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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libpsortb.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
