[med-svn] [Git][med-team/predictprotein][master] 6 commits: New upstream version 1.1.08
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 17 11:41:30 GMT 2018
Andreas Tille pushed to branch master at Debian Med / predictprotein
Commits:
91019d71 by Andreas Tille at 2018-12-17T11:09:23Z
New upstream version 1.1.08
- - - - -
529c4335 by Andreas Tille at 2018-12-17T11:09:24Z
Update upstream source from tag 'upstream/1.1.08'
Update to upstream version '1.1.08'
with Debian dir 7db7de298c8f4af98cca8e017817d63ba756b6e8
- - - - -
5d47d3fb by Andreas Tille at 2018-12-17T11:09:24Z
New upstream version
- - - - -
0970fee5 by Andreas Tille at 2018-12-17T11:11:04Z
Remove trailing whitespace in debian/changelog
- - - - -
de0fe705 by Andreas Tille at 2018-12-17T11:11:04Z
Remove trailing whitespace in debian/copyright
- - - - -
d5d9ec0d by Andreas Tille at 2018-12-17T11:12:03Z
Upload to unstable
- - - - -
17 changed files:
- ChangeLog
- INSTALL
- Makefile.am
- Makefile.in
- MakefilePP.mk
- configure
- configure.ac
- debian/changelog
- debian/copyright
- examples/Makefile.am
- examples/Makefile.in
- helper_apps/Makefile.am
- helper_apps/Makefile.in
- install-sh
- predictprotein
- resources/Makefile.am
- resources/Makefile.in
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,9 @@
+predictprotein (1.1.08) unstable; urgency=low
+
+ * Added predbind(1) prediction file handling.
+
+ -- Timothy Karl <karl at rostlab.org> Mon, 29 Oct 2018 15:25:37 +0100
+
predictprotein (1.1.07) unstable; urgency=low
* Added metastudent CCO (Cellular Component Ontology) prediction file handling.
=====================================
INSTALL
=====================================
@@ -1,8 +1,8 @@
Installation Instructions
*************************
-Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
-2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
+Inc.
Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
@@ -12,8 +12,8 @@ without warranty of any kind.
Basic Installation
==================
- Briefly, the shell commands `./configure; make; make install' should
-configure, build, and install this package. The following
+ Briefly, the shell command `./configure && make && make install'
+should configure, build, and install this package. The following
more-detailed instructions are generic; see the `README' file for
instructions specific to this package. Some packages provide this
`INSTALL' file but do not implement all of the features documented
@@ -226,6 +226,11 @@ order to use an ANSI C compiler:
and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+ HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved. Use GNU `make'
+instead.
+
On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
parse its `<wchar.h>' header file. The option `-nodtk' can be used as
a workaround. If GNU CC is not installed, it is therefore recommended
@@ -304,9 +309,10 @@ causes the specified `gcc' to be used as the C compiler (unless it is
overridden in the site shell script).
Unfortunately, this technique does not work for `CONFIG_SHELL' due to
-an Autoconf bug. Until the bug is fixed you can use this workaround:
+an Autoconf limitation. Until the limitation is lifted, you can use
+this workaround:
- CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+ CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
`configure' Invocation
======================
@@ -362,4 +368,3 @@ operates.
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.
-
=====================================
Makefile.am
=====================================
@@ -30,7 +30,7 @@ install-data-local:
pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell tr '[:lower:]' '[:upper:]' <<< "$(basename $@)") > "$@"
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
install-data-hook:
sed -i -e 's|__docdir__|$(docdir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__sysconfdir__|$(sysconfdir)|g;s|__bindir__|$(bindir)|g;' "$(DESTDIR)$(pkgdatadir)/predictproteinrc.default"
=====================================
Makefile.in
=====================================
@@ -901,7 +901,7 @@ install-data-local:
pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell tr '[:lower:]' '[:upper:]' <<< "$(basename $@)") > "$@"
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
install-data-hook:
sed -i -e 's|__docdir__|$(docdir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__sysconfdir__|$(sysconfdir)|g;s|__bindir__|$(bindir)|g;' "$(DESTDIR)$(pkgdatadir)/predictproteinrc.default"
=====================================
MakefilePP.mk
=====================================
@@ -59,6 +59,7 @@ PHDFILE:=$(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)
@@ -187,7 +188,7 @@ subcell-loc:
#
# Optional targets should never appear in other aggregate targets (such as 'interaction').
.PHONY: optional
-optional: loctree3 metadisorder psic tmhmm tmseg somena consurf
+optional: loctree3 metadisorder predbind psic tmhmm tmseg somena consurf
.PHONY: coiledcoils
coiledcoils: $(COILSFILE)
@@ -394,6 +395,13 @@ $(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: $(PREDBINDFILE)
+
+# Predbind needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run
+$(PREDBINDFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)
+ predbind -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@
+
.PHONY: metastudent
metastudent: $(METASTUDENTBPO) $(METASTUDENTCCO) $(METASTUDENTMPO)
@@ -497,6 +505,7 @@ install:
$(NORSFILE) $(NORSSUMFILE) \
$(NORSNETFILE) \
$(PHDFILE) $(PHDNOTHTMFILE) $(PHDRDBFILE) \
+ $(PREDBINDFILE) \
$(PROFTEXTFILE) $(PROFFILE) $(PROF1FILE) \
$(PROFBVALFILE) $(PROFB4SNAPFILE) \
$(PROFTMBFILE) $(PROFTMBDATFILE) \
=====================================
configure
=====================================
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for predictprotein 1.1.07.
+# Generated by GNU Autoconf 2.69 for predictprotein 1.1.08.
#
# Report bugs to <https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='predictprotein'
PACKAGE_TARNAME='predictprotein'
-PACKAGE_VERSION='1.1.07'
-PACKAGE_STRING='predictprotein 1.1.07'
+PACKAGE_VERSION='1.1.08'
+PACKAGE_STRING='predictprotein 1.1.08'
PACKAGE_BUGREPORT='https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein'
PACKAGE_URL=''
@@ -1202,7 +1202,7 @@ if test "$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 1.1.07 to adapt to many kinds of systems.
+\`configure' configures predictprotein 1.1.08 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 $ac_init_help in
- short | recursive ) echo "Configuration of predictprotein 1.1.07:";;
+ short | recursive ) echo "Configuration of predictprotein 1.1.08:";;
esac
cat <<\_ACEOF
@@ -1342,7 +1342,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-predictprotein configure 1.1.07
+predictprotein configure 1.1.08
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 1.1.07, which was
+It was created by predictprotein $as_me 1.1.08, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2223,7 +2223,7 @@ fi
# Define the identity of the package.
PACKAGE='predictprotein'
- VERSION='1.1.07'
+ VERSION='1.1.08'
cat >>confdefs.h <<_ACEOF
@@ -2876,7 +2876,7 @@ cat >>$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 1.1.07, which was
+This file was extended by predictprotein $as_me 1.1.08, 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 1.1.07
+predictprotein config.status 1.1.08
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT([predictprotein], [1.1.07], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])
+AC_INIT([predictprotein], [1.1.08], [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
=====================================
@@ -1,3 +1,11 @@
+predictprotein (1.1.08-1) unstable; urgency=medium
+
+ * New upstream version
+ * Remove trailing whitespace in debian/changelog
+ * Remove trailing whitespace in debian/copyright
+
+ -- Andreas Tille <tille at debian.org> Mon, 17 Dec 2018 12:11:04 +0100
+
predictprotein (1.1.07-4) unstable; urgency=medium
* pp-popularity-contest only suggested
@@ -159,7 +167,7 @@ predictprotein (1.0.77) unstable; urgency=low
Added reprof in alpha mode
-- Guy Yachdav <gyachdav at rostlab.org> Mon, 4 Jun 2012 21:03:15 +0200
-
+
predictprotein (1.0.76) unstable; urgency=low
* Depends on profdisis
@@ -435,7 +443,7 @@ predictprotein (1.0.36) stable; urgency=low
predictprotein (1.0.35) stable; urgency=low
- * switched from included norsp scripts to independent package
+ * switched from included norsp scripts to independent package
-- Guy Yachdav <gyachdav at rostlab.org> Thu, 23 Dec 2010 15:35:21 +0100
@@ -647,7 +655,7 @@ predictprotein (1.0.6)
* Man page had an incorrect example
-- Guy Yachdav <gyachdav at rostlab.org> Sun, 18 Jul 2010 12:56:19 +0200
-
+
predictprotein (1.0.1)
* Bug Fixes
@@ -656,7 +664,7 @@ predictprotein (1.0.1)
* Creates files into output folder and not one concatenated file
-- Guy Yachdav <gyachdav at rostlab.org> Sat, 17 Jul 2010 14:37:05 +0200
-
+
predictprotein (1.0.0)
* Initial packaged version
=====================================
debian/copyright
=====================================
@@ -23,12 +23,12 @@ Comment:
http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-July/016408.html
On 14/07/12 21:51, Kay Hofmann wrote:
> Dear Lazlo,
- >
+ >
> Like all other software I have made available (so far), the script prosite_scan.pl that you refer to is in the public domain.
> Feel free to do with it whatever you like.
- >
+ >
> Best Wishes,
- >
+ >
> Kay
.
The modifications were put under GPL-3+.
=====================================
examples/Makefile.am
=====================================
@@ -8,4 +8,4 @@ dist_docexamples_DATA = \
#
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
=====================================
examples/Makefile.in
=====================================
@@ -432,7 +432,7 @@ uninstall-am: uninstall-dist_docexamplesDATA
#
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
helper_apps/Makefile.am
=====================================
@@ -6,4 +6,4 @@ dist_helperapps_SCRIPTS = \
$(srcdir)/prosite_scan.pl
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
=====================================
helper_apps/Makefile.in
=====================================
@@ -444,7 +444,7 @@ uninstall-am: uninstall-dist_helperappsSCRIPTS
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
=====================================
install-sh
=====================================
@@ -345,34 +345,41 @@ do
# is incompatible with FreeBSD 'install' when (umask & 300) != 0.
;;
*)
+ # $RANDOM is not portable (e.g. dash); use it when possible to
+ # lower collision chance
tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
- trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+ trap 'ret=$?; rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir" 2>/dev/null; exit $ret' 0
+ # As "mkdir -p" follows symlinks and we work in /tmp possibly; so
+ # create the $tmpdir first (and fail if unsuccessful) to make sure
+ # that nobody tries to guess the $tmpdir name.
if (umask $mkdir_umask &&
- exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ $mkdirprog $mkdir_mode "$tmpdir" &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/a/b") >/dev/null 2>&1
then
if test -z "$dir_arg" || {
# Check for POSIX incompatibilities with -m.
# HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
# other-writable bit of parent directory when it shouldn't.
# FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
- ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ test_tmpdir="$tmpdir/a"
+ ls_ld_tmpdir=`ls -ld "$test_tmpdir"`
case $ls_ld_tmpdir in
d????-?r-*) different_mode=700;;
d????-?--*) different_mode=755;;
*) false;;
esac &&
- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
- ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ $mkdirprog -m$different_mode -p -- "$test_tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$test_tmpdir"`
test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
}
}
then posix_mkdir=:
fi
- rmdir "$tmpdir/d" "$tmpdir"
+ rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir"
else
# Remove any dirs left behind by ancient mkdir implementations.
- rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ rmdir ./$mkdir_mode ./-p ./-- "$tmpdir" 2>/dev/null
fi
trap '' 0;;
esac;;
=====================================
predictprotein
=====================================
@@ -75,6 +75,7 @@ our %meth_ext_hash = (
phdNotHtm => 'phd',
phdPred => 'phd',
phdRdb => 'phd',
+ predbind => 'predbind',
profAscii => 'prof',
reprof => 'reprof',
profbval => 'profbval',
@@ -651,6 +652,10 @@ 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)
+ Protein-binding
+ protein and binding
+ sites
position-specific psic* psic, clustalngz psic(1),
independent counts runNewPSIC(1),
and its base multi- clustalw(1)
=====================================
resources/Makefile.am
=====================================
@@ -2,4 +2,4 @@ pkgdataexampledir = $(pkgdatadir)/resources
dist_pkgdataexample_DATA = $(srcdir)/HtmlQuote.html $(srcdir)/HtmlHr.html
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
=====================================
resources/Makefile.in
=====================================
@@ -425,7 +425,7 @@ uninstall-am: uninstall-dist_pkgdataexampleDATA
dist-hook:
- rm -rf `find $(distdir) -name .svn`
+ rm -rf `find $(distdir) -name .git`
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
View it on GitLab: https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc
--
View it on GitLab: https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc
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