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View file @ 772dbbde
predictprotein (1.1.09) unstable; urgency=low
* predbind(1) has been renamed to prona2019(1)
* prona2019(1) target and output file have been renamed from
'predbind' to 'prona'
-- Timothy Karl <karl@rostlab.org> Mon, 18 Mar 2019 15:57:00 +0100
predictprotein (1.1.08) unstable; urgency=low
* Added predbind(1) prediction file handling.
......
MakefilePP.mk
View file @ 772dbbde
......@@ -59,10 +59,10 @@ PHDFILE:=$(INFILE:%.in=%.phdPred)
PHDRDBFILE:=$(INFILE:%.in=%.phdRdb)
# lkajan: never make PHDNOTHTMFILE a target - its creation depends on whether phd found an HTM region or not: it isn't always created
PHDNOTHTMFILE:=$(INFILE:%.in=%.phdNotHtm)
PREDBINDFILE:=$(INFILE:%.in=%.predbind)
PROFFILE:=$(INFILE:%.in=%.profRdb)
# prof output generated explicitely from one sequence - NO alignment - Chris Schaefer initiated this - B approved
PROF1FILE:=$(INFILE:%.in=%.prof1Rdb)
PRONAFILE:=$(INFILE:%.in=%.prona)
# lkajan: 20120816: profasp is now removed (https://rostlab.org/bugzilla3/show_bug.cgi?id=154)
ASPFILE:=$(INFILE:%.in=%.asp)
NORSFILE:=$(INFILE:%.in=%.nors)
......@@ -188,7 +188,7 @@ subcell-loc:
#
# Optional targets should never appear in other aggregate targets (such as 'interaction').
.PHONY: optional
optional: loctree3 metadisorder predbind psic tmhmm tmseg somena consurf
optional: loctree3 metadisorder prona psic tmhmm tmseg somena consurf
.PHONY: coiledcoils
coiledcoils: $(COILSFILE)
......@@ -395,12 +395,12 @@ $(PROFTEXTFILE): $(PROFFILE)
# conv_prof creates query.profAscii.tmp in case query.profAscii already exists - make sure it does not
rm -f $(PROFTEXTFILE); $(PROFROOT)scr/conv_prof.pl $< fileOut=$@ ascii nohtml nodet nograph
.PHONY: predbind
predbind: $(PREDBINDFILE)
.PHONY: prona
prona: $(PRONAFILE)
# Predbind needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run
$(PREDBINDFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)
predbind -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@
# ProNA needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run
$(PRONAFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)
prona2019 -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@
.PHONY: metastudent
metastudent: $(METASTUDENTBPO) $(METASTUDENTCCO) $(METASTUDENTMPO)
......@@ -505,7 +505,7 @@ install:
$(NORSFILE) $(NORSSUMFILE) \
$(NORSNETFILE) \
$(PHDFILE) $(PHDNOTHTMFILE) $(PHDRDBFILE) \
$(PREDBINDFILE) \
$(PRONAFILE) \
$(PROFTEXTFILE) $(PROFFILE) $(PROF1FILE) \
$(PROFBVALFILE) $(PROFB4SNAPFILE) \
$(PROFTMBFILE) $(PROFTMBDATFILE) \
......
configure
View file @ 772dbbde
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for predictprotein 1.1.08.
# Generated by GNU Autoconf 2.69 for predictprotein 1.1.09.
#
# Report bugs to <https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein>.
#
......@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='predictprotein'
PACKAGE_TARNAME='predictprotein'
PACKAGE_VERSION='1.1.08'
PACKAGE_STRING='predictprotein 1.1.08'
PACKAGE_VERSION='1.1.09'
PACKAGE_STRING='predictprotein 1.1.09'
PACKAGE_BUGREPORT='https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein'
PACKAGE_URL=''
......@@ -1202,7 +1202,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures predictprotein 1.1.08 to adapt to many kinds of systems.
\`configure' configures predictprotein 1.1.09 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
......@@ -1268,7 +1268,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of predictprotein 1.1.08:";;
short | recursive ) echo "Configuration of predictprotein 1.1.09:";;
esac
cat <<\_ACEOF
......@@ -1342,7 +1342,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
predictprotein configure 1.1.08
predictprotein configure 1.1.09
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
......@@ -1359,7 +1359,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by predictprotein $as_me 1.1.08, which was
It was created by predictprotein $as_me 1.1.09, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
......@@ -2223,7 +2223,7 @@ fi
# Define the identity of the package.
PACKAGE='predictprotein'
VERSION='1.1.08'
VERSION='1.1.09'
cat >>confdefs.h <<_ACEOF
......@@ -2876,7 +2876,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by predictprotein $as_me 1.1.08, which was
This file was extended by predictprotein $as_me 1.1.09, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
......@@ -2929,7 +2929,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
predictprotein config.status 1.1.08
predictprotein config.status 1.1.09
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
......
configure.ac
View file @ 772dbbde
AC_INIT([predictprotein], [1.1.08], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])
AC_INIT([predictprotein], [1.1.09], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])
AC_CONFIG_SRCDIR([predictprotein])
AM_INIT_AUTOMAKE
AC_CONFIG_FILES([Makefile] [perl/Build.PL] [examples/Makefile] [helper_apps/Makefile] [resources/Makefile])
......
debian/changelog
View file @ 772dbbde
predictprotein (1.1.09-1) unstable; urgency=medium
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.0
* Use secure URI in Homepage field.
-- Andreas Tille <tille@debian.org> Fri, 02 Aug 2019 23:05:22 +0200
predictprotein (1.1.08-1) unstable; urgency=medium
* New upstream version
......
debian/control
View file @ 772dbbde
......@@ -5,12 +5,12 @@ Uploaders: Guy Yachdav <gyachdav@rostlab.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
Build-Depends: debhelper-compat (= 12),
libmodule-build-perl
Standards-Version: 4.2.1
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/predictprotein
Vcs-Git: https://salsa.debian.org/med-team/predictprotein.git
Homepage: http://www.predictprotein.org
Homepage: https://www.predictprotein.org
Package: predictprotein
Architecture: all
......
predictprotein
View file @ 772dbbde
......@@ -75,8 +75,8 @@ our %meth_ext_hash = (
phdNotHtm => 'phd',
phdPred => 'phd',
phdRdb => 'phd',
predbind => 'predbind',
profAscii => 'prof',
prona => 'prona',
reprof => 'reprof',
profbval => 'profbval',
profb4snap => 'profbval',
......@@ -652,7 +652,7 @@ These methods are run by the target 'optional'.
protein-RNA, somena somena somena(1)
protein-DNA
interaction sites
DNA- , RNA- and predbind predbind predbind(1)
DNA- , RNA- and prona prona prona2019(1)
Protein-binding
protein and binding
sites
......