debian/0000755000000000000000000000000012222346167007173 5ustar debian/watch0000644000000000000000000000014611777522442010233 0ustar version=3 opts=pasv ftp://rostlab.org/predictprotein/predictprotein-([0-9.]+)\.tar\.gz debian uupdate debian/rules0000755000000000000000000000035412145517025010252 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 .PHONY: override_dh_compress override_dh_compress: dh_compress -Xexamples/tquick.fasta %: dh $@ get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/changelog0000644000000000000000000004222712222346040011042 0ustar 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 debian/upstream0000644000000000000000000000107411777522442010766 0ustar Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=predictprotein&component=predictprotein&resolution=--- Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein Reference: Author: Burkhrd Rost and Guy Yachdav and Jinfeng Liu Title: The PredictProtein server Journal: Nucleic Acids Research Year: 2004 Volume: 32 Number: 2 Pages: W321-W326 DOI: 10.1093/nar/gkh377 PMID: 15215403 URL: http://nar.oxfordjournals.org/content/32/suppl_2/W321.abstract eprint: http://nar.oxfordjournals.org/content/32/suppl_2/W321.full debian/control0000644000000000000000000000314612174154216010600 0ustar Source: predictprotein Section: science Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan Build-Depends: debhelper (>= 8) Standards-Version: 3.9.4 Homepage: http://www.predictprotein.org Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/predictprotein Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/predictprotein Package: predictprotein Architecture: all Depends: ${misc:Depends}, blast2, bioperl, ncoils (>= 2002-3), disulfinder, hmmer (>= 3.0), hmmer2, librg-exception-perl, librg-utils-perl (>= 1.0.24), ncbi-seg, make, metastudent, norsnet, norsp, perl, predictnls, profbval (>= 1.0.15), profisis, profphd, proftmb (>= 1.1.9-1) Recommends: pp-popularity-contest Suggests: pp-cache-mgr (>= 1.0.3), predictprotein-nonfree Description: suite of protein sequence analysis tools PredictProtein is a sequence analysis suite providing prediction of protein structure and function. . PredictProtein takes a protein sequence as input and provides the following per-residue, or whole protein annotations: * secondary structure * solvent accessibility * multiple sequence alignments * PROSITE sequence motifs * low-complexity regions * nuclear localisation signals * regions lacking regular structure (NORS) * unstructured loops * transmembrane helices * transmembrane beta barrels * coiled-coil regions * disulfide-bonds * disordered regions * B-value flexibility * protein-protein interaction sites * Gene Ontology terms debian/compat0000644000000000000000000000000211777316150010374 0ustar 8 debian/README.source0000644000000000000000000000040111777603736011361 0ustar predictprotein for Debian ========================= Uncompressed examples --------------------- dh_compress excludes examples that appear on the man page. This is in order to allow the example to work as it is pasted on the command like from the man page. debian/copyright0000644000000000000000000000547612000775670011141 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: predictprotein Upstream-Contact: Guy Yachdav Source: ftp://rostlab.org/predictprotein/ Files: debian/* Copyright: 2010 Guy Yachdav 2012 Laszlo Kajan 2012 Simon Domke License: GPL-3+ Files: helper_apps/prosite_scan.pl Copyright: 2008 Guy Yachdav (modifications) public-domain (original: ftp://lausanne.isb-sib.ch/pub/software/unix/prosite_scan/prosite_scan , author Kay Hofmann ) License: public-domain and GPL-3+ Original source (available at ftp://lausanne.isb-sib.ch/pub/software/unix/prosite_scan/prosite_scan) in public domain: 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 . Any modification to this program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". Files: * Copyright: 2010 ROSTLAB License: GPL-3+ License: GPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/source/0000755000000000000000000000000012222346167010473 5ustar debian/source/format0000644000000000000000000000001411777530301011700 0ustar 3.0 (quilt)