[med-svn] r16750 - in trunk/packages/staden/trunk/debian: . mans

Andreas Tille tille at moszumanska.debian.org
Tue Apr 22 09:51:23 UTC 2014 

Author: tille
Date: 2014-04-22 09:51:23 +0000 (Tue, 22 Apr 2014)
New Revision: 16750

Added:
   trunk/packages/staden/trunk/debian/createmanpages
   trunk/packages/staden/trunk/debian/manpages
   trunk/packages/staden/trunk/debian/mans/
   trunk/packages/staden/trunk/debian/mans/gap4.1
   trunk/packages/staden/trunk/debian/mans/gap5.1
   trunk/packages/staden/trunk/debian/mans/pregap4.1
   trunk/packages/staden/trunk/debian/mans/spin.1
   trunk/packages/staden/trunk/debian/mans/trev.1
Modified:
   trunk/packages/staden/trunk/debian/changelog
   trunk/packages/staden/trunk/debian/control
Log:
Add manpages for main programs


Modified: trunk/packages/staden/trunk/debian/changelog
===================================================================
--- trunk/packages/staden/trunk/debian/changelog	2014-04-21 20:38:19 UTC (rev 16749)
+++ trunk/packages/staden/trunk/debian/changelog	2014-04-22 09:51:23 UTC (rev 16750)
@@ -1,14 +1,8 @@
 staden (2.0.0+b10-1) UNRELEASED; urgency=low
 
   FIXME: TODO
-   it seems gap[45], pregap4, spin (not sure about trev) are the main
-   applications of staden what about hiding all those helper tools in
-      /usr/lib/staden/bin
-   and set the PATH appropriately inside the wrapper scripts gap[45],
-   pregap4 and spin?
-   This would make the package way more clean and would silence drastically
-   regarding missing manpages (which are hard to write anyway since even
-   help2man would not be able to do a reasonable job)
+  Help does not work because of missing files
+    couldn't open "/usr/share/doc/staden/manual/gap4.index": no such file or directory
 
   [ Tim Booth ]
   * Initial release to Debian (Closes: #710324)

Modified: trunk/packages/staden/trunk/debian/control
===================================================================
--- trunk/packages/staden/trunk/debian/control	2014-04-21 20:38:19 UTC (rev 16749)
+++ trunk/packages/staden/trunk/debian/control	2014-04-22 09:51:23 UTC (rev 16750)
@@ -28,7 +28,8 @@
 Depends: ${misc:Depends},
          ${shlibs:Depends},
          staden-common (= ${source:Version}),
-         staden-io-lib-utils
+         staden-io-lib-utils,
+         tklib
 Suggests: staden-doc
 Description: DNA sequence assembly (Gap4/Gap5), editing and analysis tools
  Staden is a fully developed set of DNA sequence assembly (Gap4 and

Added: trunk/packages/staden/trunk/debian/createmanpages
===================================================================
--- trunk/packages/staden/trunk/debian/createmanpages	                        (rev 0)
+++ trunk/packages/staden/trunk/debian/createmanpages	2014-04-22 09:51:23 UTC (rev 16750)
@@ -0,0 +1,22 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option="--help" \
+         --name='Genome Assembly Program (part of staden package)' \
+            --version-string="$VERSION" gap4 > $MANDIR/gap4.1
+#help2man --no-info --no-discard-stderr --help-option="--help" \
+#         --name='Genome Assembly Program (part of staden package)' \
+#            --version-string="$VERSION" gap5 > $MANDIR/gap5.1
+sed -e 's/\([Gg]ap\)4/\15/g'  -e '/^\.SH SEE ALSO/,$d' $MANDIR/gap4.1 > $MANDIR/gap5.1
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='prepare raw data from sequencing instruments for usage with gap4 (part of staden package)' \
+            --version-string="$VERSION" pregap4 > $MANDIR/pregap4.1
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name='DNA editing and analysis tool (part of staden package)' \
+            --version-string="$VERSION" spin > $MANDIR/spin.1
+help2man --no-info --no-discard-stderr --help-option="--help" \
+         --name='opening trace files (part of staden package)' \
+            --version-string="$VERSION" trev > $MANDIR/trev.1


Property changes on: trunk/packages/staden/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/staden/trunk/debian/manpages
===================================================================
--- trunk/packages/staden/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/staden/trunk/debian/manpages	2014-04-22 09:51:23 UTC (rev 16750)
@@ -0,0 +1 @@
+debian/mans/*

Added: trunk/packages/staden/trunk/debian/mans/gap4.1
===================================================================
--- trunk/packages/staden/trunk/debian/mans/gap4.1	                        (rev 0)
+++ trunk/packages/staden/trunk/debian/mans/gap4.1	2014-04-22 09:51:23 UTC (rev 16750)
@@ -0,0 +1,57 @@
+.TH GAP4 "1" "April 2014" "gap4 2.0.0+b10" "User Commands"
+.SH NAME
+gap4 \- Genome Assembly Program (part of staden package)
+.SH SYNOPSIS
+.B gap4
+[\fB\-ro\fR] [\fB\-maxseq\fR \fI<number>\fR] [\fB\-maxdb\fR \fI<number>\fR] [\fB\-skip_notes\fR] [\fI\,DATABASE_NAME.V\/\fR]
+.SH DESCRIPTION
+.P
+Gap4 is a Genome Assembly Program. The program contains all the tools
+that would be expected from an assembly program plus many unique
+features and a very easily used interface. The original version was
+described in Bonfield,J.K., Smith,K.F. and Staden,R. A new DNA sequence
+assembly program. Nucleic Acids Res. 24, 4992-4999 (1995)
+.P
+Gap4 is very big and powerful. Everybody employs a subset of options and
+has their favourite way of accessing and using them. Although there is a
+lot of it, users are encouraged to go through the whole of the
+documentation once, just to discover what is possible, and the way that
+best suits their own work. At the very least, the whole of this
+introductory chapter should be read, as in the long run, it will save
+time. 
+.SH OPTIONS
+.TP
+\fB\-ro\fR
+Read\-only
+.TP
+\fB\-maxseq\fR N
+Initial maximum total consensus length
+.TP
+\fB\-maxdb\fR N
+Initial maximum number of contigs + readings
+.TP
+\fB\-(no_)check\fR
+(Do not) run Check Database upon DB open
+.TP
+\fB\-(no_)exec_notes\fR
+(Do not) execute OPEN/CLOS notes upon database open
+.TP
+\fB\-(no_)rawdata_note\fR
+(Do not) use RAWD note instead of RAWDATA env. variable
+.TP
+\fB\-(no_)csel\fR
+(Do not) start up the contig selector upon db open
+.TP
+\fB\-display\fR
+X Display to use
+.TP
+\fB\-bitsize\fR N
+Specifies the aux file bitsize for new databases (32/64)
+.TP
+\fB\-sync\fR
+Use synchronous mode for display server (debugging)
+.TP
+\fB\-\-\fR
+End of argument list
+.SH SEE ALSO
+http://staden.sourceforge.net/manual/gap4_unix_2.html

Added: trunk/packages/staden/trunk/debian/mans/gap5.1
===================================================================
--- trunk/packages/staden/trunk/debian/mans/gap5.1	                        (rev 0)
+++ trunk/packages/staden/trunk/debian/mans/gap5.1	2014-04-22 09:51:23 UTC (rev 16750)
@@ -0,0 +1,55 @@
+.TH GAP4 "1" "April 2014" "gap5 2.0.0+b10" "User Commands"
+.SH NAME
+gap5 \- Genome Assembly Program (part of staden package)
+.SH SYNOPSIS
+.B gap5
+[\fB\-ro\fR] [\fB\-maxseq\fR \fI<number>\fR] [\fB\-maxdb\fR \fI<number>\fR] [\fB\-skip_notes\fR] [\fI\,DATABASE_NAME.V\/\fR]
+.SH DESCRIPTION
+.P
+Gap5 is a Genome Assembly Program. The program contains all the tools
+that would be expected from an assembly program plus many unique
+features and a very easily used interface. The original version was
+described in Bonfield,J.K., Smith,K.F. and Staden,R. A new DNA sequence
+assembly program. Nucleic Acids Res. 24, 4992-4999 (1995)
+.P
+Gap5 is very big and powerful. Everybody employs a subset of options and
+has their favourite way of accessing and using them. Although there is a
+lot of it, users are encouraged to go through the whole of the
+documentation once, just to discover what is possible, and the way that
+best suits their own work. At the very least, the whole of this
+introductory chapter should be read, as in the long run, it will save
+time. 
+.SH OPTIONS
+.TP
+\fB\-ro\fR
+Read\-only
+.TP
+\fB\-maxseq\fR N
+Initial maximum total consensus length
+.TP
+\fB\-maxdb\fR N
+Initial maximum number of contigs + readings
+.TP
+\fB\-(no_)check\fR
+(Do not) run Check Database upon DB open
+.TP
+\fB\-(no_)exec_notes\fR
+(Do not) execute OPEN/CLOS notes upon database open
+.TP
+\fB\-(no_)rawdata_note\fR
+(Do not) use RAWD note instead of RAWDATA env. variable
+.TP
+\fB\-(no_)csel\fR
+(Do not) start up the contig selector upon db open
+.TP
+\fB\-display\fR
+X Display to use
+.TP
+\fB\-bitsize\fR N
+Specifies the aux file bitsize for new databases (32/64)
+.TP
+\fB\-sync\fR
+Use synchronous mode for display server (debugging)
+.TP
+\fB\-\-\fR
+End of argument list

Added: trunk/packages/staden/trunk/debian/mans/pregap4.1
===================================================================
--- trunk/packages/staden/trunk/debian/mans/pregap4.1	                        (rev 0)
+++ trunk/packages/staden/trunk/debian/mans/pregap4.1	2014-04-22 09:51:23 UTC (rev 16750)
@@ -0,0 +1,19 @@
+.TH PREGAP4 "1" "April 2014" "pregap4 2.0.0+b10" "User Commands"
+.SH NAME
+pregap4 \- prepare raw data from sequencing instruments for usage with gap4 (part of staden package)
+.SH DESCRIPTION
+Before entry into a gap4 database the raw data from sequencing
+instruments needs to be passed through several processes, such as
+screening for vectors, quality evaluation, and conversion of data
+formats. Pregap4 is used to pass a batch of readings through these steps
+in an automatic way. It provides an interface for setting up and
+configuring the processing and for controlling the passage of the
+readings through each stage. The separate tasks are termed "modules" and
+each module is typically managed by a dedicated program. Pregap4 wraps
+all of these modules into a single easy to use environment, whilst
+maintaining the flexibility to select and extend the processing modules.
+It is an, as yet, unpublished replacement of the program pregap
+Bonfield, J.K. and Staden, R. Experiment files and their application
+during large-scale sequencing projects. DNA Sequence 6, 109-117 (1996). 
+.SH SEE ALSO
+http://staden.sourceforge.net/manual/pregap4_unix_2.html

Added: trunk/packages/staden/trunk/debian/mans/spin.1
===================================================================
--- trunk/packages/staden/trunk/debian/mans/spin.1	                        (rev 0)
+++ trunk/packages/staden/trunk/debian/mans/spin.1	2014-04-22 09:51:23 UTC (rev 16750)
@@ -0,0 +1,53 @@
+.TH SPIN "1" "April 2014" "spin 2.0.0+b10" "User Commands"
+.SH NAME
+spin \- DNA editing and analysis tool (part of staden package)
+.SH SYNOPSIS
+.B spin
+[options]
+.SH DESCRIPTION
+Spin is an interactive and graphical program for analysing and comparing
+sequences. It contains functions to search for restriction sites,
+consensus sequences/motifs and protein coding regions, can analyse the
+composition of the sequence and translate DNA to protein. It also
+contains functions for locating segments of similarity within and
+between sequences, and for finding global and local alignments between
+pairs of sequences. To help assess the statistical significance of
+comparisons the program can calculate tables of expected and observed
+score frequencies for each score level. Most analytical functions which
+operate on single sequences add their graphical results to a "SPIN
+Sequence Plot" that is associated with the sequence being analysed. (An
+exception is the restriction enzyme search which produces its own
+separate window.) Most functions which compare pairs of sequences add
+their results to a "SPIN Sequence Comparison Plot". The SPIN Sequence
+Plot and the SPIN Sequence Comparison Plot each have associated sequence
+display windows: the Sequence Display and the Sequence Comparison
+Display. These allow the text of the sequences to be viewed and use
+cursors to show the corresponding positions in the graphical displays.
+The graphical plots can be zoomed, and cursors or crosshairs can be used
+to locate the positions of the individual results. Plots can be
+superimposed. 
+.SH OPTIONS
+.HP
+\fB\-colormap\fR: Colormap for main window
+.TP
+\fB\-display\fR:
+Display to use
+.HP
+\fB\-geometry\fR: Initial geometry for window
+.TP
+\fB\-name\fR:
+Name to use for application
+.TP
+\fB\-sync\fR:
+Use synchronous mode for display server
+.TP
+\fB\-visual\fR:
+Visual for main window
+.TP
+\fB\-use\fR:
+Id of window in which to embed application
+.TP
+\fB\-\-\fR:
+Pass all remaining arguments through to script
+.SH SEE ALSO
+http://staden.sourceforge.net/manual/spin_unix_2.html

Added: trunk/packages/staden/trunk/debian/mans/trev.1
===================================================================
--- trunk/packages/staden/trunk/debian/mans/trev.1	                        (rev 0)
+++ trunk/packages/staden/trunk/debian/mans/trev.1	2014-04-22 09:51:23 UTC (rev 16750)
@@ -0,0 +1,53 @@
+.TH TREV "1" "April 2014" "trev 2.0.0+b10" "User Commands"
+.SH NAME
+trev \- opening trace files (part of staden package)
+.SH SYNOPSIS
+.B trev
+[\fI\-{ABI,ALF,EXP,SCF,PLN,Any}\fR] [\fB\-edits\fR \fIvalue\fR] [\fB\-editscf\fR] [\fB\-xmag\fR \fIvalue\fR] [\fB\-ymag\fB \fIvalue\fR] [\fB\-restrict\fR] [\fItracefilename\fR ...] 
+.SH DESCRIPTION
+Trace files can be opened either on the command line or from within
+Trev. In both cases it is possible to open several traces at once. In
+this case trev will add Next File, Previous File and Goto File buttons
+to allow quick navigation between traces.
+.
+On the command line, this is simply done by specifying several files.
+With the "Open" dialogue from within trev multiple files may be selected
+by dragging with the left mouse button or using shift+left button and
+control+left button to extend regions or to toggle loading of individual
+files. 
+.SH OPTIONS
+.TP
+\fB\-abi\fR/\-alf/\-ctf
+Specify input format (def. any)
+.TP
+\fB\-exp\fR/\-pln/\-ztr/\-any
+\&... " ...
+.TP
+\fB\-write_scf\fR
+Allow writing back to SCF, ZTR, CTF
+.TP
+\fB\-editscf\fR
+Synonym for \fB\-write_scf\fR
+.TP
+\fB\-xmag\fR scale
+X magnification (def. 150)
+.TP
+\fB\-ymag\fR scale
+Y magnification (def. 10)
+.TP
+\fB\-trace_scale\fR
+Set max\-trace\-value (def. 0 => auto)
+.TP
+\fB\-fofn\fR fn
+Load files from "fn"
+.TP
+\fB\-pregap_mode\fR
+Used from old pregap
+.TP
+\fB\-restrict\fR
+Used from pregap4
+.TP
+\fB\-\-\fR
+Force end of argument list
+.SH SEE ALSO
+http://staden.sourceforge.net/manual/trev_unix_2.html

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