debian/0000755000000000000000000000000012214271601007162 5ustar debian/embassy-domalign.manpages0000644000000000000000000000017011430506063014132 0ustar debian/manpages/allversusall.1e debian/manpages/domainalign.1e debian/manpages/domainrep.1e debian/manpages/seqalign.1e debian/control0000644000000000000000000000277612214271473010610 0ustar Source: embassy-domalign Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~), libx11-dev, libgd2-xpm-dev, libmysqlclient-dev, libpq-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/embassy-domalign/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/embassy-domalign/trunk/ Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN Package: embassy-domalign Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~) Recommends: emboss Suggests: embassy Description: Extra EMBOSS commands for protein domain alignment The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. . Applications in the current domalign release are allversusall (sequence similarity data from all-versus-all comparison), domainalign (generates alignments (DAF file) for nodes in a DCF file), domainrep (reorders DCF file to identify representative structures) and seqalign (extend alignments (DAF file) with sequences (DHF file)). debian/embassy-domalign.lintian-overrides0000644000000000000000000000026611567121432016007 0ustar # The embassy packages use privately some of the EMBOSS libraries. They have # the same upstream authors and are released together. embassy-domalign: binary-or-shlib-defines-rpath * debian/rules0000755000000000000000000000043511754411605010254 0ustar #!/usr/bin/make -f CFLAGS += -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib LDFLAGS += -Wl,--as-needed %: dh $@ override_dh_auto_configure: dh_auto_configure -- --enable-systemlibs debian/manpages/0000755000000000000000000000000012214271137010761 5ustar debian/manpages/domainalign.1e0000644000000000000000000001264111430506063013474 0ustar '\" t .\" Title: DOMAINALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMALIGN 0.1.0+20100721 .\" Language: English .\" .TH "DOMAINALIGN" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domainalign \- Generate alignments (DAF file) for nodes in a DCF file\&. .SH "SYNOPSIS" .HP \w'\fBdomainalign\fR\ 'u \fBdomainalign\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-pdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-keepsinglets\ \fR\fB\fItoggle\fR\fR \fB\-dafoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-singletsoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-superoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomainalign\fR\ 'u \fBdomainalign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomainalign\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .PP \fB\-pdbdir\fR \fIdirectory\fR .RS 4 This option specifies the location of domain PDB files (input)\&. A \*(Aqdomain PDB file\*(Aq contains coordinate data for a single domain from SCOP or CATH, in PDB format\&. The files are generated by using DOMAINER\&. Default value: \&./ .RE .SS "Required section" .PP \fB\-node\fR \fIlist\fR .RS 4 This option specifies the node for redundancy removal\&. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\&. For example by selecting \*(AqClass\*(Aq entries belonging to the same Class will be non\-redundant\&. Default value: 1 .RE .PP \fB\-mode\fR \fIlist\fR .RS 4 This option specifies the alignment algorithm to use\&. Default value: 1 .RE .PP \fB\-keepsinglets\fR \fItoggle\fR .RS 4 This option specifies whether to write sequences of singlet families to file\&. If you specify this option, the sequence for each singlet family are written to file (output)\&. Default value: Y .RE .SS "Output section" .PP \fB\-dafoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DAF files (domain alignment files) (output)\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The files are in clustal format and are annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ .RE .PP \fB\-singletsoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DHF files (domain hits files) for singlet sequences (output)\&. The singlets are written out as a \*(Aqdomain hits file\*(Aq \- which contains database hits (sequences) with domain classification information, in FASTA format\&. Default value: \&./ .RE .PP \fB\-superoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of structural superimposition files (output)\&. A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used\&. Default value: \&./ .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of log file (output)\&. The log file contains messages about any errors arising while domainalign ran\&. Default value: domainalign\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domainalign is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/allversusall.1e0000644000000000000000000001044111430506063013717 0ustar '\" t .\" Title: ALLVERSUSALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMALIGN 0.1.0+20100721 .\" Language: English .\" .TH "ALLVERSUSALL" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" allversusall \- Sequence similarity data from all\-versus\-all comparison\&. .SH "SYNOPSIS" .HP \w'\fBallversusall\fR\ 'u \fBallversusall\fR \fB\-seqinpath\ \fR\fB\fIdirlist\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-datoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBallversusall\fR\ 'u \fBallversusall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBallversusall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqinpath\fR \fIdirlist\fR .RS 4 Default value: \&./ .RE .PP \fB\-matrix\fR \fImatrixf\fR .RS 4 This option specifies the residue substitution matrix that is used for sequence comparison\&. Default value: EBLOSUM62 .RE .SS "Required section" .SS "Additional section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 This option specifies the gap insertion penalty\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10 .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 This option specifies the gap extension penalty\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: 0\&.5 .RE .SS "Output section" .PP \fB\-datoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of sequence similarity data files (output)\&. Default value: \&./ .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of ALLVERSUSALL log file (output)\&. The log file contains messages about any errors arising while ALLVERSUSALL ran\&. Default value: allversusall\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP allversusall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqalign.1e0000644000000000000000000001421511430506063013014 0ustar '\" t .\" Title: SEQALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMALIGN 0.1.0+20100721 .\" Language: English .\" .TH "SEQALIGN" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqalign \- Extend alignments (DAF file) with sequences (DHF file)\&. .SH "SYNOPSIS" .HP \w'\fBseqalign\fR\ 'u \fBseqalign\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dafinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-amode\ \fR\fB\fIlist\fR\fR [\fB\-forcetype\ \fR\fB\fIboolean\fR\fR] \fB\-dafoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqalign\fR\ 'u \fBseqalign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqalign\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-mode\fR \fIlist\fR .RS 4 This option specifies the mode of SEQALIGN operation\&. SEQALIGN takes as input a directory of either i\&. single sequences, ii\&. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file))\&. The user has to specify which\&. Default value: 1 .RE .PP \fB\-dhfinpath\fR \fIdirlist\fR .RS 4 This option specifies the location of sequences, e\&.g\&. DHF files (domain hits files) (input)\&. SEQALIGN takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ .RE .PP \fB\-dafinpath\fR \fIdirlist\fR .RS 4 This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQALIGN takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ .RE .PP \fB\-dhfindir\fR \fIdirectory\fR .RS 4 This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .SS "Required section" .PP \fB\-amode\fR \fIlist\fR .RS 4 This option specifies which alignment algorithm to use\&. Default value: 1 .RE .SS "Additional section" .PP \fB\-forcetype\fR \fIboolean\fR .RS 4 This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available Default value: N .RE .SS "Output section" .PP \fB\-dafoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DAF files (domain alignment files) (output)\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while SEQALIGN ran\&. Default value: seqalign\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqalign is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domainrep.1e0000644000000000000000000000713311430506063013170 0ustar '\" t .\" Title: DOMAINREP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMALIGN 0.1.0+20100721 .\" Language: English .\" .TH "DOMAINREP" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domainrep \- Reorder DCF file to identify representative structures\&. .SH "SYNOPSIS" .HP \w'\fBdomainrep\fR\ 'u \fBdomainrep\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomainrep\fR\ 'u \fBdomainrep\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomainrep\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. .RE .SS "Required section" .PP \fB\-node\fR \fIlist\fR .RS 4 This option specifies the node fore reordering the file\&. Reordering can be done for any specified node in the SCOP or CATH hierarchies\&. For example by selecting \*(AqClass\*(Aq entries belonging to the same Class will be reordered in turn\&. Default value: 1 .RE .SS "Output section" .PP \fB\-dcfoutfile\fR \fIoutfile\fR .RS 4 This option specifies the name of DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domainrep is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/watch0000644000000000000000000000015011232075302010206 0ustar version=3 opts=dversionmangle=s/\+\d+$// \ ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-(.*)\.tar\.gz debian/copyright0000644000000000000000000000232611770432700011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.0.tar.gz Files: * Copyright: Matt Blades Jon Ison (jison@ebi.ac.uk) Ranjeeva Ranasinghe License: GPL-2+ Files: debian/* Copyright: 2007-2011 Charles Plessy 2012 Andreas Tille License: GPL-2+ License: GPL-2+ 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 version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. debian/source/0000755000000000000000000000000012214271137010466 5ustar debian/source/format0000644000000000000000000000001411507156767011713 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000765612214271601011052 0ustar embassy-domalign (0.1.650-1) unstable; urgency=low * New upstream version * debian/control: - cme fix dpkg-control - Bumped versioned depends from emboss-lib - anonscm in VCS fields -- Andreas Tille Thu, 12 Sep 2013 09:51:35 +0200 embassy-domalign (0.1.0+20110714-1) unstable; urgency=low * New upstream version (upstream has applied quilt patch) Closes: #661426 * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Adapted versioned (build-)depends to latest emboss version * debian/rules: short dh * debhelper 9 (control+compat) * debian/source/format: 3.0 (quilt) * debian/copyright: DEP5 fixes -- Andreas Tille Tue, 15 May 2012 10:17:55 +0200 embassy-domalign (0.1.0+20100721-3) unstable; urgency=low * Set RPATH with “-Wl,--rpath” as GCC 4.6 does not accept “-R” anymore. (debian/rules) Closes: #625189, LP: #771115. * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * Updated debian/embassy-domsearch.lintian-overrides for lintian 2.5. * debian/copyright validated with config-edit. -- Charles Plessy Thu, 12 May 2011 11:13:56 +0900 embassy-domalign (0.1.0+20100721-2) unstable; urgency=low * Built on emboss-lib 6.3.1-6, pre-emptively depending on versions lower than 6.3.2, because backwards compatibility is sometimes broken (debian/control, debian/rules). * Set an RPATH to /usr/lib/emboss/lib for using EMBOSS private libraries (debian/rules, debian/embassy-domalign.lintian-overrides). * Use quilt since simple-patchsys is deprecated (debian/control, debian/rules, debian/patches/series). * Refreshed debian/copyright to test the latest DEP-5 format. -- Charles Plessy Wed, 22 Sep 2010 20:05:29 +0900 embassy-domalign (0.1.0+20100721-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * Build-Depends on emboss 6.3.1 (debian/control, debian/rules, closes: #591116). * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed. * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules). * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * Patched src/Makefile.am to use Debian's libexpat, using CDBS (debian/patches/enable-esystemlibs.patch, debian/rules, debian/control). -- Charles Plessy Wed, 11 Aug 2010 19:45:22 +0900 embassy-domalign (0.1.0+20100115-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * debian/control: - Build against EMBOSS 6.2 (Closes: #587113). - Checked conformance with Policy 3.8.4 (no changes needed). * debian/*manpages* refreshed. -- Charles Plessy Sat, 26 Jun 2010 18:51:56 +0900 embassy-domalign (0.1.0+20090715-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * debian/control: - Build against EMBOSS 6.1 - Checked conformance with Policy 3.8.2 (no changes needed). * debian/watch: mangle Debian version to ignore the timestamp. * Refreshed and experimeted on debian/copyright. * debian/*manpages* refreshed and moved to section 1e. -- Charles Plessy Sat, 18 Jul 2009 23:33:19 +0900 embassy-domalign (0.1.0+20080715-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * debian/control: - Updated my email address. - Build against EMBOSS 6. - Using debhelper 7. - Checked conformance with Policy 3.8.1 (no changes needed). - Corrected DM-Upload-Allowed. -- Charles Plessy Tue, 21 Apr 2009 10:12:59 +0900 embassy-domalign (0.1.0-1) unstable; urgency=low * Initial release -- Charles Plessy Wed, 26 Sep 2007 09:45:52 +0900 debian/compat0000644000000000000000000000000211770332430010364 0ustar 9