Author: plessy Date: 2010-06-26 09:55:12 +0000 (Sat, 26 Jun 2010) New Revision: 4941
Modified: trunk/packages/embassy-domalign/trunk/debian/changelog trunk/packages/embassy-domalign/trunk/debian/control trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e Log: New upstream release (last January). Modified: trunk/packages/embassy-domalign/trunk/debian/changelog =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/changelog 2010-06-26 08:52:38 UTC (rev 4940) +++ trunk/packages/embassy-domalign/trunk/debian/changelog 2010-06-26 09:55:12 UTC (rev 4941) @@ -1,3 +1,12 @@ +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 <[email protected]> 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. @@ -4,7 +13,7 @@ * 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. + * debian/watch: mangle Debian version to ignore the timestamp. * Refreshed and experimeted on debian/copyright. * debian/*manpages* refreshed and moved to section 1e. Modified: trunk/packages/embassy-domalign/trunk/debian/control =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/control 2010-06-26 08:52:38 UTC (rev 4940) +++ trunk/packages/embassy-domalign/trunk/debian/control 2010-06-26 09:55:12 UTC (rev 4941) @@ -1,13 +1,13 @@ Source: embassy-domalign Section: science Priority: optional -Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.1), libnucleus6-dev (>= 6.1), emboss-lib (>= 6.1), libx11-dev, libgd2-xpm-dev +Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.2), libnucleus6-dev (>= 6.2), emboss-lib (>= 6.2), libx11-dev, libgd2-xpm-dev Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Charles Plessy <[email protected]> Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domalign/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domalign/trunk/ -Standards-Version: 3.8.2 +Standards-Version: 3.8.4 Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN Package: embassy-domalign Modified: trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages 2010-06-26 08:52:38 UTC (rev 4940) +++ trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages 2010-06-26 09:55:12 UTC (rev 4941) @@ -1,4 +1,4 @@ debian/manpages/allversusall.1e -debian/manpages/domainrep.1e debian/manpages/domainalign.1e debian/manpages/seqalign.1e +debian/manpages/domainrep.1e Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e 2010-06-26 08:52:38 UTC (rev 4940) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e 2010-06-26 09:55:12 UTC (rev 4941) @@ -1,14 +1,23 @@ '\" t .\" Title: ALLVERSUSALL -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/17/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20090715 +.\" Source: EMBOSS 0.1.0+20100115 .\" Language: English .\" -.TH "ALLVERSUSALL" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.TH "ALLVERSUSALL" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "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 @@ -74,7 +83,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e 2010-06-26 08:52:38 UTC (rev 4940) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e 2010-06-26 09:55:12 UTC (rev 4941) @@ -1,14 +1,23 @@ '\" t .\" Title: DOMAINALIGN -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/17/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20090715 +.\" Source: EMBOSS 0.1.0+20100115 .\" Language: English .\" -.TH "DOMAINALIGN" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.TH "DOMAINALIGN" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "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 @@ -34,18 +43,18 @@ .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 -This option specifies the name of DCF file (domain classification file) (input)\&. A \'domain classification file\' 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\&. +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 \'domain PDB file\' contains coordinate data for a single domain from SCOP or CATH, in PDB format\&. The files are generated by using DOMAINER\&. Default value: \&./ +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 \'Class\' entries belonging to the same Class will be non\-redundant\&. Default value: 1 +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 @@ -61,12 +70,12 @@ .PP \fB\-dafoutdir\fR \fIoutdir\fR .RS 4 -This option specifies the location of DAF files (domain alignment files) (output)\&. A \'domain alignment file\' 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: \&./ +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 \'domain hits file\' \- which contains database hits (sequences) with domain classification information, in FASTA format\&. Default value: \&./ +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 @@ -88,7 +97,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e 2010-06-26 08:52:38 UTC (rev 4940) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e 2010-06-26 09:55:12 UTC (rev 4941) @@ -1,14 +1,23 @@ '\" t .\" Title: DOMAINREP -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/17/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20090715 +.\" Source: EMBOSS 0.1.0+20100115 .\" Language: English .\" -.TH "DOMAINREP" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.TH "DOMAINREP" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "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 @@ -34,19 +43,19 @@ .PP \fB\-dcfinfile\fR \fIinfile\fR .RS 4 -This option specifies the name of DCF file (domain classification file) (input)\&. A \'domain classification file\' 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\&. +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 \'Class\' entries belonging to the same Class will be reordered in turn\&. Default value: 1 +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 \'domain classification file\' 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 +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 @@ -58,7 +67,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e 2010-06-26 08:52:38 UTC (rev 4940) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e 2010-06-26 09:55:12 UTC (rev 4941) @@ -1,14 +1,23 @@ '\" t .\" Title: SEQALIGN -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/17/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20090715 +.\" Source: EMBOSS 0.1.0+20100115 .\" Language: English .\" -.TH "SEQALIGN" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.TH "SEQALIGN" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "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 @@ -39,17 +48,17 @@ .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 \'domain alignment file\' 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: \&./ +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 \'domain alignment file\' 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: \&./ +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 \'domain hits file\' 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: \&./ +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 @@ -67,7 +76,7 @@ .PP \fB\-dafoutdir\fR \fIoutdir\fR .RS 4 -This option specifies the location of DAF files (domain alignment files) (output)\&. A \'domain alignment file\' 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: \&./ +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 @@ -84,7 +93,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
