +1,27 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 17 Mar 2017 10:23:15 +010
+Description: Use Debian packaged libbiosquid and libhmmer2
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,6 +1,6 @@
+ # Made by me.
+
+-SUBDIRS = svmloc squid hmmer modhmm0.92b include
++SUBDIRS = svmloc modhmm0.92b
+
+ noinst_HEADERS = \
+ README
+--- a/configure.ac
++++ b/configure.ac
+@@ -66,9 +66,6 @@ AC_FUNC_STRTOD
+ AC_CHECK_FUNCS([atexit floor memmove memset pow sqrt strchr strcspn strerror strpbrk strrchr strspn strstr strtol])
+
+ AC_CONFIG_FILES([Makefile
+- hmmer/Makefile
+- squid/Makefile
+ svmloc/Makefile
+- modhmm0.92b/Makefile
+- include/Makefile])
++ modhmm0.92b/Makefile])
+ AC_OUTPUT
diff --git a/debian/patches/use_debian_packaged_libsvm.patch b/debian/patches/use_debian_packaged_libsvm.patch
new file mode 100644
index 0000000..6d1e641
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libsvm.patch
@@ -0,0 +1,76 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 17 Mar 2017 10:23:15 +010
+Description: Use Debian packaged libsvm
+
+--- a/svmloc/Makefile.am
++++ b/svmloc/Makefile.am
+@@ -3,8 +3,9 @@
+ # svmloc dir
+
+ lib_LTLIBRARIES = libsvmloc.la
+-libsvmloc_la_SOURCES = binding.cpp libsvm.cpp svmloc.cpp binding.h libsvm.h svmloc.h
++libsvmloc_la_SOURCES = binding.cpp svmloc.cpp binding.h svmloc.h
+ libsvmloc_la_LDFLAGS = -version-info 0:0:0
++libsvmloc_la_CPPFLAGS = -I/usr/include/libsvm
++
++LDADD = -lsvm
+
+-noinst_HEADERS = \
+-COPYRIGHT
+--- a/svmloc/svmloc.h
++++ b/svmloc/svmloc.h
+@@ -12,7 +12,7 @@
+ #include <stdio.h>
+ #include <string.h>
+
+-#include "libsvm.h"
++#include <svm.h>
+
+ using namespace std;
+
+--- a/svmloc/svmloc.cpp
++++ b/svmloc/svmloc.cpp
+@@ -166,7 +166,7 @@ int SVM::train(int retrain) {
+
+ // Free any old model we have.
+ if(model != NULL) {
+- svm_destroy_model(model);
++ svm_free_and_destroy_model(&model);
+ model = NULL;
+ }
+
+@@ -282,7 +282,7 @@ int SVM::loadModel(char *filename) {
+ }
+
+ if(model != NULL) {
+- svm_destroy_model(model);
++ svm_free_and_destroy_model(&model);
+ model = NULL;
+ }
+
+@@ -436,7 +436,7 @@ double SVM::crossValidate(int nfolds) {
+ sumyy += y*y;
+ sumvy += v*y;
+ }
+- svm_destroy_model(submodel);
++ svm_free_and_destroy_model(&submodel);
+ // cout << "Mean squared error = %g\n", error/(end-begin));
+ total_error += error;
+ } else {
+@@ -447,7 +447,7 @@ double SVM::crossValidate(int nfolds) {
+ double v = svm_predict(submodel,prob->x[j]);
+ if(v == prob->y[j]) ++correct;
+ }
+- svm_destroy_model(submodel);
++ svm_free_and_destroy_model(&submodel);
+ //cout << "Accuracy = " << 100.0*correct/(end-begin) << " (" <<
+ //correct << "/" << (end-begin) << endl;
+ total_correct += correct;
+@@ -502,6 +502,6 @@ int SVM::checkProbabilityModel() {
+
+ SVM::~SVM() {
+ if(x_space!=NULL) { free_x_space(); }
+- if(model != NULL) { svm_destroy_model(model); model=NULL; }
++ if(model != NULL) { svm_free_and_destroy_model(&model); model=NULL; }
+ if(prob != NULL) { free(prob); prob=NULL; }
+ }
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..6d66849
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@
+
+override_dh_auto_install:
+ dh_auto_install
+ d-shlibmove --commit \
+ --multiarch \
+ --devunversioned \
+ --exclude-la \
+ debian/tmp/usr/lib/*/libmodhmm.so
+ d-shlibmove --commit \
+ --multiarch \
+ --devunversioned \
+ --exclude-la \
+ debian/tmp/usr/lib/*/libsvmloc.so
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..acf4a7a
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Nancy Y. Yu and James R. Wagner and Matthew R. Laird and Gabor Melli and Sébastien Rey and Raymond Lo and Phuong Dao and S. Cenk Sahinalp and Martin Ester and Leonard J. Foster and F. S. Brinkman
+ Title: "PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes"
+ Journal: Bioinformatics
+ Year: 2010
+ Volume: 26
+ Number: 13
+ Pages: 1608-1615
+ DOI: 10.1093/bioinformatics/btq249
+ PMID: 20472543
+ URL: https://academic.oup.com/bioinformatics/article/26/13/1608/201357/PSORTb-3-0-improved-protein-subcellular
+ eprint: https://academic.oup.com/bioinformatics/article-pdf/26/13/1608/516044/btq249.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..8032d9c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ http://www.psort.org/downloads .*/libpsortb-(\d[.\d]+)\.tar\.gz
--
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