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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 <[email protected]> - -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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
