[med-svn] [acedb] 01/07: Package acedb-other-dotter and acedb-other-belvu are now transitional packages to install dotter and belvu from seqtools source package
Andreas Tille
tille at debian.org
Tue Dec 19 12:24:33 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository acedb.
commit f1a4807e4164748c789078ebb7c893df0e055e51
Author: Andreas Tille <tille at debian.org>
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 <Erik.Sonnhammer at cgb.ki.se>
-.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 <moeller at debian.org> 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 <tille at debian.org> 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
-Erik.Sonnhammer at cgb.ki.se
-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 <tille at debian.org>
+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
--
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