Loading ChangeLog +6 −0 Original line number Diff line number Diff line 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. Loading INSTALL +12 −7 Original line number Diff line number Diff line 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 Loading @@ -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 Loading Loading @@ -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 Loading Loading @@ -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 ====================== Loading Loading @@ -362,4 +368,3 @@ operates. `configure' also accepts some other, not widely useful, options. Run `configure --help' for more details. Makefile.am +1 −1 Original line number Diff line number Diff line Loading @@ -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)$(pkgdatadir)/predictproteinrc.default" Loading Makefile.in +1 −1 Original line number Diff line number Diff line Loading @@ -901,7 +901,7 @@ install-data-local: pod2man -c 'User Commands' -r "$(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)$(pkgdatadir)/predictproteinrc.default" Loading MakefilePP.mk +10 −1 Original line number Diff line number Diff line Loading @@ -59,6 +59,7 @@ PHDFILE:=$(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) Loading Loading @@ -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) Loading Loading @@ -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) Loading Loading @@ -497,6 +505,7 @@ install: $(NORSFILE) $(NORSSUMFILE) \ $(NORSNETFILE) \ $(PHDFILE) $(PHDNOTHTMFILE) $(PHDRDBFILE) \ $(PREDBINDFILE) \ $(PROFTEXTFILE) $(PROFFILE) $(PROF1FILE) \ $(PROFBVALFILE) $(PROFB4SNAPFILE) \ $(PROFTMBFILE) $(PROFTMBDATFILE) \ Loading Loading
ChangeLog +6 −0 Original line number Diff line number Diff line 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. Loading
INSTALL +12 −7 Original line number Diff line number Diff line 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 Loading @@ -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 Loading Loading @@ -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 Loading Loading @@ -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 ====================== Loading Loading @@ -362,4 +368,3 @@ operates. `configure' also accepts some other, not widely useful, options. Run `configure --help' for more details.
Makefile.am +1 −1 Original line number Diff line number Diff line Loading @@ -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)$(pkgdatadir)/predictproteinrc.default" Loading
Makefile.in +1 −1 Original line number Diff line number Diff line Loading @@ -901,7 +901,7 @@ install-data-local: pod2man -c 'User Commands' -r "$(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)$(pkgdatadir)/predictproteinrc.default" Loading
MakefilePP.mk +10 −1 Original line number Diff line number Diff line Loading @@ -59,6 +59,7 @@ PHDFILE:=$(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) Loading Loading @@ -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) Loading Loading @@ -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) Loading Loading @@ -497,6 +505,7 @@ install: $(NORSFILE) $(NORSSUMFILE) \ $(NORSNETFILE) \ $(PHDFILE) $(PHDNOTHTMFILE) $(PHDRDBFILE) \ $(PREDBINDFILE) \ $(PROFTEXTFILE) $(PROFFILE) $(PROF1FILE) \ $(PROFBVALFILE) $(PROFB4SNAPFILE) \ $(PROFTMBFILE) $(PROFTMBDATFILE) \ Loading
