[med-svn] r10621 - in trunk/packages/saint/trunk/debian: . patches

Fri Apr 27 09:54:18 UTC 2012

Author: tille
Date: 2012-04-27 09:54:18 +0000 (Fri, 27 Apr 2012)
New Revision: 10621

Added:
   trunk/packages/saint/trunk/debian/manpages
   trunk/packages/saint/trunk/debian/saint-int-ctrl.1
   trunk/packages/saint/trunk/debian/saint-reformat.1
   trunk/packages/saint/trunk/debian/saint-spc-ctrl.1
   trunk/packages/saint/trunk/debian/saint-spc-noctrl-matrix.1
   trunk/packages/saint/trunk/debian/saint-spc-noctrl.1
Modified:
   trunk/packages/saint/trunk/debian/README.Debian
   trunk/packages/saint/trunk/debian/changelog
   trunk/packages/saint/trunk/debian/copyright
   trunk/packages/saint/trunk/debian/patches/fix-makefile.patch
   trunk/packages/saint/trunk/debian/rules
Log:
Upstream has confirmed GPL license so it makes some sense to keep on working on this package


Modified: trunk/packages/saint/trunk/debian/README.Debian
===================================================================

--- trunk/packages/saint/trunk/debian/README.Debian	2012-04-27 08:07:39 UTC (rev 10620)
+++ trunk/packages/saint/trunk/debian/README.Debian	2012-04-27 09:54:18 UTC (rev 10621)
@@ -1,6 +1,20 @@
 SAINT for Debian
 ================
 
+Documentation:
+--------------
+
+You can download a PDF file with more detailed instructions than you
+can read in the relevant man pages at
+
+   http://sourceforge.net/projects/saint-apms/files/
+
+which is called saint-vignette-<YYYYMonDD>.pdf.
+
+
+Other Hint:
+-----------
+
 The description speaks explicitly about the program ProHits which
 can be found here:
 

Modified: trunk/packages/saint/trunk/debian/changelog
===================================================================
--- trunk/packages/saint/trunk/debian/changelog	2012-04-27 08:07:39 UTC (rev 10620)
+++ trunk/packages/saint/trunk/debian/changelog	2012-04-27 09:54:18 UTC (rev 10621)
@@ -1,4 +1,4 @@
-saint (2.3.2-1) UNRELEASED; urgency=low
+saint (2.3.3-1) UNRELEASED; urgency=low
 
   * Initial Release  (Closes: #?)
 

Modified: trunk/packages/saint/trunk/debian/copyright
===================================================================
--- trunk/packages/saint/trunk/debian/copyright	2012-04-27 08:07:39 UTC (rev 10620)
+++ trunk/packages/saint/trunk/debian/copyright	2012-04-27 09:54:18 UTC (rev 10621)
@@ -5,25 +5,17 @@
 
 Files: *
 Copyright: © 2010-2012 Hyung Won Choi <hyung_won_choi at nuhs.edu.sg>
-License: GPL-2+
-Comment:
- From: Hyung Won Choi <hyung_won_choi at nuhs.edu.sg>
- To: Andreas Tille <andreas at fam-tille.de>
- Date: Wed, 25 Apr 2012 06:36:29 +0800
- Subject: RE: Saint for Debian
- .
- There should be a gnu license statement in the header files.
- I will go check when I go to office today.
+License: GPL-3+
 
 Files: debian/*
 Copyright: © 2012 Andreas Tille <tille at debian.org>
-License: GPL-2+
+License: GPL-3+
 
-License: GPL-2+
+License: GPL-3+
  This program is free software; you can redistribute it
  and/or modify it under the terms of the GNU General Public
  License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later
+ version 3 of the License, or (at your option) any later
  version.
  .
  This program is distributed in the hope that it will be
@@ -38,6 +30,6 @@
  Boston, MA  02110-1301 USA
  .
  On Debian systems, the full text of the GNU General Public
- License version 2 can be found in the file
- `/usr/share/common-licenses/GPL-2'.
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
 

Added: trunk/packages/saint/trunk/debian/manpages
===================================================================
--- trunk/packages/saint/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/saint/trunk/debian/manpages	2012-04-27 09:54:18 UTC (rev 10621)
@@ -0,0 +1 @@
+debian/*.1

Modified: trunk/packages/saint/trunk/debian/patches/fix-makefile.patch
===================================================================
--- trunk/packages/saint/trunk/debian/patches/fix-makefile.patch	2012-04-27 08:07:39 UTC (rev 10620)
+++ trunk/packages/saint/trunk/debian/patches/fix-makefile.patch	2012-04-27 09:54:18 UTC (rev 10621)
@@ -1,5 +1,5 @@
---- SAINT_v2.3.2.orig/Makefile
-+++ SAINT_v2.3.2/Makefile
+--- SAINT_v2.3.3.orig/Makefile
++++ SAINT_v2.3.3/Makefile
 @@ -29,7 +29,7 @@
  
  clean:

Modified: trunk/packages/saint/trunk/debian/rules
===================================================================
--- trunk/packages/saint/trunk/debian/rules	2012-04-27 08:07:39 UTC (rev 10620)
+++ trunk/packages/saint/trunk/debian/rules	2012-04-27 09:54:18 UTC (rev 10621)
@@ -10,3 +10,7 @@
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -rf bin
+
+get-orig-source:
+	mkdir -p ../tarballs
+	uscan --verbose --force-download --repack --rename --destdir=../tarballs

Added: trunk/packages/saint/trunk/debian/saint-int-ctrl.1
===================================================================
--- trunk/packages/saint/trunk/debian/saint-int-ctrl.1	                        (rev 0)
+++ trunk/packages/saint/trunk/debian/saint-int-ctrl.1	2012-04-27 09:54:18 UTC (rev 10621)
@@ -0,0 +1,12 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.8.
+.TH saint-int-ctrl "1" "April 2012" "User Commands"
+.SH NAME
+saint-int-ctrl \- suport continuous measurements in SAINT
+.SH DESCRIPTION
+usage: saint\-int\-ctrl [interactionFile] [preyFile] [baitFile] [nburnin] [niter]
+.SH "SEE ALSO"
+You can download a PDF file with more detailed instructions from
+.IP
+http://sourceforge.net/projects/saint-apms/files/
+.P
+which is called saint-vignette-<YYYYMonDD>.pdf.

Added: trunk/packages/saint/trunk/debian/saint-reformat.1
===================================================================
--- trunk/packages/saint/trunk/debian/saint-reformat.1	                        (rev 0)
+++ trunk/packages/saint/trunk/debian/saint-reformat.1	2012-04-27 09:54:18 UTC (rev 10621)
@@ -0,0 +1,15 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.8.
+.TH SAINT-SPC-REFORMAT "1" "April 2012" "User Commands"
+.SH NAME
+saint-spc-reformat \- imputs missing data and cleans up duplicate entries
+.SH DESCRIPTION
+usage: saint\-spc\-reformat [interactionFile] [preyFile] [baitFile]
+usage: saint\-spc\-reformat [interactionFile] [preyFile] [baitFile] [# Control]
+.PP
+usage: saint\-spc\-reformat [interactionFile] [preyFile] [baitFile] [# Control]
+.SH "SEE ALSO"
+You can download a PDF file with more detailed instructions from
+.IP
+http://sourceforge.net/projects/saint-apms/files/
+.P
+which is called saint-vignette-<YYYYMonDD>.pdf.

Added: trunk/packages/saint/trunk/debian/saint-spc-ctrl.1
===================================================================
--- trunk/packages/saint/trunk/debian/saint-spc-ctrl.1	                        (rev 0)
+++ trunk/packages/saint/trunk/debian/saint-spc-ctrl.1	2012-04-27 09:54:18 UTC (rev 10621)
@@ -0,0 +1,54 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.8.
+.TH "SAINT-SPC-CTRL" "1" "April 2012" "User Commands"
+.SH NAME
+saint-spc-ctrl \- run SAINT with control data
+.SH SYNOPSIS
+.B saint-spc-ctrl
+.I [interactionFile] [preyFile] [baitFile] [nburnin] [niter] [lowMode] [minFold] [normalize]
+.SH DESCRIPTION
+.IP
+nburnin = 2000: number of burn\-in iterations in MCMC.
+.IP
+niter = 10000: number of main iterations in MCMC.
+.IP
+lowMode = 0/1 : exclude extremely high counts in the model.
+.IP
+\- If baits are densely connected or dataset is small (few baits), use 1.
+.IP
+\- otherwise, use 0.
+.IP
+minFold = 0/1 : forcing separation between true and false distributions.
+.IP
+\- If user wishes to allow typical contaminants with significant
+.IP
+differential enrichment over control purifications, use 0.
+.IP
+\- otherwise, use 1.
+.IP
+normalize = 0/1 : divide the counts by the total spectral counts in each IP.
+.IP
+nburnin = 2000: number of burn\-in iterations in MCMC.
+.IP
+niter = 10000: number of main iterations in MCMC.
+.IP
+lowMode = 0/1 : exclude extremely high counts in the model.
+.IP
+\- If baits are densely connected or dataset is small (few baits), use 1.
+.IP
+\- otherwise, use 0.
+.IP
+minFold = 0/1 : forcing separation between true and false distributions.
+.IP
+\- If user wishes to allow typical contaminants with significant
+.IP
+differential enrichment over control purifications, use 0.
+.IP
+\- otherwise, use 1.
+.IP
+normalize = 0/1 : divide the counts by the total spectral counts in each IP.
+.SH "SEE ALSO"
+You can download a PDF file with more detailed instructions from
+.IP
+http://sourceforge.net/projects/saint-apms/files/
+.P
+which is called saint-vignette-<YYYYMonDD>.pdf.

Added: trunk/packages/saint/trunk/debian/saint-spc-noctrl-matrix.1
===================================================================
--- trunk/packages/saint/trunk/debian/saint-spc-noctrl-matrix.1	                        (rev 0)
+++ trunk/packages/saint/trunk/debian/saint-spc-noctrl-matrix.1	2012-04-27 09:54:18 UTC (rev 10621)
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.8.
+.TH SAINT-SPC-NOCTRL-MATRIX "1" "April 2012" "User Commands"
+.SH NAME
+saint-spc-noctrl-matrix \- run SAINT for a (large-scale, matrix-formatted) dataset without control purification
+.SH SYNOPSIS
+.B saint-spc-noctrl-matrix
+.I [interactomeData] [output file] [nburnin] [niter] [ff]
+.P
+.B saint-spc-noctrl-matrix
+.I [interactomeData] [output file] [nburnin] [niter] [ff] [useAbundance(0/1)] [useLength(0/1)] [useCoverage(0/1)]
+.SH "SEE ALSO"
+You can download a PDF file with more detailed instructions from
+.IP
+http://sourceforge.net/projects/saint-apms/files/
+.P
+which is called saint-vignette-<YYYYMonDD>.pdf.

Added: trunk/packages/saint/trunk/debian/saint-spc-noctrl.1
===================================================================
--- trunk/packages/saint/trunk/debian/saint-spc-noctrl.1	                        (rev 0)
+++ trunk/packages/saint/trunk/debian/saint-spc-noctrl.1	2012-04-27 09:54:18 UTC (rev 10621)
@@ -0,0 +1,24 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.8.
+.TH SAINT-SPC-NOCTRL "1" "April 2012" "saint-spc-noctrl " "User Commands"
+.SH NAME
+saint-spc-noctrl \- run SAINT scoring algorithm for protein-protein interaction data using label free quantitative proteomics data
+.SH SYNOPSIS
+.B saint-spc-noctrl
+.I [interactionFile] [preyFile] [baitFile] [nburnin] [niter] [fthres] [fgroup] [var] [normalize]
+.SH DESCRIPTION
+.PP
+\fB\-burnin\fR and iter: burn\-in period and main iteration of MCMC
+.PP
+\fB\-fthres\fR: frequency threshold above which probability is set to 0
+.PP
+\fB\-fgroup\fR: frequency boundary dividing high and low frequency groups
+.PP
+\fB\-var\fR: binary [0/1] indicator for modeling variance of the count data distributions
+.PP
+\fB\-normalize\fR: whether to normalize the counts by total spectral counts
+.SH "SEE ALSO"
+You can download a PDF file with more detailed instructions from
+.IP
+http://sourceforge.net/projects/saint-apms/files/
+.P
+which is called saint-vignette-<YYYYMonDD>.pdf.


