[med-svn] [Git][med-team/bandage][master] 8 commits: Add myself as uploader

Andreas Tille gitlab at salsa.debian.org
Mon Aug 27 10:30:55 BST 2018 

Andreas Tille pushed to branch master at Debian Med / bandage


Commits:
1d0fb8c5 by Andreas Tille at 2018-08-27T09:30:43Z
Add myself as uploader

- - - - -
7078744d by Andreas Tille at 2018-08-27T09:30:43Z
debhelper 11

- - - - -
ef41870e by Andreas Tille at 2018-08-27T09:30:43Z
Point Vcs fields to salsa.debian.org

- - - - -
5a49c535 by Andreas Tille at 2018-08-27T09:30:43Z
Standards-Version: 4.2.0

- - - - -
e366d27f by Andreas Tille at 2018-08-27T09:30:43Z
Do not confuse qmake by providing two different project files

- - - - -
5f347a90 by Andreas Tille at 2018-08-27T09:30:43Z
Install to /usr/bin instead of /usr/local/bin

- - - - -
211ab66e by Andreas Tille at 2018-08-27T09:30:43Z
Standards-Version: 4.2.1

- - - - -
de4aacc5 by Andreas Tille at 2018-08-27T09:30:43Z
Add manpage

- - - - -


9 changed files:

- + debian/Bandage.1
- debian/changelog
- debian/compat
- debian/control
- + debian/createmanpages
- + debian/manpages
- + debian/patches/fix_target_path.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/Bandage.1
=====================================
@@ -0,0 +1,292 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH BANDAGE "1" "August 2018" "Bandage 0.8.1" "User Commands"
+.SH NAME
+Bandage \- Bioinformatics Application for Navigating De novo Assembly Graphs Easily
+.SH SYNOPSIS
+.B Bandage
+\fI\,<command> \/\fR[\fI\,options\/\fR]
+.SH DESCRIPTION
+Bandage is a GUI program that allows users to interact with the assembly
+graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and
+others..
+.SH OPTIONS
+.SS Commands
+.TP
+<blank>      Launch the Bandage GUI
+.TP
+load
+Launch the Bandage GUI and load a graph file
+.TP
+info
+Display information about a graph
+.TP
+image
+Generate an image file of a graph
+.TP
+querypaths
+Output graph paths for BLAST queries
+.TP
+reduce
+Save a subgraph of a larger graph
+.SS Options
+.TP
+\fB\-\-help\fR
+View this help message
+.TP
+\fB\-\-helpall\fR
+View all command line settings
+.TP
+\fB\-\-version\fR
+View Bandage version number
+.SS Settings
+The following options configure the Bandage settings that are available in the Bandage GUI.
+.TP
+Colours can be specified using hex values, with or without an alpha channel, (e.g. #FFB6C1 or #7FD2B48C) or using standard colour names (e.g. red, yellowgreen or skyblue).
+Note that hex colours will
+either need to be enclosed in quotes (e.g. "#FFB6C1") or have the hash symbol escaped (e.g. \e#FFB6C1).
+.PP
+.B Graph scope
+.PP
+These settings control the graph scope.  If the aroundnodes scope is used, then the \fB\-\-nodes\fR option must also be used.  If the aroundblast scope is used, a BLAST query must be given with the \fB\-\-query\fR
+option
+.TP
+\fB\-\-scope\fR <scope>
+Graph scope, from one of the following options: entire, aroundnodes, aroundblast, depthrange (default: entire)
+.TP
+\fB\-\-nodes\fR <list>
+A comma\-separated list of starting nodes for the aroundnodes scope (default: none)
+.TP
+\fB\-\-partial\fR
+Use partial node name matching (default: exact node name matching)
+.TP
+\fB\-\-distance\fR <int>
+The number of node steps away to draw for the aroundnodes and aroundblast scopes (0 to 100, default: 0)
+.TP
+\fB\-\-mindepth\fR <float>
+The minimum allowed depth for the depthrange scope (0 to 1e+6, default: 10)
+.TP
+\fB\-\-maxdepth\fR <float>
+The maximum allowed depth for the depthrange scope (0 to 1e+6, default: 100)
+.TP
+\fB\-\-double\fR
+Draw graph in double mode (default: off)
+.PP
+.B Graph size
+.TP
+\fB\-\-nodelen\fR <float>
+Node length per megabase (0 to 1e+6, default: auto)
+.TP
+\fB\-\-minnodlen\fR <float>
+Minimum node length (1 to 100, default: 5)
+.TP
+\fB\-\-edgelen\fR <float>
+Edge length (0.1 to 100, default: 5)
+.TP
+\fB\-\-edgewidth\fR <float>
+Edge width (0.1 to 100, default: 1.5)
+.TP
+\fB\-\-doubsep\fR <float>
+Double mode separation (0 to 100, default: 2)
+.PP
+.B Graph layout
+.TP
+\fB\-\-nodseglen\fR <float>
+Node segment length (1 to 1000, default: 20)
+.TP
+\fB\-\-iter\fR <int>
+Graph layout iterations (0 to 4, default: 2)
+.TP
+\fB\-\-linear\fR
+Linear graph layout (default: off)
+.PP
+.B Graph appearance
+.TP
+\fB\-\-edgecol\fR <col>
+Colour for edges (default: black)
+.TP
+\fB\-\-outcol\fR <col
+Colour for node outlines (default: black)
+.TP
+\fB\-\-outline\fR <float>
+Node outline thickness (0 to 100, default: 0)
+.TP
+\fB\-\-selcol\fR <col>
+Colour for selections (default: blue)
+.TP
+\fB\-\-noaa\fR
+Disable antialiasing (default: antialiasing on)
+.TP
+\fB\-\-singlearr\fR
+Show node arrowheads in single mode (default: nodes are only displayed with arrowheads in double mode)
+.PP
+.B Text appearance
+.TP
+\fB\-\-textcol\fR <col>
+Colour for label text (default: black)
+.TP
+\fB\-\-toutcol\fR <col>
+Colour for text outline (default: white)
+.TP
+\fB\-\-toutline\fR <float>
+Surround text with an outline with this thickness (0 to 10, default: 1.5)
+.TP
+\fB\-\-centre\fR
+Node labels appear at the centre of the node (default: off, node labels appear over visible parts of nodes)
+.PP
+.B Node width
+.PP
+Node widths are determined using the following formula:
+.IP
+a*b*((c/d)^e\-1)+1
+.IP
+a = average node width
+.IP
+b = depth effect on width
+.IP
+c = node depth
+.IP
+d = mean depth
+.IP
+e = power of depth effect on width
+.TP
+\fB\-\-nodewidth\fR <float>
+Average node width (0.5 to 1000, default: 5)
+.TP
+\fB\-\-depwidth\fR <float>
+Depth effect on width (0 to 1, default: 0.5)
+.TP
+\fB\-\-deppower\fR <float>
+Power of depth effect on width (0 to 1, default: 0.5)
+.PP
+.B Node labels
+.TP
+\fB\-\-names\fR
+Label nodes with name (default: off)
+.TP
+\fB\-\-lengths\fR
+Label nodes with length (default: off)
+.TP
+\fB\-\-depth\fR
+Label nodes with depth (default: off)
+.TP
+\fB\-\-blasthits\fR
+Label BLAST hits (default: off)
+.TP
+\fB\-\-fontsize\fR <int>
+Font size for node labels (1 to 100, default: 12)
+.PP
+.B Node colours
+.TP
+\fB\-\-colour\fR <scheme>
+Node colouring scheme, from one of the following options: random, uniform, depth, blastsolid, blastrainbow (default: random if \fB\-\-query\fR option not used, blastsolid if \fB\-\-query\fR
+option used)
+.PP
+.B Random colour scheme
+.PP
+These settings only apply when the random colour scheme is used.
+.TP
+\fB\-\-ransatpos\fR <int>
+Positive node saturation (0 to 255, default: 127)
+.TP
+\fB\-\-ransatneg\fR <int>
+Negative node saturation (0 to 255, default: 127)
+.TP
+\fB\-\-ranligpos\fR <int>
+Positive node lightness (0 to 255, default: 150)
+.TP
+\fB\-\-ranligneg\fR <int>
+Negative node lightness (0 to 255, default: 90)
+.TP
+\fB\-\-ranopapos\fR <int>
+Positive node opacity (0 to 255, default: 255)
+.TP
+\fB\-\-ranopaneg\fR <int>
+Negative node opacity (0 to 255, default: 255)
+.PP
+.B Uniform colour scheme
+.PP
+These settings only apply when the uniform colour scheme is used.
+.TP
+\fB\-\-unicolpos\fR <col>
+Positive node colour (default: firebrick)
+.TP
+\fB\-\-unicolneg\fR <col>
+Negative node colour (default: maroon)
+.TP
+\fB\-\-unicolspe\fR <col>
+Special node colour (default: green)
+.PP
+.B Depth colour scheme
+.PP
+These settings only apply when the depth colour scheme is used.
+.TP
+\fB\-\-depcollow\fR <col>
+Colour for nodes with depth below the low depth value (default: black)
+.TP
+\fB\-\-depcolhi\fR <col>
+Colour for nodes with depth above the high depth value (default: red)
+.TP
+\fB\-\-depvallow\fR <float>
+Low depth value (0 to 1e+6, default: auto)
+.TP
+\fB\-\-depvalhi\fR <float>
+High depth value (0 to 1e+6, default: auto)
+.PP
+.B BLAST search
+.TP
+\fB\-\-query\fR <fastafile>
+A FASTA file of either nucleotide or protein sequences to be used as BLAST queries (default: none)
+.TP
+\fB\-\-blastp\fR <param>
+Parameters to be used by blastn and tblastn when conducting a BLAST search in Bandage (default: none). Format BLAST parameters exactly as they would be used for blastn/tblastn on
+the command line, and enclose them in quotes.
+.TP
+\fB\-\-alfilter\fR <int>
+Alignment length filter for BLAST hits. Hits with shorter alignments will be excluded (1 to 1e+6, default: off)
+.TP
+\fB\-\-qcfilter\fR <float>
+Query coverage filter for BLAST hits. Hits with less coverage will be excluded (0 to 100, default: off)
+.TP
+\fB\-\-ifilter\fR <float>
+Identity filter for BLAST hits. Hits with less identity will be excluded (0 to 100, default: off)
+.TP
+\fB\-\-evfilter\fR <sci>
+E\-value filter for BLAST hits. Hits with larger e\-values will be excluded (1e\-999 to 9.9e1, default: off)
+.TP
+\fB\-\-bsfilter\fR <float>
+Bit score filter for BLAST hits. Hits with lower bit scores will be excluded (0 to 1e+6, default: off)
+.PP
+.B BLAST query paths
+.PP
+These settings control how Bandage searches for query paths after conducting a BLAST search.
+.TP
+\fB\-\-pathnodes\fR <int>
+The number of allowed nodes in a BLAST query path (1 to 50, default: 6)
+.TP
+\fB\-\-minpatcov\fR <float>
+Minimum fraction of a BLAST query which must be covered by a query path (0.3 to 1, default: 0.9)
+.TP
+\fB\-\-minhitcov\fR <float>
+Minimum fraction of a BLAST query which must be covered by BLAST hits in a query path (0.3 to 1, default: 0.9)
+.TP
+\fB\-\-minmeanid\fR <float>
+Minimum mean identity of BLAST hits in a query path (0 to 1, default: 0.5)
+.TP
+\fB\-\-maxevprod\fR <sci>
+Maximum e\-value product for all BLAST hits in a query path (1e\-999 to 9.9e1, default: 1e\-10)
+.TP
+\fB\-\-minpatlen\fR <float>
+Minimum allowed relative path length as compared to the query (0 to 10000, default: 0.95)
+.TP
+\fB\-\-maxpatlen\fR <float>
+Maximum allowed relative path length as compared to the query (0 to 10000, default: 1.05)
+.TP
+\fB\-\-minlendis\fR <int>
+Minimum allowed length discrepancy (in bases) between a BLAST query and its path in the graph (\fB\-1e\fR+6 to 1e+6, default: off)
+.TP
+\fB\-\-maxlendis\fR <int>
+Maximum allowed length discrepancy (in bases) between a BLAST query and its path in the graph (\fB\-1e\fR+6 to 1e+6, default: off)
+.SH SEE ALSO
+Online Bandage help: https://github.com/rrwick/Bandage/wiki
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.


=====================================
debian/changelog
=====================================
@@ -2,4 +2,4 @@ bandage (0.8.1-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #872622)
 
- -- DMPT <debian-med-packaging at lists.alioth.debian.org>  Tue, 15 Aug 2017 16:57:55 +0200
+ -- Andreas Tille <tille at debian.org>  Sun, 26 Aug 2018 21:01:25 +0200


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11


=====================================
debian/control
=====================================
@@ -1,14 +1,15 @@
 Source: bandage
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Cédric Lood <cedric.lood at kuleuven.be>
+Uploaders: Cédric Lood <cedric.lood at kuleuven.be>,
+           Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                qtbase5-dev,
                libqt5svg5-dev
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bandage.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bandage.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/bandage
+Vcs-Git: https://salsa.debian.org/med-team/bandage.git
 Homepage: https://rrwick.github.io/Bandage
 
 Package: bandage


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,27 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//'`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=Bandage
+help2man --no-info --no-discard-stderr --help-option=" --helpall" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/patches/fix_target_path.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 26 Aug 2018 19:57:42 +0200
+Description: Install binary to /usr/bin
+
+--- a/Bandage.pro
++++ b/Bandage.pro
+@@ -24,7 +24,7 @@ TEMPLATE = app
+ 
+ CONFIG += c++11
+ 
+-target.path += /usr/local/bin
++target.path += /usr/bin
+ INSTALLS += target
+ 
+ INCLUDEPATH += ui


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 fix_include_vars_makefile.patch
+fix_target_path.patch


=====================================
debian/rules
=====================================
@@ -16,8 +16,14 @@ include /usr/share/dpkg/default.mk
 # export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 export QT_SELECT = qt5
+
 %:
 	dh $@
 
-#get-orig-source:
-#	. debian/get-orig-source
+override_dh_auto_configure:
+	# see https://lists.debian.org/debian-mentors/2018/08/msg00206.html
+	#   --> thus move the other .pro file that confuses qmake out of the way
+	mv BandageTests.pro BandageTests.pro_do_not_use
+	dh_auto_configure
+	# restore original status of source dir
+	mv BandageTests.pro_do_not_use BandageTests.pro



View it on GitLab: https://salsa.debian.org/med-team/bandage/compare/17b69fde8952a60b95226696db1095d2e07b2d5e...de4aacc5b2915121fa109660c21c8829cefcf1b4

-- 
View it on GitLab: https://salsa.debian.org/med-team/bandage/compare/17b69fde8952a60b95226696db1095d2e07b2d5e...de4aacc5b2915121fa109660c21c8829cefcf1b4
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