debian/0000775000000000000000000000000012300163043007160 5ustar debian/copyright0000664000000000000000000000235011776574747011154 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: hmmer Upstream-Contact: Sean Eddy Source: ftp://selab.janelia.org/pub/software/hmmer/ Files: debian/* Copyright: 1998, John Lapeyre License: GPL-2+ Files: * Copyright: Copyright (C) 1992-2003 HHMI/Washington University School of Medicine License: GPL-2+ License: GPL-2+ 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 2 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/README.Debian0000664000000000000000000000114711776574747011265 0ustar hmmer2 for Debian ----------------- This hmmer2 package has been built with POSIX multithreading support (--enable-threads), Large File Support (--enable-lfs) and Parallel Virtual Machine (--enable-pvm) enabled. -- Nelson A. de Oliveira Tue, 08 Aug 2006 23:07:12 -0300 Notes on how this package is tested: The HMMER programs are tested when we assemble our binary packages in our build network, using the standard upstream tests. You can consult the results in the build logs: ‘http://buildd.debian.org/hmmer2’. -- Charles Plessy Wed, 16 Dec 2009 13:52:24 +0900 debian/README.source0000664000000000000000000000106012010243655011342 0ustar hmmer2 for Debian ================= Repackaged Upstream Source -------------------------- The non-policy-compliant 'get-orig-source' target is provided to build the upstream tarball. The problem with the upstream tarball is that upstream packs a pdf (Userguide.pdf) without sources. In 'get-orig-source' this file is deleted from the archive. I have decided to keep d/watch and use uscan in 'get-orig-source' in order to keep the process simpler, sacrificing the "get-orig-source [...] may be invoked in any directory" requirement of the policy (point 4.9). debian/hmmer2-doc.docs0000664000000000000000000000001212010243655011766 0ustar tutorial/ debian/hmmer2.NEWS0000664000000000000000000000106711775616577011112 0ustar hmmer (2.3.2-3) unstable; urgency=low Hmmer dependency on biosquid has been downgraded to recommends, as there is no need for this upgrade path anymore. -- Nelson A. de Oliveira Tue, 31 Jul 2007 16:18:00 -0300 hmmer (2.3.2-1) unstable; urgency=low Some binaries from the old hmmer (version 2.1.4) have been split between two packages: hmmer and biosquid. To maintain all binaries included on the older hmmer, the new hmmer package depends on biosquid. -- Nelson A. de Oliveira Tue, 08 Aug 2006 23:07:12 -0300 debian/changelog0000664000000000000000000001163012300163036011035 0ustar hmmer2 (2.3.2-7ubuntu1) trusty; urgency=low * Use autotools-dev for arm64. -- Daniel T Chen Sun, 16 Feb 2014 11:23:45 -0500 hmmer2 (2.3.2-7) unstable; urgency=low * Team upload * debian/control: - Removed myself from the Uploaders. - Removed obsolete DM-Upload-Allowed field. - Use canonical VCS URLs. - Normalised using config-model-edit. - Build-depend on libperl4-corelibs-perl (Closes: #730921). * Conforms with Policy 3.9.5. -- Charles Plessy Sun, 01 Dec 2013 09:26:43 +0900 hmmer2 (2.3.2-6) unstable; urgency=low [Charles Plessy] * Enabled upstream checks in debian/rules. * Documented how the package is tested in debian/README.Debian * Switched Debhelper to mode 7 (debian/compat, debian/control). * Gathered some metadata about upstream in debian/upstream-metadata.yaml. * Checked conformance with Policy 3.8.3 and incremented Standards-Version in debian/control to reflect it. [Laszlo Kajan] * Debhelper 8. * Policy version 3.9.3. * Renaming hmmer version 2 to hmmer2 in order to allow coexistence with hmmer (>=3) in wheezy. * Renaming binaries and man pages: hmmalign => hmm2align hmmbuild => hmm2build hmmcalibrate => hmm2calibrate hmmconvert => hmm2convert hmmemit => hmm2emit hmmfetch => hmm2fetch hmmindex => hmm2index hmmpfam => hmm2pfam hmmsearch => hmm2search hmmcalibrate-pvm => hmm2calibrate-pvm hmmpfam-pvm => hmm2pfam-pvm hmmsearch-pvm => hmm2search-pvm in order to allow coexistence with those from hmmer (>=3). (Closes: #680539) * debian/rules: remove binary without source documentation Userguide.pdf in get-orig-source target -- Laszlo Kajan Mon, 09 Jul 2012 17:46:31 +0200 hmmer (2.3.2-5) unstable; urgency=low * Changed the doc-base section according to the new policy. * debian/control: - Added myself as Uploader. - Increased priority to `optional' - Standards-Version: 3.8.0 (no changes needed) -- Charles Plessy Sun, 06 Jul 2008 23:49:23 +0900 hmmer (2.3.2-4) unstable; urgency=low * Moved Homepage tag from long description to tags * Removed XB-Tag because it is actually not used by debtags * Added myself as Uploader * Standards-Version: 3.7.3 (no changes needed) * Added Vcs-Browser, Vcs-Svn * DM-Upload-Allowed: yes -- Andreas Tille Tue, 26 Feb 2008 20:40:17 +0100 hmmer (2.3.2-3) unstable; urgency=low * Updated hmmer homepage (Closes: #435396). Thanks to Charles Plessy; * Updated watch file; * Moved Matthew Vernon to Uploaders and set Maintainer to Debian-Med Packaging Team ; * Downgraded biosquid to recommends. -- Nelson A. de Oliveira Tue, 31 Jul 2007 15:15:23 -0300 hmmer (2.3.2-2) unstable; urgency=medium * Changed my email address; * Changing priority to extra, instead optional (hmmer has a dependency on pvm and libpmv3 -- Policy 2.5); * Added tags on debian/control; * Medium urgency to get the package with the correct priority on Etch. -- Nelson A. de Oliveira Wed, 6 Dec 2006 16:27:06 -0200 hmmer (2.3.2-1) unstable; urgency=low * New upstream version (Closes: #261293); * Documentation is split in a new package (Closes: #233374, #175481); * "getseq" is not shipped anymore with hmmer, since it was renamed to "sfetch" (Closes: #197658); * New package hmmer-pvm, with PVM enabled binaries; * The package is again non-Debian native; * Using CDBS; * Using debhelper compatibility level 5; * Updated Standards-Version to 3.7.2; * Added doc-base and watch file; * Updated copyright file; * Added me as co-maintainer. From Matthew Vernon: "If you're keen to take hmmer, take it; I'm writing up my thesis at the moment, so my time for Debian is somewhat limited; I took on hmmer because it was orphaned at the time, and I wanted it to stay in the distribution." -- Nelson A. de Oliveira Tue, 15 Aug 2006 17:30:32 -0300 hmmer (2.1.4) unstable; urgency=low * Change section to science -- Matthew Vernon Tue, 10 Apr 2001 02:51:17 +0100 hmmer (2.1.3) unstable; urgency=low * Move from /usr/man to /usr/share/man (closes: #91171) * Move from /usr/doc to /usr/share/doc (closes: #91494) -- Matthew Vernon Mon, 09 Apr 2001 16:12:21 +0100 hmmer (2.1.2) unstable; urgency=low * New maintainer -- Matthew Vernon Tue, 07 Dec 1999 16:30:35 +0000 hmmer (2.1.1-1) unstable; urgency=low * New upstream version. -- John Lapeyre Tue, 30 Mar 1999 16:50:05 -0700 hmmer (2.0-1) unstable; urgency=low * Initial Release. -- John Lapeyre Thu, 13 Aug 1998 21:48:53 -0700 debian/hmmer2-pvm.10000664000000000000000000000113112010243655011236 0ustar .TH HMMER-PVM 1 "Tue, 08 Aug 2006 20:00:00 -0300" .SH NAME hmmer2-pvm \- HMMER utilities for PVM clusters .SH DESCRIPTION Information on how to use the programs .B hmmcalibrate-pvm , .B hmmpfam-pvm and .B hmmsearch-pvm is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf). .PP .SH SEE ALSO .BR hmmer2 (1), .BR hmmer (1) .SH AUTHOR HMMER was written by Sean Eddy. .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/docs0000664000000000000000000000000610761065313010041 0ustar NOTES debian/patches/0000775000000000000000000000000012246501114010613 5ustar debian/patches/userguidepdf0000664000000000000000000001345212010243655013233 0ustar Description: corrections to man pages The WWW home of hmmer (URL) is updated. Also, as we now do not include Userguide.pdf in this package, references to that are changed to ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf . . No need to forward this patch as it tackles issues with the way this hmmer version is packaged for Debian. Author: Laszlo Kajan Forwarded: no --- a/00README +++ b/00README @@ -14,8 +14,9 @@ o Getting HMMER - WWW home: http://hmmer.wustl.edu/ + WWW home: http://hmmer.janelia.org/ Distribution: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/ + User's Guide: ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf o Installing HMMER --- a/documentation/man/hmmalign.man +++ b/documentation/man/hmmalign.man @@ -129,9 +129,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmbuild.man +++ b/documentation/man/hmmbuild.man @@ -438,9 +438,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmcalibrate.man +++ b/documentation/man/hmmcalibrate.man @@ -135,9 +135,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmconvert.man +++ b/documentation/man/hmmconvert.man @@ -86,9 +86,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmemit.man +++ b/documentation/man/hmmemit.man @@ -91,9 +91,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmfetch.man +++ b/documentation/man/hmmfetch.man @@ -56,9 +56,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmindex.man +++ b/documentation/man/hmmindex.man @@ -37,9 +37,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmpfam.man +++ b/documentation/man/hmmpfam.man @@ -282,9 +282,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/documentation/man/hmmsearch.man +++ b/documentation/man/hmmsearch.man @@ -249,9 +249,8 @@ pages: see .B hmmer2(1). .PP -For complete documentation, see the user guide that came with the -distribution (Userguide.pdf); or see the HMMER web page, -http://hmmer.wustl.edu/. +For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, +http://hmmer.janelia.org/. .SH COPYRIGHT --- a/INSTALL +++ b/INSTALL @@ -3,7 +3,7 @@ ------------------------------------------ These are quick installation instructions. For complete documentation, -see the Installation chapter in the HMMER User's Guide (Userguide.pdf). +see the Installation chapter in the HMMER User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf). For a source distribution (hmmer-2.3.2.tar.gz): --- a/documentation/man/hmmer.man +++ b/documentation/man/hmmer.man @@ -73,7 +73,7 @@ with the software distribution, which includes a tutorial introduction and more detailed descriptions of the programs. -See http://hmmer.wustl.edu/ for on-line documentation and +See http://hmmer.janelia.org/ for on-line documentation and the current HMMER release. .PP --- a/NOTES +++ b/NOTES @@ -1,5 +1,5 @@ HMMER 2.3.2 release notes -http://hmmer.wustl.edu/ +http://hmmer.janelia.org/ SRE, Fri Oct 3 14:04:44 2003 ________________________________________________________________ debian/patches/series0000664000000000000000000000003612010243655012031 0ustar version2-manpage userguidepdf debian/patches/version2-manpage0000664000000000000000000003770211776576050013746 0ustar Description: rename binaries in man pages Binaries are renamed in man pages to match their new file names. . No need to forward this patch as it tackles issues with the way hmmer versions are packaged for Debian. Author: Laszlo Kajan Forwarded: no --- a/documentation/man/hmmer.man +++ b/documentation/man/hmmer.man @@ -1,4 +1,4 @@ -.TH "hmmer" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmmer2" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP @@ -6,41 +6,41 @@ .SH SYNOPSIS .TP -.B hmmalign +.B hmm2align Align multiple sequences to a profile HMM. .TP -.B hmmbuild +.B hmm2build Build a profile HMM from a given multiple sequence alignment. .TP -.B hmmcalibrate +.B hmm2calibrate Determine appropriate statistical significance parameters for a profile HMM prior to doing database searches. .TP -.B hmmconvert +.B hmm2convert Convert HMMER profile HMMs to other formats, such as GCG profiles. .TP -.B hmmemit +.B hmm2emit Generate sequences probabilistically from a profile HMM. .TP -.B hmmfetch +.B hmm2fetch Retrieve an HMM from an HMM database .TP -.B hmmindex +.B hmm2index Create a binary SSI index for an HMM database .TP -.B hmmpfam +.B hmm2pfam Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the query sequence). .TP -.B hmmsearch +.B hmm2search Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled family). --- a/documentation/man/hmmalign.man +++ b/documentation/man/hmmalign.man @@ -1,18 +1,18 @@ -.TH "hmmalign" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2align" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmalign - align sequences to an HMM profile +hmm2align - align sequences to an HMM profile .SH SYNOPSIS -.B hmmalign +.B hmm2align .I [options] -.I hmmfile +.I hmm2file .I seqfile .SH DESCRIPTION -.B hmmalign +.B hmm2align reads an HMM file from .I hmmfile and a set of sequences from @@ -26,7 +26,7 @@ accepted by HMMER. If it is in a multiple alignment format (e.g. Stockholm, MSF, SELEX, ClustalW), the existing alignment is ignored (i.e., the sequences are read as if they were -unaligned - hmmalign will align them the way it wants). +unaligned - hmm2align will align them the way it wants). .SH OPTIONS @@ -76,7 +76,7 @@ .I is held fixed. This allows you to align sequences to a model with -.B hmmalign +.B hmm2align and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is defined by a "map" kept @@ -110,7 +110,7 @@ .I is held fixed. This allows you to align sequences to a model with -.B hmmalign +.B hmm2align and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, @@ -127,7 +127,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmbuild.man +++ b/documentation/man/hmmbuild.man @@ -1,18 +1,18 @@ -.TH "hmmbuild" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2build" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmbuild - build a profile HMM from an alignment +hmm2build - build a profile HMM from an alignment .SH SYNOPSIS -.B hmmbuild +.B hmm2build .I [options] .I hmmfile .I alignfile .SH DESCRIPTION -.B hmmbuild +.B hmm2build reads a multiple sequence alignment file .I alignfile , builds a new profile HMM, and saves the HMM in @@ -311,7 +311,7 @@ weights (PB weights) are more efficient. At or above a certain threshold sequence number .I -.B hmmbuild +.B hmm2build will switch from GSC, BLOSUM, or Voronoi weights to PB weights. To disable this switching behavior (at the cost of compute time, set @@ -436,7 +436,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmcalibrate.man +++ b/documentation/man/hmmcalibrate.man @@ -1,17 +1,17 @@ -.TH "hmmcalibrate" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2calibrate" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmcalibrate - calibrate HMM search statistics +hmm2calibrate - calibrate HMM search statistics .SH SYNOPSIS -.B hmmcalibrate +.B hmm2calibrate .I [options] .I hmmfile .SH DESCRIPTION -.B hmmcalibrate +.B hmm2calibrate reads an HMM file from .I hmmfile, scores a large number of synthesized random sequences with it, fits an @@ -21,13 +21,13 @@ now including the EVD parameters. .PP -.B hmmcalibrate +.B hmm2calibrate may take several minutes (or longer) to run. While it is running, a temporary file called .I hmmfile.xxx is generated in your working directory. If you abort -.B hmmcalibrate +.B hmm2calibrate prematurely (ctrl-C, for instance), your original .I hmmfile will be untouched, and you should delete the @@ -94,7 +94,7 @@ .B --pvm Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program -.B hmmcalibrate-pvm +.B hmm2calibrate-pvm must be installed on all the PVM nodes. Optional PVM support must have been compiled into HMMER. @@ -120,12 +120,12 @@ .B time() to generate a different seed for each run, which means that two different runs of -.B hmmcalibrate +.B hmm2calibrate on the same HMM will give slightly different results. You can use this option to generate reproducible results for different -.B hmmcalibrate +.B hmm2calibrate runs on the same HMM. @@ -133,7 +133,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmconvert.man +++ b/documentation/man/hmmconvert.man @@ -1,18 +1,18 @@ -.TH "hmmconvert" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2convert" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmconvert - convert between profile HMM file formats +hmm2convert - convert between profile HMM file formats .SH SYNOPSIS -.B hmmconvert +.B hmm2convert .I [options] .I oldhmmfile .I newhmmfile .SH DESCRIPTION -.B hmmconvert +.B hmm2convert reads an HMM file from .I oldhmmfile in any HMMER format, and writes it to a new file @@ -66,7 +66,7 @@ already exists, and .I -A is not being used to append to the file, -hmmconvert will refuse to clobber the existing +hmm2convert will refuse to clobber the existing file unless .I -F is used. @@ -84,7 +84,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmemit.man +++ b/documentation/man/hmmemit.man @@ -1,17 +1,17 @@ -.TH "hmmemit" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2emit" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmemit - generate sequences from a profile HMM +hmm2emit - generate sequences from a profile HMM .SH SYNOPSIS -.B hmmemit +.B hmm2emit .I [options] .I hmmfile .SH DESCRIPTION -.B hmmemit +.B hmm2emit reads an HMM file from .I hmmfile containing one or more HMMs, @@ -22,9 +22,9 @@ This can be useful for various applications in which one needs a simulation of sequences consistent with a sequence family consensus. -.pp +.PP By default, -.B hmmemit +.B hmm2emit generates 10 sequences and outputs them in FASTA (unaligned) format. .SH OPTIONS @@ -78,7 +78,7 @@ .B time() to generate a different seed for each run, which means that two different runs of -.B hmmemit +.B hmm2emit on the same HMM will give slightly different results. You can use this option to generate reproducible results. @@ -89,7 +89,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmfetch.man +++ b/documentation/man/hmmfetch.man @@ -1,18 +1,18 @@ -.TH "hmmfetch" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2fetch" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmfetch - retrieve an HMM from an HMM database +hmm2fetch - retrieve an HMM from an HMM database .SH SYNOPSIS -.B hmmfetch +.B hmm2fetch .I [options] .I database .I name .SH DESCRIPTION -.B hmmfetch +.B hmm2fetch is a small utility that retrieves an HMM called .I name from a HMMER model database called @@ -20,7 +20,7 @@ in a new format, and prints that model to standard output. For example, -.I hmmfetch Pfam rrm +.I hmm2fetch Pfam rrm retrieves the RRM (RNA recognition motif) model from Pfam, if the environment variable HMMERDB is set to the location of the Pfam database. @@ -29,7 +29,7 @@ .PP The database must have an associated GSI index file. To index an HMM database, use the program -.B hmmindex. +.B hmm2index. .SH OPTIONS @@ -47,14 +47,14 @@ called .B foo, you would do -.B hmmfetch -n 0 foo. +.B hmm2fetch -n 0 foo. .SH SEE ALSO Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmindex.man +++ b/documentation/man/hmmindex.man @@ -1,26 +1,26 @@ -.TH "hmmindex" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2index" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmindex - create a binary SSI index for an HMM database +hmm2index - create a binary SSI index for an HMM database .SH SYNOPSIS -.B hmmindex +.B hmm2index .I [options] .I database .SH DESCRIPTION -.B hmmindex +.B hmm2index is a utility that creates a binary SSI ("squid sequence index" format) index for an HMM database file called .I database. The new index file is named .IR database.ssi. An SSI index file is required for -.B hmmfetch +.B hmm2fetch to work, and also for the PVM implementation of -.B hmmpfam. +.B hmm2pfam. .SH OPTIONS @@ -35,7 +35,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmpfam.man +++ b/documentation/man/hmmpfam.man @@ -1,18 +1,18 @@ -.TH "hmmpfam" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2pfam" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmpfam - search one or more sequences against an HMM database +hmm2pfam - search one or more sequences against an HMM database .SH SYNOPSIS -.B hmmpfam +.B hmm2pfam .I [options] .I hmmfile .I seqfile .SH DESCRIPTION -.B hmmpfam +.B hmm2pfam reads a sequence file .I seqfile and compares each sequence in it, one at a time, against all the HMMs in @@ -65,7 +65,7 @@ Specify that models and sequence are nucleic acid, not protein. Other HMMER programs autodetect this; but because of the order in which -.B hmmpfam +.B hmm2pfam accesses data, it can't reliably determine the correct "alphabet" by itself. @@ -134,7 +134,7 @@ to --globT --domT , but the GA1 and GA2 cutoffs are read from each HMM in .I hmmfile -individually. hmmbuild puts these cutoffs there +individually. hmm2build puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these @@ -148,7 +148,7 @@ to --globT --domT , but the TC1 and TC2 cutoffs are read from each HMM in .I hmmfile -individually. hmmbuild puts these cutoffs there +individually. hmm2build puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these @@ -162,7 +162,7 @@ to --globT --domT , but the NC1 and NC2 cutoffs are read from each HMM in .I hmmfile -individually. hmmbuild puts these cutoffs there +individually. hmm2build puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these @@ -246,7 +246,7 @@ .B --pvm Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program -.B hmmpfam-pvm +.B hmm2pfam-pvm must be installed on all the PVM nodes. The HMM database .I hmmfile @@ -254,7 +254,7 @@ .IR hmmfile. gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program -.BR hmmindex .) +.BR hmm2index .) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of @@ -280,7 +280,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, --- a/documentation/man/hmmsearch.man +++ b/documentation/man/hmmsearch.man @@ -1,18 +1,18 @@ -.TH "hmmsearch" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" +.TH "hmm2search" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP -hmmsearch - search a sequence database with a profile HMM +hmm2search - search a sequence database with a profile HMM .SH SYNOPSIS -.B hmmsearch +.B hmm2search .I [options] .I hmmfile .I seqfile .SH DESCRIPTION -.B hmmsearch +.B hmm2search reads an HMM from .I hmmfile and searches @@ -28,7 +28,7 @@ has been configured for the site. .PP -.B hmmsearch +.B hmm2search may take minutes or even hours to run, depending on the size of the sequence database. It is a good idea to redirect the output to a file. @@ -121,7 +121,7 @@ Use Pfam GA (gathering threshold) score cutoffs. Equivalent to --globT --domT , but the GA1 and GA2 cutoffs -are read from the HMM file. hmmbuild puts these cutoffs there +are read from the HMM file. hmm2build puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these @@ -133,7 +133,7 @@ .B --cut_tc Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to --globT --domT , but the TC1 and TC2 cutoffs -are read from the HMM file. hmmbuild puts these cutoffs there +are read from the HMM file. hmm2build puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these @@ -145,7 +145,7 @@ .B --cut_nc Use Pfam NC (noise cutoff) score cutoffs. Equivalent to --globT --domT , but the NC1 and NC2 cutoffs -are read from the HMM file. hmmbuild puts these cutoffs there +are read from the HMM file. hmm2build puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these @@ -229,7 +229,7 @@ .B --pvm Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program -.B hmmsearch-pvm +.B hmm2search-pvm must be installed on all the PVM nodes. Optional PVM support must have been compiled into HMMER. @@ -247,7 +247,7 @@ Master man page, with full list of and guide to the individual man pages: see -.B hmmer(1). +.B hmmer2(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, debian/hmmer2-pvm.README.Debian0000664000000000000000000000053312010243655013221 0ustar hmmer2-pvm for Debian -------------------- Please, read the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf), to see how to configure properly Hmmer on a PVM cluster. -- Nelson A. de Oliveira Tue, 08 Aug 2006 23:07:12 -0300 debian/hmmer2-pvm.manpages0000664000000000000000000000002411775616577012721 0ustar debian/hmmer2-pvm.1 debian/watch0000664000000000000000000000012411775616414010232 0ustar version=3 ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-([0-9.]+)\.tar\.gz debian/hmmer2-pvm.install0000664000000000000000000000016311775616577012600 0ustar debian/tmp/bin/hmm2calibrate-pvm usr/bin debian/tmp/bin/hmm2pfam-pvm usr/bin debian/tmp/bin/hmm2search-pvm usr/bin debian/hmmer2-pvm.links0000664000000000000000000000033711775616577012255 0ustar usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2calibrate-pvm.1.gz usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2pfam-pvm.1.gz usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2search-pvm.1.gz debian/upstream0000664000000000000000000000072511775616414010773 0ustar Contact: http://selab.janelia.org/people/eddys/contact.html DOI: 10.1093/bioinformatics/14.9.755 Name: HMMER Homepage: http://hmmer.janelia.org PMID: 9918945 Reference: Author: Eddy, SR Title: Profile hidden Markov models Journal: Bioinformatics Volume: 14 Number: 9 Pages: 755-763 Year: 1998 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755 Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz debian/control0000664000000000000000000000553712300163007010575 0ustar Source: hmmer2 Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Matthew Vernon , Nelson A. de Oliveira , Andreas Tille , Laszlo Kajan Section: science Priority: optional Build-Depends: debhelper (>= 8), pvm-dev, autotools-dev, libperl4-corelibs-perl Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/hmmer2/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/hmmer2/trunk/ Homepage: http://hmmer.janelia.org/ Package: hmmer2 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: biosquid Suggests: hmmer2-doc (>= ${source:Version}), hmmer2-pvm (>= ${binary:Version}) Description: profile hidden Markov models for protein sequence analysis HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries. . Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family. Package: hmmer2-pvm Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, pvm Suggests: hmmer2-doc (>= ${binary:Version}) Description: HMMER programs with PVM (Parallel Virtual Machine) support HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries. . Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family. . This package contains HMMER programs compiled with PVM support. Package: hmmer2-doc Architecture: all Section: doc Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: hmmer2 (>= ${source:Version}), xpdf-reader | pdf-viewer Description: profile hidden Markov models for protein sequence analysis (docs) HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries. . Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family. . This package contains documents and example files for the hmmer2 package. debian/source/0000775000000000000000000000000012246501114010464 5ustar debian/source/format0000664000000000000000000000001411776574747011727 0ustar 3.0 (quilt) debian/compat0000664000000000000000000000000211775616414010402 0ustar 8 debian/hmmer2.install0000664000000000000000000000050311775616577011776 0ustar debian/tmp/share usr debian/tmp/bin/hmm2align usr/bin debian/tmp/bin/hmm2build usr/bin debian/tmp/bin/hmm2calibrate usr/bin debian/tmp/bin/hmm2convert usr/bin debian/tmp/bin/hmm2emit usr/bin debian/tmp/bin/hmm2fetch usr/bin debian/tmp/bin/hmm2index usr/bin debian/tmp/bin/hmm2pfam usr/bin debian/tmp/bin/hmm2search usr/bin debian/rules0000775000000000000000000000322512300163020010235 0ustar #!/usr/bin/make -f # DH_VERBOSE=1 export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) # lkajan: The following violates point 4.9 of the Debian policy: "get-orig-source [...] may be invoked in any directory [...]" as uscan needs to find the watch file. .PHONY: get-orig-source get-orig-source: set -e; \ t=$$(mktemp -d) || exit 1; \ trap "rm -rf -- '$$t'" EXIT; \ pwd; \ uscan --no-conf --force-download --rename --destdir "$$t"; \ ( cd "$$t"; \ gunzip *.tar.gz; \ tar --owner=root --group=root --mode=a+rX --delete -f *.tar --wildcards 'hmmer-*/Userguide.pdf'; \ xz --best *.tar; \ ); \ mv $$t/*.tar.xz ./ .PHONY: override_dh_auto_configure override_dh_auto_configure: dh_auto_configure -- --enable-threads --enable-lfs --enable-pvm .PHONY: override_dh_auto_install override_dh_auto_install: dh_auto_install -- prefix=$(CURDIR)/debian/tmp # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: rename 's/^hmm/hmm2/;' $(CURDIR)/debian/tmp/bin/* cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm/hmm2/;' * cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' $(CURDIR)/debian/tmp/share/man/man1/* .PHONY: override_dh_installchangelogs override_dh_installchangelogs: dh_installchangelogs -k 00README %: dh $@ --parallel --with autotools-dev