Author: lkajan-guest Date: 2012-02-22 10:46:19 +0000 (Wed, 22 Feb 2012) New Revision: 9749
Added: trunk/packages/sift/trunk/debian/patches/ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path trunk/packages/sift/trunk/debian/patches/series trunk/packages/sift/trunk/debian/watch Modified: trunk/packages/sift/trunk/debian/ trunk/packages/sift/trunk/debian/changelog trunk/packages/sift/trunk/debian/control trunk/packages/sift/trunk/debian/links trunk/packages/sift/trunk/debian/rules Log: Soons changes, Laszlo committing on behalf of him Property changes on: trunk/packages/sift/trunk/debian ___________________________________________________________________ Added: svn:ignore + *.substvars files *.debhelper.log Modified: trunk/packages/sift/trunk/debian/changelog =================================================================== --- trunk/packages/sift/trunk/debian/changelog 2012-02-21 18:10:57 UTC (rev 9748) +++ trunk/packages/sift/trunk/debian/changelog 2012-02-22 10:46:19 UTC (rev 9749) @@ -1,3 +1,10 @@ +sift (4.0.3b-2) lucid; urgency=low + + * Update to new upstream + * Re-hack build rules + + -- H. Soon Gweon (Key for package building) <[email protected]> Mon, 20 Feb 2012 18:01:12 +0000 + sift (3.0-1) UNRELEASED; urgency=low * Initial release (Closes: #????) Modified: trunk/packages/sift/trunk/debian/control =================================================================== --- trunk/packages/sift/trunk/debian/control 2012-02-21 18:10:57 UTC (rev 9748) +++ trunk/packages/sift/trunk/debian/control 2012-02-22 10:46:19 UTC (rev 9749) @@ -2,9 +2,10 @@ Section: science Priority: extra Maintainer: Laszlo Kajan <[email protected]> -Build-Depends: debhelper (>= 7) +Uploaders: H. Soon Gweon <[email protected]>, Tim Booth <[email protected]> +Build-Depends: debhelper (>= 7), libblimps3-dev Standards-Version: 3.9.1 -Homepage: http://blocks.fhcrc.org/sift/SIFT_help.html +Homepage: http://sift.jcvi.org Package: sift Architecture: any Modified: trunk/packages/sift/trunk/debian/links =================================================================== --- trunk/packages/sift/trunk/debian/links 2012-02-21 18:10:57 UTC (rev 9748) +++ trunk/packages/sift/trunk/debian/links 2012-02-22 10:46:19 UTC (rev 9749) @@ -1 +1,3 @@ -usr/bin/sift_for_submitting_fasta_seq.csh usr/bin/sift +usr/lib/sift/bin/SIFT_exome_nssnvs.pl usr/bin/SIFT_exome_nssnvs.pl +#usr/lib/sift/bin/sift_for_submitting_fasta_seq.csh usr/bin/sift +#usr/lib/sift/bin/consensus_to_seq usr/bin/consensus_to_seq Added: trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path =================================================================== --- trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path (rev 0) +++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-22 10:46:19 UTC (rev 9749) @@ -0,0 +1,31 @@ +--- a/bin/SIFT_exome_nssnvs.pl ++++ b/bin/SIFT_exome_nssnvs.pl +@@ -1,4 +1,8 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl ++ ++#Location of all the SIFT grot on Debian. ++use lib '/usr/lib/sift/bin'; ++ + use List::Util qw[min max]; + use File::Copy; + use Getopt::Std; +--- a/bin/SIFT_exome_indels.pl ++++ b/bin/SIFT_exome_indels.pl +@@ -1,4 +1,6 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl ++ ++use lib '/usr/lib/sift/bin'; + + # This program is licensed to you under the Fred + # Hutchinos Cancer Research Center (FHCRC) +@@ -12,7 +14,7 @@ + use Tie::IxHash; + use File::Copy; + use Getopt::Std; +-$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.1'; ++$ENV{'SIFT_HOME'} = '/usr/share/sift'; + $SIFT_HOME = $ENV{'SIFT_HOME'}; + use vars qw($opt_i $opt_c $opt_d $opt_o); + getopts("i:c:d:o:"); Added: trunk/packages/sift/trunk/debian/patches/series =================================================================== --- trunk/packages/sift/trunk/debian/patches/series (rev 0) +++ trunk/packages/sift/trunk/debian/patches/series 2012-02-22 10:46:19 UTC (rev 9749) @@ -0,0 +1 @@ +fix_perl_interpreter_and_lib_path Modified: trunk/packages/sift/trunk/debian/rules =================================================================== --- trunk/packages/sift/trunk/debian/rules 2012-02-21 18:10:57 UTC (rev 9748) +++ trunk/packages/sift/trunk/debian/rules 2012-02-22 10:46:19 UTC (rev 9749) @@ -9,83 +9,25 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 +%: + dh --with quilt $@ +override_dh_auto_clean: + rm -rf bin/linux + rm -rf bin/solaris + ( cd bin ; rm -f choose_seqs_via_psiblastseedmedian consensus_to_seq psiblast_res_to_fasta_dbpairwise \ + clump_output_alignedseq fastaseqs info_on_seqs seqs_from_psiblast_res ) +override_dh_auto_build: + ( cd src ; \ + for f in `grep '^\./cccb' compile.csh | cut -d ' ' -f 2` ; do \ + gcc -O2 -o $$f $$f.c -lblimps -lm -I/usr/include/blimps ; \ + mv $$f ../bin ; \ + done ) +override_dh_install: + dh_install -X.svn bin /usr/lib/sift/ + #Below command simply replaced with -X above + #find debian/sift -type d -name '.svn' -prune -exec rm -rf '{}' ';' + #Links are created by debian/links -configure: configure-stamp -configure-stamp: - dh_testdir - # Add here commands to configure the package. - - touch configure-stamp - - -build: build-stamp - -build-stamp: configure-stamp - dh_testdir - - # Add here commands to compile the package. - $(MAKE) prefix=/usr - #docbook-to-man debian/sift.sgml > sift.1 - - touch $@ - -clean: - dh_testdir - dh_testroot - rm -f build-stamp configure-stamp - - # Add here commands to clean up after the build process. - $(MAKE) prefix=/usr distclean - - dh_clean - -install: build - dh_testdir - dh_testroot - dh_prep - dh_installdirs - - # Add here commands to install the package into debian/sift. - $(MAKE) DESTDIR=$(CURDIR)/debian/sift prefix=/usr install - - -# Build architecture-independent files here. -binary-indep: build install -# We have nothing to do by default. - -# Build architecture-dependent files here. -binary-arch: build install - dh_testdir - dh_testroot - dh_installchangelogs ChangeLog - dh_installdocs - dh_installexamples -# dh_install -# dh_installmenu -# dh_installdebconf -# dh_installlogrotate -# dh_installemacsen -# dh_installpam -# dh_installmime -# dh_python -# dh_installinit -# dh_installcron -# dh_installinfo - dh_installman - dh_link - dh_strip - dh_compress - dh_fixperms -# dh_perl -# dh_makeshlibs - dh_installdeb - dh_shlibdeps - dh_gencontrol - dh_md5sums - dh_builddeb - -binary: binary-indep binary-arch -.PHONY: build clean binary-indep binary-arch binary install configure Added: trunk/packages/sift/trunk/debian/watch =================================================================== --- trunk/packages/sift/trunk/debian/watch (rev 0) +++ trunk/packages/sift/trunk/debian/watch 2012-02-22 10:46:19 UTC (rev 9749) @@ -0,0 +1,6 @@ +version=3 +# This is a variant HTTP format which allows direct specification of +# the homepage: +# Homepage Pattern [Version [Action]] +http://sift.jcvi.org \ + www/sift([0-9][0-9a-z.]*)\.tar\.[gzbl2]{2,3} _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
