[med-svn] r11656 - in trunk/packages/hmmer2/trunk/debian: . patches source
Laszlo Kajan
lkajan-guest at alioth.debian.org
Mon Jul 9 15:33:59 UTC 2012
Author: lkajan-guest
Date: 2012-07-09 15:33:59 +0000 (Mon, 09 Jul 2012)
New Revision: 11656
Added:
trunk/packages/hmmer2/trunk/debian/patches/
trunk/packages/hmmer2/trunk/debian/patches/series
trunk/packages/hmmer2/trunk/debian/patches/version2-manpage
trunk/packages/hmmer2/trunk/debian/source/
trunk/packages/hmmer2/trunk/debian/source/format
Modified:
trunk/packages/hmmer2/trunk/debian/README.Debian
trunk/packages/hmmer2/trunk/debian/changelog
trunk/packages/hmmer2/trunk/debian/copyright
trunk/packages/hmmer2/trunk/debian/rules
Log:
fixed all Lintian issues; renamed man pages and binaries to hmm2*
Modified: trunk/packages/hmmer2/trunk/debian/README.Debian
===================================================================
--- trunk/packages/hmmer2/trunk/debian/README.Debian 2012-07-09 15:02:15 UTC (rev 11655)
+++ trunk/packages/hmmer2/trunk/debian/README.Debian 2012-07-09 15:33:59 UTC (rev 11656)
@@ -6,7 +6,7 @@
-- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 08 Aug 2006 23:07:12 -0300
-Notes on how this pacakge is tested:
+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
Modified: trunk/packages/hmmer2/trunk/debian/changelog
===================================================================
--- trunk/packages/hmmer2/trunk/debian/changelog 2012-07-09 15:02:15 UTC (rev 11655)
+++ trunk/packages/hmmer2/trunk/debian/changelog 2012-07-09 15:33:59 UTC (rev 11656)
@@ -1,4 +1,4 @@
-hmmer2 (2.3.2-1) UNRELEASED; urgency=low
+hmmer2 (2.3.2-6) UNRELEASED; urgency=low
[Charles Plessy]
* Enabled upstream checks in debian/rules.
@@ -9,9 +9,11 @@
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 (s/hmm/hmm2/):
+ * Renaming binaries and man pages:
hmmalign => hmm2align
hmmbuild => hmm2build
@@ -22,6 +24,10 @@
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).
Modified: trunk/packages/hmmer2/trunk/debian/copyright
===================================================================
--- trunk/packages/hmmer2/trunk/debian/copyright 2012-07-09 15:02:15 UTC (rev 11655)
+++ trunk/packages/hmmer2/trunk/debian/copyright 2012-07-09 15:33:59 UTC (rev 11656)
@@ -1,29 +1,34 @@
-This package was debianized by John Lapeyre <lapeyre at physics.arizona.edu> on
-Thu, 13 Aug 1998 21:48:53 -0700.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: hmmer
+Upstream-Contact: Sean Eddy <eddy at genetics.wustl.edu>
+Source: ftp://selab.janelia.org/pub/software/hmmer/
-It was downloaded from ftp://selab.janelia.org/pub/software/hmmer/
+Files: debian/*
+Copyright: 1998, John Lapeyre <lapeyre at physics.arizona.edu>
+License: GPL-2+
-HMMER - Biological sequence analysis with profile hidden Markov models
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Files: *
+Copyright: Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+License: GPL-2+
-Upstream author: Sean Eddy <eddy at genetics.wustl.edu>
-
-License:
-
- This package 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 package 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 complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
+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'.
Added: trunk/packages/hmmer2/trunk/debian/patches/series
===================================================================
--- trunk/packages/hmmer2/trunk/debian/patches/series (rev 0)
+++ trunk/packages/hmmer2/trunk/debian/patches/series 2012-07-09 15:33:59 UTC (rev 11656)
@@ -0,0 +1 @@
+version2-manpage
Added: trunk/packages/hmmer2/trunk/debian/patches/version2-manpage
===================================================================
--- trunk/packages/hmmer2/trunk/debian/patches/version2-manpage (rev 0)
+++ trunk/packages/hmmer2/trunk/debian/patches/version2-manpage 2012-07-09 15:33:59 UTC (rev 11656)
@@ -0,0 +1,605 @@
+--- 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 <f>
+ 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 <f>
+ 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 <n>
+-.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 <GA1> --domT <GA2>, 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 <TC1> --domT <TC2>, 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 <NC1> --domT <NC2>, 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 <GA1> --domT <GA2>, 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 <TC1> --domT <TC2>, 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 <NC1> --domT <NC2>, 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,
Modified: trunk/packages/hmmer2/trunk/debian/rules
===================================================================
--- trunk/packages/hmmer2/trunk/debian/rules 2012-07-09 15:02:15 UTC (rev 11655)
+++ trunk/packages/hmmer2/trunk/debian/rules 2012-07-09 15:33:59 UTC (rev 11656)
@@ -1,8 +1,29 @@
#!/usr/bin/make -f
+# DH_VERBOSE=1
-include /usr/share/cdbs/1/class/autotools.mk
-include /usr/share/cdbs/1/rules/debhelper.mk
+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)
-DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-lfs --enable-pvm
-DEB_MAKE_INSTALL_TARGET := install prefix=$(CURDIR)/debian/tmp
-DEB_MAKE_CHECK_TARGET = check
+.PHONY: override_dh_auto_configure
+override_dh_auto_configure:
+ dh_auto_configure -- --enable-threads --enable-lfs --enable-pvm
+
+.PHONY: override_dh_auto_install
+override_dh_auto_install:
+ dh_auto_install -- prefix=$(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
Added: trunk/packages/hmmer2/trunk/debian/source/format
===================================================================
--- trunk/packages/hmmer2/trunk/debian/source/format (rev 0)
+++ trunk/packages/hmmer2/trunk/debian/source/format 2012-07-09 15:33:59 UTC (rev 11656)
@@ -0,0 +1 @@
+3.0 (quilt)
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