[med-svn] r4210 - trunk/packages/alien-hunter/trunk/debian

[Andreas Tille]

Author: tille
Date: 2009-10-14 11:52:01 +0000 (Wed, 14 Oct 2009)
New Revision: 4210

Added:
   trunk/packages/alien-hunter/trunk/debian/alien_hunter.1
   trunk/packages/alien-hunter/trunk/debian/manpages
Removed:
   trunk/packages/alien-hunter/trunk/debian/docs
Modified:
   trunk/packages/alien-hunter/trunk/debian/install
   trunk/packages/alien-hunter/trunk/debian/rules
Log:
Do not install useless upstream REAMD which basically describes installation; added manpage


Added: trunk/packages/alien-hunter/trunk/debian/alien_hunter.1
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/alien_hunter.1	                        (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/alien_hunter.1	2009-10-14 11:52:01 UTC (rev 4210)
@@ -0,0 +1,73 @@
+.\" Originally generated by help2man 1.36.
+.TH ALIEN_HUNTER "1" "October 2009" "alien_hunter 1.7" "User Commands"
+.SH NAME
+alien_hunter \- Interpolated Variable Order Motifs for identification of horizontally acquired DNA
+
+.SH SYNOPSIS
+.B alien_hunter \fI<sequence.file>\fR \fI<output.file>\fR [\fIOptions\fR]
+
+.SH DESCRIPTION
+.PP
+Alien_hunter is an application for the prediction of putative Horizontal
+Gene Transfer (HGT) events with the implementation of Interpolated
+Variable Order Motifs (IVOMs). An IVOM approach exploits compositional
+biases using variable order motif distributions and captures more
+reliably the local composition of a sequence compared to fixed-order
+methods. Optionally the predictions can be parsed into a 2-state 2nd
+order Hidden Markov Model (HMM), in a change-point detection framework,
+to optimize the localization of the boundaries of the predicted regions.
+The predictions (embl format) can be automatically loaded into Artemis
+genome viewer freely available at:
+http://www.sanger.ac.uk/Software/Artemis/.
+.PP
+INPUT: raw genomic sequence PREDICTION: HGT regions based on Interpolated Variable Order Motifs (IVOMs)
+arguments:
+.TP
+<sequence.file>
+raw genomic sequence
+.TP
+<output.file>
+filename for output data
+
+.PP
+Optional arguments:
+.TP
+\-a
+to load the prediction file into Artemis
+.TP
+\-c
+optimize predicted boundaries with a change\-point detection 2 state 2nd order HMM
+
+.PP
+Output files:
+.TP
+<output.file>
+predictions (tab file) in embl format
+.TP
+<output.file>.opt
+optimized (HMM) predictions (tab file) in embl format
+.TP
+<output.file>.plot
+predictions in Artemis User Plot format to be loaded manually using Graph \-> Add User Plot...
+.TP
+<output.file>.opt.plot
+optimized (HMM) predictions in Artemis User Plot format to be loaded manually using Graph \-> Add User Plot...
+.TP
+<output.file>.sco
+the scores over all the sliding windows \- for score distribution check
+
+.PP
+Note: Predictions that overlap with rRNA operon are mentioned in the note qualifier
+
+.SH SEE ALSO
+
+The manuscript describing the alien_hunter algorithm is available from
+Bioinformatics: Interpolated variable order motifs for identification of
+horizontally acquired DNA: revisiting the Salmonella pathogenicity
+islands.  Vernikos GS, Parkhill J Bioinformatics. 2006;. PMID: 16837528
+
+.SH "AUTHOR"
+.PP
+This manual page was written by Andreas Tille <tille at debian\.com> for the Debian(TM)
+system (but may be used by others)\. This man page is released under the same conditions
+as the software, that is GPL\.

Deleted: trunk/packages/alien-hunter/trunk/debian/docs
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/docs	2009-10-14 11:06:32 UTC (rev 4209)
+++ trunk/packages/alien-hunter/trunk/debian/docs	2009-10-14 11:52:01 UTC (rev 4210)
@@ -1 +0,0 @@
-README

Modified: trunk/packages/alien-hunter/trunk/debian/install
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/install	2009-10-14 11:06:32 UTC (rev 4209)
+++ trunk/packages/alien-hunter/trunk/debian/install	2009-10-14 11:52:01 UTC (rev 4210)
@@ -1,4 +1,5 @@
-*.pm        /usr/share/perl5
-PAI_scripts /usr/share/perl5
-*.pl        /usr/share/alien_hunter
-*.class     /usr/share/alien_hunter
+*.pm          usr/share/perl5
+PAI_scripts   usr/share/perl5
+*.pl          usr/share/alien_hunter
+*.class       usr/share/alien_hunter
+alien_hunter  usr/bin

Added: trunk/packages/alien-hunter/trunk/debian/manpages
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/manpages	2009-10-14 11:52:01 UTC (rev 4210)
@@ -0,0 +1 @@
+debian/alien_hunter.1

Modified: trunk/packages/alien-hunter/trunk/debian/rules
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/rules	2009-10-14 11:06:32 UTC (rev 4209)
+++ trunk/packages/alien-hunter/trunk/debian/rules	2009-10-14 11:52:01 UTC (rev 4210)
@@ -2,6 +2,9 @@
 # debian/rules for alien-hunter
 # Andreas Tille <tille at debian.org>, GPL
 
+version=$(shell dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d- -f1 )
+executable=alien_hunter
+
 %:
 	dh --with quilt $@
 
@@ -9,7 +12,7 @@
 	CLASSPATH=/usr/share/java/biojava.jar javac -Xlint:deprecation -Xlint:unchecked *.java
 
 override_dh_auto_clean:
-	rm -f *.class
+	rm -f *.class $(executable).1
 
 get-orig-source:
 	. debian/get-orig-source