[med-svn] r7787 - in trunk/packages: . eigensoft eigensoft/trunk eigensoft/trunk/debian eigensoft/trunk/debian/patches eigensoft/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Wed Sep 14 10:23:28 UTC 2011
Author: moeller
Date: 2011-09-14 10:23:28 +0000 (Wed, 14 Sep 2011)
New Revision: 7787
Added:
trunk/packages/eigensoft/
trunk/packages/eigensoft/trunk/
trunk/packages/eigensoft/trunk/debian/
trunk/packages/eigensoft/trunk/debian/README.Debian
trunk/packages/eigensoft/trunk/debian/README.source
trunk/packages/eigensoft/trunk/debian/changelog
trunk/packages/eigensoft/trunk/debian/compat
trunk/packages/eigensoft/trunk/debian/control
trunk/packages/eigensoft/trunk/debian/copyright
trunk/packages/eigensoft/trunk/debian/docs
trunk/packages/eigensoft/trunk/debian/eigensoft.install
trunk/packages/eigensoft/trunk/debian/patches/
trunk/packages/eigensoft/trunk/debian/patches/atlasLinkNotNeeded.patch
trunk/packages/eigensoft/trunk/debian/patches/g772gfortran.patch
trunk/packages/eigensoft/trunk/debian/patches/series
trunk/packages/eigensoft/trunk/debian/rules
trunk/packages/eigensoft/trunk/debian/source/
trunk/packages/eigensoft/trunk/debian/source/format
trunk/packages/eigensoft/trunk/debian/watch
Log:
Hello,
the 2009 binaries provided by upstream do not work on any recent Debian
system. Well, any fairly recent Linux system will complain. But it
compiles nicely, still, just there was the atlas library that blas and
lapack are sufficient to take care of and today one uses gfortran and
no longer g77 with its g2c library. So, I happily let you all share my
build instructions. However, we would need to find someone else to bring
the package into Debian, which seems like very much worthwhile to do.
The copyright is completely unclear for the moment. And we need something
that resembles a man page. Please use the get-orig-source target for
download .. saves you some trouble.
W: eigensoft: new-package-should-close-itp-bug
W: eigensoft: wrong-bug-number-in-closes l3:#nnnn
E: eigensoft: helper-templates-in-copyright
E: eigensoft: helper-templates-in-copyright
E: eigensoft: helper-templates-in-copyright
W: eigensoft: copyright-has-url-from-dh_make-boilerplate
E: eigensoft: copyright-contains-dh_make-todo-boilerplate
W: eigensoft: binary-without-manpage usr/bin/eigenstrat.big.perl
W: eigensoft: binary-without-manpage usr/bin/eigenstratQTL.big.perl
W: eigensoft: binary-without-manpage usr/bin/evec2pca.perl
W: eigensoft: binary-without-manpage usr/bin/gc.perl
W: eigensoft: binary-without-manpage usr/bin/smarteigenstrat.perl
W: eigensoft: binary-without-manpage usr/bin/smartpca.perl
W: eigensoft: unusual-interpreter usr/share/eigenstrat/POPGEN/HGDP.X.perl #!/usr/bin
Cheers,
Steffen
Property changes on: trunk/packages/eigensoft/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/eigensoft/trunk/debian/README.Debian
===================================================================
--- trunk/packages/eigensoft/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/README.Debian 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,7 @@
+eigensoft for Debian
+--------------------
+
+Help for finalising this package would be much appreciated. The license
+needs to be clarified with upstream and a series of man pages are missing.
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 14 Sep 2011 10:35:55 +0200
Added: trunk/packages/eigensoft/trunk/debian/README.source
===================================================================
--- trunk/packages/eigensoft/trunk/debian/README.source (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/README.source 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,7 @@
+eigensoft for Debian
+--------------------
+
+Patches removed the explicit notion of the Atlas library and helped
+with a transition from g77 to gfortran, which allowed to omit the g2c
+library dependency, which is no longer existing.
+
Added: trunk/packages/eigensoft/trunk/debian/changelog
===================================================================
--- trunk/packages/eigensoft/trunk/debian/changelog (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/changelog 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,5 @@
+eigensoft (3.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn).
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 14 Sep 2011 10:35:55 +0200
Added: trunk/packages/eigensoft/trunk/debian/compat
===================================================================
--- trunk/packages/eigensoft/trunk/debian/compat (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/compat 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1 @@
+8
Added: trunk/packages/eigensoft/trunk/debian/control
===================================================================
--- trunk/packages/eigensoft/trunk/debian/control (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/control 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,26 @@
+Source: eigensoft
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0),
+ gfortran,
+ libblas-dev,
+ liblapack-dev
+Standards-Version: 3.9.2
+Homepage: http://genepath.med.harvard.edu/~reich/Software.htm
+#Vcs-Git: git://git.debian.org/collab-maint/eigenstrat.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/eigenstrat.git;a=summary
+
+Package: eigensoft
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl
+Description: reduction of population bias for genetic analyses
+ The EIGENSOFT package combines functionality from the group's population
+ genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
+ method (Price et al. 2006). The EIGENSTRAT method uses principal components
+ analysis to explicitly model ancestry differences between cases and
+ controls along continuous axes of variation; the resulting correction is
+ specific to a candidate marker's variation in frequency across ancestral
+ populations, minimizing spurious associations while maximizing power to
+ detect true associations. The EIGENSOFT package has a built-in plotting
+ script and supports multiple file formats and quantitative phenotypes.
Added: trunk/packages/eigensoft/trunk/debian/copyright
===================================================================
--- trunk/packages/eigensoft/trunk/debian/copyright (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/copyright 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,36 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: eigenstrat
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+License: GPL-2+
+ This package 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.
+ .
+ This package 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 program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/eigensoft/trunk/debian/docs
===================================================================
--- trunk/packages/eigensoft/trunk/debian/docs (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/docs 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1 @@
+README
Added: trunk/packages/eigensoft/trunk/debian/eigensoft.install
===================================================================
--- trunk/packages/eigensoft/trunk/debian/eigensoft.install (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/eigensoft.install 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,4 @@
+bin/* usr/bin
+CONVERTF usr/share/eigenstrat
+EIGENSTRAT usr/share/eigenstrat
+POPGEN usr/share/eigenstrat
Added: trunk/packages/eigensoft/trunk/debian/patches/atlasLinkNotNeeded.patch
===================================================================
--- trunk/packages/eigensoft/trunk/debian/patches/atlasLinkNotNeeded.patch (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/patches/atlasLinkNotNeeded.patch 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,30 @@
+Index: eigenstrat-3.0/src/Makefile
+===================================================================
+--- eigenstrat-3.0.orig/src/Makefile 2011-09-14 11:51:57.597092399 +0200
++++ eigenstrat-3.0/src/Makefile 2011-09-14 11:53:41.913609546 +0200
+@@ -87,10 +87,10 @@
+ rm -f $(PROGS) $(PERLPROGS)
+
+ $(M1): nicklib $(M1O)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1) $(M1O) $(NLIB) -L/broad/tools/lib64 -lm -llapack -latlas -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1) $(M1O) $(NLIB) -L/broad/tools/lib64 -lm -llapack -l$(BLAS) -Wimplicit
+
+ $(M1Z): nicklib $(M1ZO)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1Z) $(M1ZO) $(NLIB) -L/broad/tools/lib64 -lm -latlas -llapack -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1Z) $(M1ZO) $(NLIB) -L/broad/tools/lib64 -lm -llapack -l$(BLAS) -Wimplicit
+
+ $(M2): nicklib $(M2O)
+ gcc -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M2) $(M2O) $(NLIB) -Wimplicit
+@@ -105,10 +105,10 @@
+ gcc -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M5) $(M5O) $(NLIB) -Wimplicit
+
+ $(M6): nicklib $(M6O)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M6) $(M6O) $(NLIB) -L/broad/tools/lib64 -lm -latlas -llapack -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M6) $(M6O) $(NLIB) -L/broad/tools/lib64 -lm -llapack -l$(BLAS) -Wimplicit
+
+ $(M7): nicklib $(M7O)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M7) $(M7O) $(NLIB) -L/broad/tools/lib64 -lm -latlas -llapack -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M7) $(M7O) $(NLIB) -L/broad/tools/lib64 -lm -llapack -l$(BLAS) -Wimplicit
+
+ $(M8): nicklib $(M8O)
+ gcc -I$(IDIR) $(DEBUG_OPTIONS) -o $(M8) $(M8O) $(NLIB) -lm -Wimplicit
Added: trunk/packages/eigensoft/trunk/debian/patches/g772gfortran.patch
===================================================================
--- trunk/packages/eigensoft/trunk/debian/patches/g772gfortran.patch (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/patches/g772gfortran.patch 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,43 @@
+Index: eigenstrat-3.0/src/Makefile
+===================================================================
+--- eigenstrat-3.0.orig/src/Makefile 2011-09-14 11:27:28.565807868 +0200
++++ eigenstrat-3.0/src/Makefile 2011-09-14 11:30:59.594854531 +0200
+@@ -21,7 +21,7 @@
+
+ # CC=/util/bin/gcc
+ CC=gcc
+-FF=g77
++FF=gfortran
+
+ CFLAGS= -c -pthread -I$(IDIR) -I$(IDIR3) -Wimplicit
+ OBJ=strsubs.o sortit.o vsubs.o statsubs.o linsubs.o getpars.o xsearch.o gauss.o gds.o
+@@ -87,10 +87,10 @@
+ rm -f $(PROGS) $(PERLPROGS)
+
+ $(M1): nicklib $(M1O)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1) $(M1O) $(NLIB) -L/broad/tools/lib64 -lg2c -lm -llapack -latlas -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1) $(M1O) $(NLIB) -L/broad/tools/lib64 -lm -llapack -latlas -l$(BLAS) -Wimplicit
+
+ $(M1Z): nicklib $(M1ZO)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1Z) $(M1ZO) $(NLIB) -L/broad/tools/lib64 -lm -lg2c -latlas -llapack -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1Z) $(M1ZO) $(NLIB) -L/broad/tools/lib64 -lm -latlas -llapack -l$(BLAS) -Wimplicit
+
+ $(M2): nicklib $(M2O)
+ gcc -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M2) $(M2O) $(NLIB) -Wimplicit
+@@ -105,13 +105,13 @@
+ gcc -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M5) $(M5O) $(NLIB) -Wimplicit
+
+ $(M6): nicklib $(M6O)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M6) $(M6O) $(NLIB) -L/broad/tools/lib64 -lg2c -lm -latlas -llapack -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M6) $(M6O) $(NLIB) -L/broad/tools/lib64 -lm -latlas -llapack -l$(BLAS) -Wimplicit
+
+ $(M7): nicklib $(M7O)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M7) $(M7O) $(NLIB) -L/broad/tools/lib64 -lg2c -lm -latlas -llapack -l$(BLAS) -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M7) $(M7O) $(NLIB) -L/broad/tools/lib64 -lm -latlas -llapack -l$(BLAS) -Wimplicit
+
+ $(M8): nicklib $(M8O)
+- gcc -I$(IDIR) $(DEBUG_OPTIONS) -o $(M8) $(M8O) $(NLIB) -lg2c -lm -Wimplicit
++ gcc -I$(IDIR) $(DEBUG_OPTIONS) -o $(M8) $(M8O) $(NLIB) -lm -Wimplicit
+
+ $(M9): nicklib $(M9O)
+ gcc -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M9) $(M9O) $(NLIB) -Wimplicit
Added: trunk/packages/eigensoft/trunk/debian/patches/series
===================================================================
--- trunk/packages/eigensoft/trunk/debian/patches/series (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/patches/series 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,2 @@
+g772gfortran.patch
+atlasLinkNotNeeded.patch
Added: trunk/packages/eigensoft/trunk/debian/rules
===================================================================
--- trunk/packages/eigensoft/trunk/debian/rules (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/rules 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,34 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ $(MAKE) FF=gfortran DEBUG_OPTIONS=-g -C src all
+
+override_dh_clean:
+ dh_clean
+ $(MAKE) -C src clean
+ rm -fr smartinclude smartlib smarttables
+
+VERSION=3.0
+get-orig-source:
+ [ ! -r ../EIG$(VERSION) ] || wget http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG$(VERSION).tar.gz -O ../EIG$(VERSION).tar.gz
+ rm -rf ../eigensoft-$(VERSION)
+ mkdir ../eigensoft-$(VERSION)
+ cd ../eigensoft-$(VERSION) && tar xzf ../EIG$(VERSION).tar.gz
+ find ../eigensoft-$(VERSION)/bin -type f | grep -v '.perl$$' | xargs -r rm
+ find ../eigensoft-$(VERSION)/POPGEN -type f | grep -v '.perl$$' | xargs -r chmod -x
+ find ../eigensoft-$(VERSION)/CONVERTF -type f | grep -v '.perl$$' | xargs -r chmod -x
+ find ../eigensoft-$(VERSION)/EIGENSTRAT -type f | grep -v '.perl$$' | xargs -r chmod -x
+ make -C ../eigensoft-$(VERSION)/src clean
+ cd .. && tar cjf eigensoft_$(VERSION).orig.tar.bz2 eigensoft-$(VERSION)
Property changes on: trunk/packages/eigensoft/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/eigensoft/trunk/debian/source/format
===================================================================
--- trunk/packages/eigensoft/trunk/debian/source/format (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/source/format 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/eigensoft/trunk/debian/watch
===================================================================
--- trunk/packages/eigensoft/trunk/debian/watch (rev 0)
+++ trunk/packages/eigensoft/trunk/debian/watch 2011-09-14 10:23:28 UTC (rev 7787)
@@ -0,0 +1,8 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG([0-9.]+)\.tar\.gz
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