Andreas Tille pushed to branch upstream at Debian Med / predictprotein
Commits: 863084e3 by Andreas Tille at 2019-08-02T21:05:09Z New upstream version 1.1.09 - - - - - 5 changed files: - ChangeLog - MakefilePP.mk - configure - configure.ac - predictprotein Changes: ===================================== ChangeLog ===================================== @@ -1,3 +1,11 @@ +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 <[email protected]> Mon, 18 Mar 2019 15:57:00 +0100 + predictprotein (1.1.08) unstable; urgency=low * Added predbind(1) prediction file handling. ===================================== MakefilePP.mk ===================================== @@ -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) $(PROFTMBDATFILE) \ ===================================== configure ===================================== @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for predictprotein 1.1.08. +# Generated by GNU Autoconf 2.69 for predictprotein 1.1.09. # # Report bugs to <https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein>. # @@ -580,8 +580,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='predictprotein' PACKAGE_TARNAME='predictprotein' -PACKAGE_VERSION='1.1.08' -PACKAGE_STRING='predictprotein 1.1.08' +PACKAGE_VERSION='1.1.09' +PACKAGE_STRING='predictprotein 1.1.09' PACKAGE_BUGREPORT='https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein' PACKAGE_URL='' @@ -1202,7 +1202,7 @@ if test "$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 ===================================== @@ -1,4 +1,4 @@ -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]) ===================================== predictprotein ===================================== @@ -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 View it on GitLab: https://salsa.debian.org/med-team/predictprotein/commit/863084e30f360f170ff5cb31ab5afac9de19731d -- View it on GitLab: https://salsa.debian.org/med-team/predictprotein/commit/863084e30f360f170ff5cb31ab5afac9de19731d You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
