Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/ChangeLog
+++ b/ChangeLog
+predictprotein (1.1.08) unstable; urgency=low
+
+  * Added predbind(1) prediction file handling.
+
+ -- Timothy Karl <karl@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.

--- a/INSTALL
+++ b/INSTALL
 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.
-
--- a/Makefile.am
+++ b/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"

--- a/Makefile.in
+++ b/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"

--- a/MakefilePP.mk
+++ b/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) \

--- a/configure
+++ b/configure
 #! /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\\"


--- a/configure.ac
+++ b/configure.ac
-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])

--- a/debian/changelog
+++ b/debian/changelog
+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@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@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@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@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@rostlab.org>  Sat, 17 Jul 2010 14:37:05 +0200
-	
+
 predictprotein (1.0.0)

  * Initial packaged version

--- a/debian/copyright
+++ b/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+.

--- a/examples/Makefile.am
+++ b/examples/Makefile.am
@@ -8,4 +8,4 @@ dist_docexamples_DATA = \
 #

 dist-hook:
-	rm -rf `find $(distdir) -name .svn`
+	rm -rf `find $(distdir) -name .git`
--- a/examples/Makefile.in
+++ b/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.

--- a/helper_apps/Makefile.am
+++ b/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`
--- a/helper_apps/Makefile.in
+++ b/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.

--- a/install-sh
+++ b/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;;

--- a/predictprotein
+++ b/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)

--- a/resources/Makefile.am
+++ b/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`
--- a/resources/Makefile.in
+++ b/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.