[med-svn] r4210 - trunk/packages/alien-hunter/trunk/debian
Andreas Tille
tille at alioth.debian.org
Wed Oct 14 11:52:01 UTC 2009
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
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