debian/0000755000000000000000000000000012152610622007163 5ustar debian/saint-spc-ctrl.10000644000000000000000000000323312151612127012112 0ustar .\" 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-.pdf. debian/manpages0000644000000000000000000000001312151612127010674 0ustar debian/*.1 debian/control0000644000000000000000000000216212151612127010570 0ustar Source: saint Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 9), libgsl0-dev Standards-Version: 3.9.4 Homepage: http://saint-apms.sourceforge.net/Main.html Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/saint/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/saint/trunk/ Package: saint Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Significance Analysis of INTeractome SAINT implements the scoring algorithm for protein-protein interaction data using label free quantitative proteomics data in AP-MS experiments. It was used for spectral count data in the yeast kinase interactome work not incorporating control purification, as well as a generalized implementation for spectral count data with and without control purification. . Alternatively, you can also run SAINT in combination with ProHits. . The package was written for either doing analysis without or with control IPs and debian/copyright0000644000000000000000000000247212151612127011124 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: SAINT Upstream-Contact: Hyung Won Choi Source: https://sourceforge.net/projects/saint-apms/files/ Files-Excluded: __MACOSX/ .DS_Store */.DS_Store */*/.DS_Store *~ *.pdf Files: * Copyright: © 2010-2012 Hyung Won Choi License: GPL-3+ Files: debian/* Copyright: © 2012 Andreas Tille License: GPL-3+ 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 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. debian/changelog0000644000000000000000000000123412152455571011047 0ustar saint (2.3.4+dfsg-2) unstable; urgency=low * add patch ld-as-needed.patch from Julian Taylor (Closes: #710364) -- Thorsten Alteholz Sat, 01 Jun 2013 22:00:00 +0200 saint (2.3.4+dfsg-1) unstable; urgency=low * new upstream version * debian/control: bump standard to 3.9.4 (no changes needed) [Andreas Tille] * debian/copyright: - Add Files-Excluded to document what was removed from original source -- Thorsten Alteholz Thu, 16 May 2013 21:20:00 +0200 saint (2.3.3-1) unstable; urgency=low * Initial Release (Closes: #671224) -- Andreas Tille Tue, 24 Apr 2012 22:18:38 +0200 debian/compat0000644000000000000000000000000212151612127010362 0ustar 9 debian/watch0000644000000000000000000000021012151612127010206 0ustar version=3 opts=dversionmangle=s/\+dfsg[0-9]*// \ http://sf.net/saint-apms/SAINT_v\.?([.\d]+)\.zip \ debian debian/get-orig-source debian/saint-spc-noctrl-matrix.10000644000000000000000000000124412151612127013751 0ustar .\" 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-.pdf. debian/upstream0000644000000000000000000000232312151612127010747 0ustar Reference: - Author: A. Breitkreutz and H. Choi and J.R. Sharom and L. Boucher and V. Neduva and B. Larsen and Z.Y. Lin and B.J. Breitkreutz and C. Stark and G. Liu and J. Ahn and D. Dewar-Darch and T. Reguly and X. Tang and R. Almeida and Z.S. Qin and T. Pawson and A.-C. Gingras and A.I. Nesvizhskii and M. Tyers Title: A global protein kinase and phosphatase interaction network in yeast Journal: Science Year: 2010 Volume: 328 Number: 5981 Pages: 1043-6 DOI: 10.1126/science.1176495 PMID: 20489023 URL: http://www.mendeley.com/research/global-protein-kinase-phosphatase-interaction-network-yeast-49/ ISSN: 00368075 - Author: Hyungwon Choi and Brett Larsen and Zhen-Yuan Lin and Ashton Breitkreutz and Dattatreya Mellacheruvu and Damian Fermin and Zhaohui S Qin and Mike Tyers and Anne-Claude Gingras and Alexey I Nesvizhskii Title: "SAINT: probabilistic scoring of affinity purification–mass spectrometry data" Journal: Nature Methods Year: 2010 Volume: 8 Pages: 70–73 DOI: 10.1038/nmeth.1541 PMID: 21131968 URL: http://www.nature.com/nmeth/journal/v8/n1/abs/nmeth.1541.html eprint: http://www.nature.com/nmeth/journal/v8/n1/full/nmeth.1541.html debian/saint-spc-noctrl.10000644000000000000000000000176412151612127012456 0ustar .\" 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-.pdf. debian/saint-reformat.10000644000000000000000000000117712151612127012207 0ustar .\" 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-.pdf. debian/get-orig-source0000755000000000000000000000234412151612127012130 0ustar #!/bin/sh # get source for SAINT because upstream archive is bloated by macosx specific # stuff which breaks dpkg-buildpackage # -> http://lists.debian.org/debian-qa/2012/04/msg00057.html set -e NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` UCNAME=`echo $NAME | tr [a-z] [A-Z]` if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${UCNAME}.*?\1?"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi mkdir -p ../tarballs cd ../tarballs upstream="${UCNAME}_v${VERSION}" unzip -q ../${upstream}.zip rm -rf __MACOSX # once we are changing the tarball anyway we could fix some other nasty things # this will be suggested upstream for the future find ${upstream} -name .DS_Store -delete find ${upstream} -name "*~" -type f -delete find ${upstream} -name "*.c" -type f -exec chmod a-x \{\} \; find ${upstream} -name "*.h" -type f -exec chmod a-x \{\} \; GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf "$NAME"_"$VERSION"+dfsg.orig.tar.gz "${upstream}" rm -rf "$upstream" debian/patches/0000755000000000000000000000000012152610620010610 5ustar debian/patches/ld-as-needed.patch0000644000000000000000000000333112151612633014060 0ustar Description: fix build failure with ld --as-needed libraries need to be placed after objects needing them --- a/Makefile +++ b/Makefile @@ -43,7 +43,7 @@ all: makeDirs \ saint-reformat: $(CC) $(CFLAGS) -c $(SRC)/SAINTreformat/*.c $(SRC)/SAINTreformat/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-reformat + $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-reformat $(LIBS) rm $(BUILD)/*.o @echo @echo @@ -52,7 +52,7 @@ saint-reformat: saint-spc-noctrl-matrix: $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl-matrix/*.c $(SRC)/SAINTspc-noctrl-matrix/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl-matrix + $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl-matrix $(LIBS) rm $(BUILD)/*.o @echo @echo @@ -60,7 +60,7 @@ saint-spc-noctrl-matrix: saint-spc-noctrl: $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl/*.c $(SRC)/SAINTspc-noctrl/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl + $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl $(LIBS) rm $(BUILD)/*.o @echo @echo @@ -69,7 +69,7 @@ saint-spc-noctrl: saint-spc-ctrl: $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-ctrl/*.c $(SRC)/SAINTspc-ctrl/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-ctrl + $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-ctrl $(LIBS) rm $(BUILD)/*.o @echo @echo @@ -78,7 +78,7 @@ saint-spc-ctrl: saint-int-ctrl: $(CC) $(CFLAGS) -c $(SRC)/SAINTint-ctrl/*.c $(SRC)/SAINTint-ctrl/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-int-ctrl + $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-int-ctrl $(LIBS) rm $(BUILD)/*.o @echo @echo debian/patches/series0000644000000000000000000000004612151613241012026 0ustar fix-makefile.patch ld-as-needed.patch debian/patches/fix-makefile.patch0000644000000000000000000000423212151612127014176 0ustar Author: Thorsten Alteholz + Andreas Tille Description: add hardening flags to makefile and fix clean target Index: SAINT_v2.3.4/Makefile =================================================================== --- SAINT_v2.3.4.orig/Makefile 2013-05-16 21:11:02.000000000 +0200 +++ SAINT_v2.3.4/Makefile 2013-05-16 21:12:28.000000000 +0200 @@ -14,8 +14,8 @@ CC = gcc CXX = g++ -CFLAGS = -g -O3 -CXXFLAGS = $(CFLAGS) +CFLAGS += -g -O3 +CXXFLAGS += $(CFLAGS) #--------------------------------------------------------------------------------- # any extra libraries we wish to link with the projects @@ -29,7 +29,7 @@ clean: rm -rf $(BUILD) - rm $(SRC)/*/*.gch + rm -f $(SRC)/*/*.gch all: makeDirs \ saint-reformat \ @@ -43,7 +43,7 @@ saint-reformat: $(CC) $(CFLAGS) -c $(SRC)/SAINTreformat/*.c $(SRC)/SAINTreformat/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-reformat + $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-reformat rm $(BUILD)/*.o @echo @echo @@ -52,7 +52,7 @@ saint-spc-noctrl-matrix: $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl-matrix/*.c $(SRC)/SAINTspc-noctrl-matrix/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl-matrix + $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl-matrix rm $(BUILD)/*.o @echo @echo @@ -60,7 +60,7 @@ saint-spc-noctrl: $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl/*.c $(SRC)/SAINTspc-noctrl/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl + $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl rm $(BUILD)/*.o @echo @echo @@ -69,7 +69,7 @@ saint-spc-ctrl: $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-ctrl/*.c $(SRC)/SAINTspc-ctrl/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-spc-ctrl + $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-ctrl rm $(BUILD)/*.o @echo @echo @@ -78,7 +78,7 @@ saint-int-ctrl: $(CC) $(CFLAGS) -c $(SRC)/SAINTint-ctrl/*.c $(SRC)/SAINTint-ctrl/*.h mv *.o $(BUILD) - $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-int-ctrl + $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-int-ctrl rm $(BUILD)/*.o @echo @echo debian/README.Debian0000644000000000000000000000112112151612127011220 0ustar 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-.pdf. Other Hint: ----------- The description speaks explicitly about the program ProHits which can be found here: http://prohitsms.com/Prohits_download/list.php Just tell the Debian Med team, whether you are interested in a package of ProHits. -- Andreas Tille Tue, 24 Apr 2012 22:18:38 +0200 debian/saint-int-ctrl.10000644000000000000000000000072612151612127012123 0ustar .\" 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 \- support 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-.pdf. debian/rules0000755000000000000000000000050612151612127010245 0ustar #!/usr/bin/make -f %: dh $@ override_dh_auto_build: # Tweak hardening flags into the Makefile make all CFLAGS='$(CPPFLAGS) $(CFLAGS) $(LDFLAGS)' override_dh_auto_clean: dh_auto_clean rm -rf bin get-orig-source: # repack in debian/get-orig-source to avoid trouble with dirty archive uscan --verbose --force-download debian/source/0000755000000000000000000000000012152610620010461 5ustar debian/source/format0000644000000000000000000000001412151612127011672 0ustar 3.0 (quilt) debian/install0000644000000000000000000000001612151612127010552 0ustar bin/* usr/bin