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commit f1a4807e4164748c789078ebb7c893df0e055e51 Author: Andreas Tille <[email protected]> Date: Tue Dec 19 13:05:00 2017 +0100 Package acedb-other-dotter and acedb-other-belvu are now transitional packages to install dotter and belvu from seqtools source package --- debian/acedb-other-belvu.install | 1 - debian/acedb-other-belvu.manpages | 1 - debian/acedb-other-dotter.install | 1 - debian/acedb-other-dotter.manpages | 1 - debian/belvu.1 | 111 ------------------------------- debian/changelog | 7 +- debian/control | 40 +++++------ debian/dotter.1 | 79 ---------------------- debian/patches/no_dotter_and_belvu.patch | 79 ++++++++++++++++++++++ debian/patches/series | 1 + 10 files changed, 102 insertions(+), 219 deletions(-) diff --git a/debian/acedb-other-belvu.install b/debian/acedb-other-belvu.install deleted file mode 100644 index e55b614..0000000 --- a/debian/acedb-other-belvu.install +++ /dev/null @@ -1 +0,0 @@ -usr/bin/belvu diff --git a/debian/acedb-other-belvu.manpages b/debian/acedb-other-belvu.manpages deleted file mode 100644 index afc297c..0000000 --- a/debian/acedb-other-belvu.manpages +++ /dev/null @@ -1 +0,0 @@ -debian/belvu.1 diff --git a/debian/acedb-other-dotter.install b/debian/acedb-other-dotter.install deleted file mode 100644 index 41f36b5..0000000 --- a/debian/acedb-other-dotter.install +++ /dev/null @@ -1 +0,0 @@ -usr/bin/dotter diff --git a/debian/acedb-other-dotter.manpages b/debian/acedb-other-dotter.manpages deleted file mode 100644 index 8b3e258..0000000 --- a/debian/acedb-other-dotter.manpages +++ /dev/null @@ -1 +0,0 @@ -debian/dotter.1 diff --git a/debian/belvu.1 b/debian/belvu.1 deleted file mode 100644 index be0a2f0..0000000 --- a/debian/belvu.1 +++ /dev/null @@ -1,111 +0,0 @@ -.\" This file was generated by help2man 1.36 and then -.\" manually tweaked a bit. -.TH BELVU "1" "August 2009" "belvu 2.19" "User Commands" -.SH NAME -belvu \- View multiple alignments in good\-looking colours. -.SH SYNOPSIS -belvu [options] <multiple_alignment>|\- [X options] -.IP -<multiple_alignment>|\- = alignment file or pipe. -.SH DESCRIPTION -Belvu presents multiple sequence alignments in a colourful -biologically interpretable manner. -.SH OPTIONS -\fB\-c\fR Print Conservation table. -.HP -\fB\-l\fR <file> Load color code file. -.HP -\fB\-L\fR <file> Load Markup color code file. -.HP -\fB\-m\fR <file> Read file with matching sequence segments. -.HP -\fB\-r\fR Read alignment in 'raw' format (Name sequence). -.HP -\fB\-R\fR Do not parse coordinates when reading alignment. -.HP -\fB\-o\fR <format> Write alignment or tree to stdout in this format and exit. -.IP -Valid formats: MSF, Mul(Stockholm), Selex, -.IP -FastaAlign, Fasta, tree. -.HP -\fB\-n\fR <cutoff> Make non\-redundant to <cutoff> %identity at startup. -.HP -\fB\-Q\fR <cutoff> Remove columns more gappy than <cutoff>. -.HP -\fB\-q\fR <cutoff> Remove sequences more gappy than <cutoff>. -.TP -\fB\-P\fR -Remove partial sequences at startup. -.TP -\fB\-C\fR -Don't write coordinates to saved file. -.TP -\fB\-z\fR <char> -Separator char between name and coordinates in saved file. -.TP -\fB\-a\fR -Show alignment annotations on screen (Stockholm format only). -.TP -\fB\-p\fR -Output random model probabilites for HMMER. -.IP -(Based on all residues.) -.TP -\fB\-S\fR <order> -Sort sequences in this order. -.IP -a \-> alphabetically -o \-> by Swissprot organism, alphabetically -s \-> by score -n \-> by Neighbor\-joining tree -u \-> by UPGMA tree -S \-> by similarity to first sequence -i \-> by identity to first sequence -.TP -\fB\-s\fR <file> -Read in file of scores. -.HP -\fB\-T\fR <method> Start up with tree calculated by method: -.IP -n \-> Neighbor\-joining -u \-> UPGMA -N \-> Neighbor\-joining, only show tree -U \-> UPGMA, only show tree -c \-> Don't color tree by organism -o \-> Don't display sequence coordinates in tree -s \-> Use Storm & Sonnhammer distance correction -r \-> Use uncorrected distances -.TP -\fB\-b\fR <#> -Print out # bootstrapped trees and exit -.IP -(Negative value \-> display bootstrap trees on screen) -.TP -\fB\-O\fR <label> -Read organism info after this label (default OS) -.TP -\fB\-t\fR <title> -Set window title. -.TP -\fB\-g\fR -Draw grid line (for debugging). -.TP -\fB\-u\fR -Start up with uncoloured alignment (faster). -.TP -\fB\-h\fR -Show this help. -.TP -\fB\-v\fR -Show version info. -.IP -Some X options: -\fB\-acefont\fR <font> Main font. -\fB\-font\fR <font> Menu font. -.SH "SEE ALSO" -For documentation, see: http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html -.SH AUTHOR -Erik Sonnhammer <[email protected]> -.SH VERSION -Version 2.16, compiled Aug 18 2009 diff --git a/debian/changelog b/debian/changelog index 1eafe3c..37b124c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,10 +1,15 @@ acedb (4.9.39+dfsg.02-2) UNRELEASED; urgency=medium + [ Steffen Moeller ] * debian/upstream/metadata: - Added references to registries - yamllint cleanliness - -- Steffen Moeller <[email protected]> Mon, 18 Sep 2017 01:06:46 +0200 + [ Andreas Tille ] + * Package acedb-other-dotter and acedb-other-belvu are now transitional + packages to install dotter and belvu from seqtools source package + + -- Andreas Tille <[email protected]> Tue, 19 Dec 2017 13:00:46 +0100 acedb (4.9.39+dfsg.02-1) unstable; urgency=medium diff --git a/debian/control b/debian/control index 2640fb1..adbfce1 100644 --- a/debian/control +++ b/debian/control @@ -19,32 +19,24 @@ Vcs-Git: https://anonscm.debian.org/git/debian-med/acedb.git Homepage: http://www.acedb.org/ Package: acedb-other-dotter -Architecture: any -Depends: ${shlibs:Depends}, - ${misc:Depends} -Provides: dotter -Description: visualisation of sequence similarity - For the analysis of biological sequences, a general principle is to - compare corresponding regions between related proteins, RNA or DNA. - . - Dotter, as an interactive dotplot with varying thresholds, displays - graphically the similarity of DNA or protein sequence to itself or - another sequence. +Architecture: all +Depends: ${misc:Depends}, + dotter +Description: transitional package for dotter + This is a transitional package to ease upgrades to the new dotter + executable now maintained in the seqtools source package. The + dotter executable in the acedb package was unmaintained for years + and seqtools contains the maintained code. Package: acedb-other-belvu -Architecture: any -Depends: ${shlibs:Depends}, - ${misc:Depends} -Provides: belvu -Description: multiple sequence alignment editor - For the analysis of biological sequences, a general principle is to - corresponding regions between related proteins, RNA or DNA. Written - next to each other, corresponding positions above each other, one has - prepared an alignment. - . - Belvu is best known for its perfect implementation of the Stockholm - format of multiple sequence alignments, since upstream is maintaining - that. That is for instance used in the Pfam and Rfam databases. +Architecture: all +Depends: ${misc:Depends}, + belvu +Description: transitional package for belvu + This is a transitional package to ease upgrades to the new belvu + executable now maintained in the seqtools source package. The + belvu executable in the acedb package was unmaintained for years + and seqtools contains the maintained code. Package: acedb-other Architecture: any diff --git a/debian/dotter.1 b/debian/dotter.1 deleted file mode 100644 index 3b97508..0000000 --- a/debian/dotter.1 +++ /dev/null @@ -1,79 +0,0 @@ -.\" This file was generated by help2man 1.37.1 and then manually edited. -.TH DOTTER: "1" "July 2010" -.SH NAME -dotter \- Sequence dotplots with image enhancement tools. -.SH SYNOPSIS -dotter [options] <horizontal_sequence> <vertical_sequence> [X options] -.SH DESCRIPTION -.IP -Reference: Sonnhammer ELL & Durbin R (1995). A dot\-matrix program -with dynamic threshold control suited for genomic DNA and protein -sequence analysis. Gene 167(2):GC1\-10. -.TP -.TP -Allowed types: -Protein \- Protein -DNA \- DNA -DNA \- Protein -.IP -Options: -.TP -\fB\-b\fR <file> -Batch mode, write dotplot to <file> -.TP -\fB\-l\fR <file> -Load dotplot from <file> -.TP -\fB\-m\fR <float> -Memory usage limit in Mb (default 0.5) -.TP -\fB\-z\fR <int> -Set zoom (compression) factor -.TP -\fB\-p\fR <int> -Set pixel factor manually (ratio pixelvalue/score) -.TP -\fB\-W\fR <int> -Set sliding window size. (K => Karlin/Altschul estimate) -.TP -\fB\-M\fR <file> -Read in score matrix from <file> (Blast format; Default: Blosum62). -.TP -\fB\-F\fR <file> -Read in sequences and data from <file> (replaces sequencefiles). -.TP -\fB\-f\fR <file> -Read feature segments from <file> -.TP -\fB\-H\fR -Do not calculate dotplot at startup. -.TP -\fB\-R\fR -Reversed Greyramp tool at start. -.TP -\fB\-r\fR -Reverse and complement horizontal_sequence (DNA vs Protein) -.TP -\fB\-D\fR -Don't display mirror image in self comparisons -.TP -\fB\-w\fR -For DNA: horizontal_sequence top strand only (Watson) -.TP -\fB\-c\fR -For DNA: horizontal_sequence bottom strand only (Crick) -.TP -\fB\-q\fR <int> -Horizontal_sequence offset -.TP -\fB\-s\fR <int> -Vertical_sequence offset -.IP -Some X options: -\fB\-acefont\fR <font> Main font. -\fB\-font\fR <font> Menu font. -.SH SEE ALSO -http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info. -.SH AUTHOR [email protected] -Version 3.1, compiled Jul 10 2010 diff --git a/debian/patches/no_dotter_and_belvu.patch b/debian/patches/no_dotter_and_belvu.patch new file mode 100644 index 0000000..ffcb92a --- /dev/null +++ b/debian/patches/no_dotter_and_belvu.patch @@ -0,0 +1,79 @@ +Description: Package acedb-other-dotter and acedb-other-belvu are now + transitional packages to install dotter and belvu from seqtools source + package + . + So do not even build these binaries +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 19 Dec 2017 13:00:46 +0100 + +--- a/wmake/makefile ++++ b/wmake/makefile +@@ -49,7 +49,7 @@ ace : $(ACE_BIN) + ACEMBLY_BIN = makeSCF xacembly tacembly gifacemblyserver + acembly : libstaden.a $(ACEMBLY_BIN) + +-OTHER_BIN = blixem blixelect dotter belvu jade2ace efetch \ ++OTHER_BIN = blixem blixelect jade2ace efetch \ + gnbk gnbkclient genefeatures + other : $(OTHER_BIN) + +@@ -82,7 +82,7 @@ xace xremote tace giface taql \ + aceserver gifaceserver aceclient xaceclient \ + saceserver sgifaceserver saceclient sxaceclient sace_build \ + libstaden.a makeSCF xacembly tacembly gifacemblyserver \ +-blixem blixelect dotter belvu jade2ace efetch gnbk gnbkclient \ ++blixem blixelect jade2ace efetch gnbk gnbkclient \ + makeUserPasswd acediff acediffsorted pmapace diskdump diskfix metacheck homonym tagcount \ + xtest coltest giftest boxtest md5test acelibtest \ + tace5 xace5 xacembly5 tacembly5 \ +--- a/wtools/MAKE_INSTALL ++++ b/wtools/MAKE_INSTALL +@@ -110,13 +110,13 @@ srcname='source' + srcpattern='./makefile ./w*' + binname='binary' + staticbinname='STATIC_binary' +-binpattern='./acediff ./dotter ./giface ./tace ./tagcount ./taql ./xace ./xremote' ++binpattern='./acediff ./giface ./tace ./tagcount ./taql ./xace ./xremote' + servername='server' + staticservername='STATIC_server' + serverpattern='./makeUserPasswd ./saceclient ./saceserver ./sgifaceserver ./sxaceclient' + blixemname='blixem' + staticblixemname='STATIC_blixem' +-blixempattern='./dotter ./blixem ./belvu' ++blixempattern='./blixem ' + helpname='help' + helppattern='./*' + docname='doc' +--- a/wmake/truemake ++++ b/wmake/truemake +@@ -620,7 +620,7 @@ acembly : libstaden.a tacembly xacembly + gifacemblyserver\ + gnbk gnbkclient + +-other : blixem belvu dotter efetch \ ++other : blixem efetch \ + pmapace tagcount diskdump diskfix \ + xtest coltest genefeatures \ + libfree.a \ +@@ -1246,10 +1246,6 @@ blixem : $(GRAPHXWIN_DEPEND) libfree.a b + blixem.o : blxview.c + $(COMPILER) $(USEROPTS) $(IDIR) -D$(NAME) -c -o $@ blxview.c + +-dotter : $(GRAPHXWIN_DEPEND) libfree.a dotter.o dotterMain.o dotterKarlin.o translate.o blxparser.o blixem.o +- $(LINKER) -o dotter dotter.o dotterKarlin.o dotterMain.o \ +- translate.o blxparser.o blixem.o -L. $(GRAPHXWIN_LIBS) -lfree $(XWIN_LIBS) $(LIBS) +- + + # I have removed this optimisation stuff from dotter for now because you cannot + # debug properly with it, EG +@@ -1262,10 +1258,6 @@ dotter.o: dotter.c + belvu.o: belvu.c + $(COMPILER) $(USEROPTS) -O2 -g3 $(IDIR) -D$(NAME) -c -o $@ belvu.c + +-belvu : $(GRAPHXWIN_DEPEND) libfree.a belvu.o +- $(LINKER) -o belvu belvu.o \ +- -L. $(GRAPHXWIN_LIBS) -lfree $(XWIN_LIBS) $(LIBS) +- + efetch : efetch.o dbidx.o + $(LINKER) -o efetch efetch.o dbidx.o + diff --git a/debian/patches/series b/debian/patches/series index 3137719..7a444e6 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -8,3 +8,4 @@ hardening.patch fix_hardening_errors.patch mayhem.patch spelling.patch +no_dotter_and_belvu.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/acedb.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
