predictprotein (1.1.07-2) unstable; urgency=medium [ Tatiana Malygina ] * Team upload. * cme fix dpkg-control * add hardening [ Andreas Tille ] * d/watch: version=4 * debhelper 10 -- Tatiana Malygina Fri, 08 Jul 2016 22:17:25 +0300 predictprotein (1.1.07-1) unstable; urgency=medium * New upstream version * Build-Depends: libmodule-build-perl Closes: #789640 -- Andreas Tille Fri, 03 Jul 2015 09:28:44 +0200 predictprotein (1.1.06-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * debhelper 9 * d/copyright: Move "Files: *" section on top to fit DEP5 -- Andreas Tille Thu, 02 Oct 2014 11:25:18 +0200 predictprotein (1.1.01-1) unstable; urgency=low [ Guy Yachdav ] * New upstream release: integrated somena(1) [ Andreas Tille ] * Priority: optional * Removed README.source since this it just explains usual practice * cme fix dpkg-control * correct DEP5 syntax and content of debian/copyright -- Andreas Tille Wed, 02 Apr 2014 21:41:04 +0200 predictprotein (1.0.99-1) UNRELEASED; urgency=low * New upstream release: integrated reprof(1) -- Guy Yachdav Fri, 28 Mar 2014 02:50:16 +0100 predictprotein (1.0.98) UNRELEASED; urgency=low * New upstream release: integrated TMSEG(1) -- Guy Yachdav Mon, 10 Mar 2014 20:43:12 +0100 predictprotein (1.0.97~bpo70+1) UNRELEASED; urgency=low * New upstream release: mapped lc3 extensions to method. -- Guy Yachdav Wed, 26 Feb 2014 23:38:17 +0100 predictprotein (1.0.95-1~bpo70+1) UNRELEASED; urgency=low * New upstream release: upgraded to loctree3 (lc3) -- Guy Yachdav Tue, 11 Feb 2014 20:47:22 +0100 predictprotein (1.0.94-1) unstable; urgency=low * New upstream release: fixes "FTBFS: POD errors" (Closes: #724122). -- Laszlo Kajan Mon, 30 Sep 2013 21:07:08 +0200 predictprotein (1.0.92-1~bpo70+1) unstable; urgency=low * New upstream release. -- Laszlo Kajan Mon, 10 Jun 2013 20:08:19 +0200 predictprotein (1.0.90-1) unstable; urgency=low * New upstream release -- Guy Yachdav Thu, 24 Jan 2013 16:20:44 +0100 predictprotein (1.0.88-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Wed, 05 Dec 2012 14:57:26 +0100 predictprotein (1.0.87-1) unstable; urgency=low * New upstream release. -- Laszlo Kajan Wed, 19 Sep 2012 17:54:23 +0200 predictprotein (1.0.86-1) unstable; urgency=low * Initial release (Closes: #680610) * profdisis now runs in succinct mode -- Guy Yachdav Mon, 13 Aug 2012 17:38:28 +0200 predictprotein (1.0.80-1) UNRELEASED; urgency=low * Removed profglobe. * Fixed lowcompseg-renamed-to-ncbi-seg issue. -- Laszlo Kajan Fri, 06 Jul 2012 14:25:47 +0200 predictprotein (1.0.79-1) UNRELEASED; urgency=low * reprof integration moved to its own branch while experimental. * metadisorder a Suggests: because it is non-redistributable for all. * Removing disis Suggests per Burkhard's request: we do not trust the method any more, Yanay had some funny results with the packaged version. * Cleaned up Suggests. * Depends on ncbi-seg now (the new name for lowcompseg). -- Laszlo Kajan Fri, 06 Jul 2012 11:40:43 +0200 predictprotein (1.0.78) unstable; urgency=low * Added --print-ext-method-map cmd line argument. * Removed unnecessary libnhgri-blastall-perl dependency. * profcon is no longer a dependency of any sort. * hmm3pfam is now a default target. Promoted Suggests: of hmmer to Depends:. * disis back to Suggests and an optional target because of svm-light5 dependency that can not make it into Debian (non-redistributable). -- Laszlo Kajan Tue, 19 Jun 2012 11:24:31 +0200 predictprotein (1.0.77) unstable; urgency=low * [Laszlo Kajan ] Demoting pp-cache-mgr dependency to Suggests - as this pack is not necessary for the default configuration and should not be pulled in automatically because of 'Recommends'. * [Guy Yachdav ] Added reprof in alpha mode -- Guy Yachdav Mon, 4 Jun 2012 21:03:15 +0200 predictprotein (1.0.76) unstable; urgency=low * Depends on profdisis -- Laszlo Kajan Tue, 21 Feb 2012 14:06:07 +0100 predictprotein (1.0.75) unstable; urgency=low * profdisis target now in 'all' as svm-light5 is now redistributable by us -- Laszlo Kajan Tue, 21 Feb 2012 13:29:31 +0100 predictprotein (1.0.74) unstable; urgency=low * fixed proftmb Makefile rule bug -- Laszlo Kajan Fri, 17 Feb 2012 17:12:45 +0100 predictprotein (1.0.73) unstable; urgency=low * Reconfigure to work with HHomp-compatible (newer) proftmb. -- Laszlo Kajan Fri, 17 Feb 2012 16:03:47 +0100 predictprotein (1.0.72) unstable; urgency=low * Changed section to non-free/science. * Updated manpage. -- Laszlo Kajan Sat, 17 Dec 2011 02:27:11 +0100 predictprotein (1.0.71) unstable; urgency=low * output dir for examples now /tmp/pp -- Laszlo Kajan Thu, 15 Dec 2011 22:10:11 +0100 predictprotein (1.0.70) unstable; urgency=low * removed profchop dependency as we never actually called it -- Laszlo Kajan Thu, 15 Dec 2011 22:09:07 +0100 predictprotein (1.0.69) unstable; urgency=low * hmm3pfam moved to be an optional target because Bio-Linux dependencies can not handle the upgrade to version 3 of it -- Laszlo Kajan Thu, 15 Dec 2011 21:47:21 +0100 predictprotein (1.0.68) unstable; urgency=low * conflicts with coiledcoils -- Laszlo Kajan Thu, 27 Oct 2011 20:24:16 +0200 predictprotein (1.0.67) unstable; urgency=low * dep now on ncoils as a replacement of coiledcoils -- Laszlo Kajan Sat, 22 Oct 2011 11:18:12 +0200 predictprotein (1.0.66) unstable; urgency=low * the error.log generated by occational blast in psic is now handled -- Laszlo Kajan Fri, 21 Oct 2011 13:12:47 +0200 predictprotein (1.0.65) unstable; urgency=low * --prosite-dat to give loctree the prosite.dat database path -- Laszlo Kajan Fri, 21 Oct 2011 12:07:18 +0200 predictprotein (1.0.64) unstable; urgency=low * exposed new loctree cmd line arg for Swiss-Prot keyword-to-accession 'index' -- Laszlo Kajan Tue, 18 Oct 2011 16:58:36 +0200 predictprotein (1.0.63) unstable; urgency=low * updated cache_merge logic: now no merging occurs when the cache is empty * fixed DESTDIR vulnerability due to lack of quoting in Makefile - DESTDIR now accepts all valid paths -- Laszlo Kajan Mon, 19 Sep 2011 17:57:01 +0200 predictprotein (1.0.62) unstable; urgency=low * Merging, when --target is used, is now default only when there already is something in the cache. -- Laszlo Kajan Mon, 19 Sep 2011 17:55:26 +0200 predictprotein (1.0.61) unstable; urgency=low * fixed --output-dir bug when it is not a fully qualified path -- Laszlo Kajan Thu, 15 Sep 2011 15:44:48 +0200 predictprotein (1.0.60) unstable; urgency=low * fixed --target switching on cache merging when nouse-cache is given * added ~/.predictproteinrc to the conf file list -- Laszlo Kajan Tue, 28 Jun 2011 17:42:29 +0200 predictprotein (1.0.59) unstable; urgency=low * removed >> 8 from $? error reporting in predictprotein -- Laszlo Kajan Fri, 03 Jun 2011 14:13:55 +0200 predictprotein (1.0.58) unstable; urgency=low * added code to recover STDERR of blast calls and disulfinder in case of failure even if not in debug mode -- Laszlo Kajan Fri, 20 May 2011 22:13:21 +0200 predictprotein (1.0.57) unstable; urgency=low * fixed exit 255 bug -- Laszlo Kajan Wed, 18 May 2011 22:35:50 +0200 predictprotein (1.0.56) unstable; urgency=low * more rigorous cleaning up after ppc_lock -- Laszlo Kajan Wed, 18 May 2011 14:05:32 +0200 predictprotein (1.0.55) unstable; urgency=low * blastall error.log is now automatically removed -- Laszlo Kajan Sun, 15 May 2011 20:16:02 +0200 predictprotein (1.0.54) unstable; urgency=low * clustalw results from psic are now retained in cache - gzipped * switch make to workdir with -C now - this makes targets like query.asp work * --cache-merge cache merging implemented, this is now ON by default in case use_cache is in effect -- Laszlo Kajan Thu, 05 May 2011 21:49:16 +0200 predictprotein (1.0.53) unstable; urgency=low * .hssp80 is removed from light_cache list because Esmeralda needs it -- Laszlo Kajan Wed, 20 Apr 2011 18:24:11 +0200 predictprotein (1.0.52) unstable; urgency=low * Added light_cache config file value to control caching of big and rarely needed files. With light_cache set to 1 .safBlastPsi .safBlastPsi80 .hssp and .hssp80 are not stored into the cache -- Laszlo Kajan Fri, 15 Apr 2011 14:17:24 +0200 predictprotein (1.0.51) unstable; urgency=low * now uses runNewPSIC.pl from the rost-runpsic package -- Laszlo Kajan Tue, 12 Apr 2011 12:33:33 +0200 predictprotein (1.0.50) unstable; urgency=low * added --makedebug cmd line argument to trigger --debug of make -- Laszlo Kajan Fri, 11 Mar 2011 15:37:14 +0100 predictprotein (1.0.49) unstable; urgency=low * proper license presentation in debconf -- Laszlo Kajan Wed, 09 Mar 2011 11:41:26 +0100 predictprotein (1.0.48) unstable; urgency=low * added debconf check for non-profitness * changed license to academi ala ppmi license -- Laszlo Kajan Wed, 09 Mar 2011 10:53:44 +0100 predictprotein (1.0.47) unstable; urgency=low * >& now correctly -- Laszlo Kajan Wed, 02 Mar 2011 13:08:31 +0100 predictprotein (1.0.46) unstable; urgency=low * dash compatible shell syntax -- Laszlo Kajan Wed, 02 Mar 2011 10:37:40 +0100 predictprotein (1.0.45) stable; urgency=low * message when pp-popcon is not installed -- Laszlo Kajan Mon, 28 Feb 2011 17:56:33 +0100 predictprotein (1.0.44) stable; urgency=low * pp man page mentions popularity contest * in popularity contest * coils-wrap.pl now uses proper tmp dir * removed prodom but kept cmd line arg for compatibility -- Laszlo Kajan Fri, 18 Feb 2011 13:27:52 +0100 predictprotein (1.0.43) stable; urgency=low * pp-cache-mgr is only recommended now, not a dep; loctree and tmhmm are suggests -- Laszlo Kajan Thu, 27 Jan 2011 23:40:18 +0100 predictprotein (1.0.42) stable; urgency=low * added predictnls dependency -- Laszlo Kajan Thu, 27 Jan 2011 16:35:13 +0100 predictprotein (1.0.41) stable; urgency=low * silenced disulfinder * psic now runs with blastpgp results on big80: .blastPsiOutTmp -- Laszlo Kajan Fri, 21 Jan 2011 16:32:52 +0100 predictprotein (1.0.40) stable; urgency=low * psicexe default changed to /usr/share/librg-utils-perl/runNewPSIC.pl * no more snapfun dependency * added 'make', 'perl' dependency -- Laszlo Kajan Wed, 19 Jan 2011 17:12:42 +0100 predictprotein (1.0.39) stable; urgency=low * --cpu 4 corrected on hmmscan -- Laszlo Kajan Mon, 17 Jan 2011 23:36:54 +0100 predictprotein (1.0.38) stable; urgency=low * made loctree recommended 'cause it depends on the non-redistributable SignalP * extended debian/control with paragraphs about tmhmm and loctree * took tmhmm and loctree out of the default target all:, these are now in the optional: target * new config file option: default_targets to control targets made when none is given on the cmd line -- Laszlo Kajan Mon, 17 Jan 2011 17:58:02 +0100 predictprotein (1.0.37) stable; urgency=low * made tmhmm a suggested package and not a dependency -- Guy Yachdav Sun, 16 Jan 2011 16:59:06 +0100 predictprotein (1.0.36) stable; urgency=low * tidied up MakefilePP.mk: changed references to profnors to norsp -- Laszlo Kajan Tue, 04 Jan 2011 11:08:05 +0100 predictprotein (1.0.35) stable; urgency=low * switched from included norsp scripts to independent package -- Guy Yachdav Thu, 23 Dec 2010 15:35:21 +0100 predictprotein (1.0.34) stable; urgency=low * norsnet now on disorder target * ... -- Laszlo Kajan Tue, 14 Dec 2010 15:34:32 +0100 predictprotein (1.0.33) stable; urgency=low * all blasts now 2>/dev/null if not debug -- Laszlo Kajan Tue, 19 Oct 2010 14:38:04 +0200 predictprotein (1.0.32) stable; urgency=low * --numresmax: maximum sequence length allowed I think convert_seq fails for a seq over 19000. Marco's swissprot analysis: TOTAL NUMBER OF SEQUENCES = 12,265,120 0-1000 11,962,876 0.975 1000-2000 261,633 0.021 2000-3000 25,677 0.002 3000-4000 9,944 0 4000-5000 2,735 0 5000-6000 1,060 0 6000-7000 428 0 7000-8000 366 0 8000-9000 164 0 9000-10000 65 0 >10000 171 0 -- Laszlo Kajan Tue, 19 Oct 2010 14:38:04 +0200 predictprotein (1.0.31) stable; urgency=low * --profnumresmin: minimum sequence length required by prof. Sequences shorter than this will make predictprotein fail with 254 This value is 17 by default, configurable from the cmd line or config file. -- Laszlo Kajan Thu, 14 Oct 2010 16:43:48 +0200 predictprotein (1.0.30) stable; urgency=low * silenced warnings of %.blastpSwissM8 blastall call (e.g. 'Selenocysteine (U) at position 59 replaced by X') -- Laszlo Kajan Thu, 14 Oct 2010 09:28:27 +0200 predictprotein (1.0.29) stable; urgency=low * MakefilePP now properly defined rules producing multiple targets - now ready for -j >1 runs -- Laszlo Kajan Wed, 13 Oct 2010 18:39:59 +0200 predictprotein (1.0.28) stable; urgency=low * psic call with --quiet -- Laszlo Kajan Tue, 12 Oct 2010 17:31:17 +0200 predictprotein (1.0.27) stable; urgency=low * added configuration options for pfam databases -- Laszlo Kajan Mon, 11 Oct 2010 14:17:13 +0200 predictprotein (1.0.26) stable; urgency=low * added required version to hmmer dep -- Laszlo Kajan Sat, 09 Oct 2010 14:11:34 +0200 predictprotein (1.0.25) stable; urgency=low * added missing dependencies -- Laszlo Kajan Sat, 09 Oct 2010 14:01:48 +0200 predictprotein (1.0.24) stable; urgency=low * fixed tmhmm work dir issue - not current dir but tmp dir now -- Laszlo Kajan Fri, 08 Oct 2010 23:31:44 +0200 predictprotein (1.0.23) stable; urgency=low * added psic from snap * added loctree with all 3 organism 'types' * added hmmer2 and 3 * added prof runs on fasta sequence only (no alignment) * added tmhmm -- Laszlo Kajan Fri, 08 Oct 2010 13:59:43 +0200 predictprotein (1.0.22) stable; urgency=low * Sequence now converted to upper case before fed into pipeline * Copf now explicitely told to expect FASTA format input file (where appropriate) -- Laszlo Kajan Mon, 20 Sep 2010 17:13:20 +0200 predictprotein (1.0.21) stable; urgency=low * Makefile.am now correctly modifies predictprotein with version number * Debian native now * Unfortunate dependency on discontinued librg-pp-cachemgr-perl removed -- Laszlo Kajan Fri, 17 Sep 2010 15:11:28 +0200 predictprotein (1.0.20) * Silenced 'wrong parsin htm file??\nctHtm=$ctHtm' * Corrected some grammar issues * Reorganized predictprotein - only for more logical code, no change in what it does -- Laszlo Kajan Mon, 16 Aug 2010 21:25:17 +0200 predictprotein (1.0.19) * Introduced config file and cmd line params to control: bigblastdb big80blastdb swissblastdb prodomblastdb prositeconvdat -- Laszlo Kajan Mon, 16 Aug 2010 19:05:18 +0200 predictprotein (1.0.18) * silenced nors.pl * MD make rules according to Avner's original runMD.pl are now included but are not used -- Laszlo Kajan Thu, 12 Aug 2010 20:30:57 +0200 predictprotein (1.0.17) * file restore logic moved to cache module -- Laszlo Kajan Fri, 23 Jul 2010 13:23:00 +0200 predictprotein (1.0.16) * redirecting standard output of make of methods to /dev/null if not --debug -- Laszlo Kajan Fri, 23 Jul 2010 13:23:00 +0200 predictprotein (1.0.15) * fixed filter_blastp_big.pl e-179 error -- Laszlo Kajan Fri, 23 Jul 2010 13:23:00 +0200 predictprotein (1.0.14) * fixed syntax error -- Laszlo Kajan Fri, 23 Jul 2010 13:23:00 +0200 predictprotein (1.0.13) * Another example on man page * predictprotein works with cache now -- Laszlo Kajan Fri, 23 Jul 2010 13:23:00 +0200 predictprotein (1.0.12) * New examples -- Laszlo Kajan Thu, 22 Jul 2010 09:35:05 +0200 predictprotein (1.0.11) * filter_blastp_big.pl -> helper apps -- Laszlo Kajan Wed, 21 Jul 2010 21:53:30 +0200 predictprotein (1.0.10) * Helper apps now installed as scripts -- Laszlo Kajan Wed, 21 Jul 2010 21:53:30 +0200 predictprotein (1.0.9) * predictnls params now correctly given (were paths for fileSummary and fileTrace, boolean is expected) -- Laszlo Kajan Wed, 21 Jul 2010 21:53:30 +0200 predictprotein (1.0.8) * Man pages -- Laszlo Kajan Wed, 21 Jul 2010 21:53:30 +0200 predictprotein (1.0.7) * System now compatible with cmd line interface of the cache manager and queue manager -- Laszlo Kajan Wed, 21 Jul 2010 21:53:30 +0200 predictprotein (1.0.6) * Paths for prof, proftmb are now resolved through the config file * Added more version information about the package * Man page had an incorrect example -- Guy Yachdav Sun, 18 Jul 2010 12:56:19 +0200 predictprotein (1.0.1) * Bug Fixes * No longer relies on RG:PP * Runs profdisis * Creates files into output folder and not one concatenated file -- Guy Yachdav Sat, 17 Jul 2010 14:37:05 +0200 predictprotein (1.0.0) * Initial packaged version -- Guy Yachdav Wed, 28 Apr 2010 15:33:11 +0200