Author: lkajan-guest Date: 2012-02-23 18:22:34 +0000 (Thu, 23 Feb 2012) New Revision: 9767
Added: trunk/packages/sift/trunk/debian/README.source Modified: trunk/packages/sift/trunk/debian/changelog trunk/packages/sift/trunk/debian/control trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path trunk/packages/sift/trunk/debian/rules Log: documented patch in the header Added: trunk/packages/sift/trunk/debian/README.source =================================================================== --- trunk/packages/sift/trunk/debian/README.source (rev 0) +++ trunk/packages/sift/trunk/debian/README.source 2012-02-23 18:22:34 UTC (rev 9767) @@ -0,0 +1,15 @@ +sift for Debian +----------------- + +Patches +....... +Patches are documented in the headers. + +Autobuilding +............ +The FHCRC NONCOMMERCIAL LICENSE does not prohibit building the source. It +also does not prohibit the distribution of the binary software on a +royalty-free basis. + +# vim:et:ts=2: + Modified: trunk/packages/sift/trunk/debian/changelog =================================================================== --- trunk/packages/sift/trunk/debian/changelog 2012-02-23 17:54:29 UTC (rev 9766) +++ trunk/packages/sift/trunk/debian/changelog 2012-02-23 18:22:34 UTC (rev 9767) @@ -4,4 +4,5 @@ * Re-hack build rules * Initial release (Closes: #660272) - -- H. Soon Gweon (Key for package building) <[email protected]> Mon, 20 Feb 2012 18:01:12 +0000 + -- Laszlo Kajan <[email protected]> Thu, 23 Feb 2012 18:55:23 +0100 + Modified: trunk/packages/sift/trunk/debian/control =================================================================== --- trunk/packages/sift/trunk/debian/control 2012-02-23 17:54:29 UTC (rev 9766) +++ trunk/packages/sift/trunk/debian/control 2012-02-23 18:22:34 UTC (rev 9767) @@ -1,9 +1,10 @@ Source: sift -Section: science +Section: non-free/science +XS-Autobuild: yes Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: H. Soon Gweon <[email protected]>, Laszlo Kajan <[email protected]>, Tim Booth <[email protected]> -Build-Depends: debhelper (>= 7), libblimps3-dev +Build-Depends: debhelper (>= 7.0.50~), libblimps3-dev, quilt (>= 0.46-7~) Standards-Version: 3.9.2 Homepage: http://sift.jcvi.org Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/sift/trunk/ Modified: trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path =================================================================== --- trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-23 17:54:29 UTC (rev 9766) +++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-23 18:22:34 UTC (rev 9767) @@ -1,7 +1,12 @@ +* Fix perl interpreter paths. +* Support parallel build of binaries. +* Enhance verbosity in csh scripts for bug hunting. +* Add blast processors argument SIFT_for_submitting_fasta_seq.csh . +* Trailing whitespace removed from lines. Index: sift-4.0.3b/bin/SIFT_exome_nssnvs.pl =================================================================== ---- sift-4.0.3b.orig/bin/SIFT_exome_nssnvs.pl 2012-02-23 18:08:31.099044430 +0100 -+++ sift-4.0.3b/bin/SIFT_exome_nssnvs.pl 2012-02-23 18:08:32.615044433 +0100 +--- sift-4.0.3b.orig/bin/SIFT_exome_nssnvs.pl 2010-03-08 19:08:59.000000000 +0100 ++++ sift-4.0.3b/bin/SIFT_exome_nssnvs.pl 2012-02-23 18:57:19.447044528 +0100 @@ -1,4 +1,8 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -32,8 +37,8 @@ my $num_coords_per_split = 1000; Index: sift-4.0.3b/bin/SIFT_exome_indels.pl =================================================================== ---- sift-4.0.3b.orig/bin/SIFT_exome_indels.pl 2012-02-23 18:08:31.127044460 +0100 -+++ sift-4.0.3b/bin/SIFT_exome_indels.pl 2012-02-23 18:08:32.619044541 +0100 +--- sift-4.0.3b.orig/bin/SIFT_exome_indels.pl 2010-03-08 19:00:00.000000000 +0100 ++++ sift-4.0.3b/bin/SIFT_exome_indels.pl 2012-02-23 18:57:19.451044490 +0100 @@ -1,4 +1,6 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -62,8 +67,8 @@ chmod 0777, $tmp; Index: sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl =================================================================== ---- sift-4.0.3b.orig/bin/perlscripts/get_BLINK_seq.pl 2012-02-23 18:08:31.159044429 +0100 -+++ sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl 2012-02-23 18:08:32.631044576 +0100 +--- sift-4.0.3b.orig/bin/perlscripts/get_BLINK_seq.pl 2010-03-08 18:59:21.000000000 +0100 ++++ sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl 2012-02-23 18:57:19.467044434 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -72,8 +77,8 @@ use LWP::UserAgent; Index: sift-4.0.3b/bin/seqs_chosen_via_median_info.csh =================================================================== ---- sift-4.0.3b.orig/bin/seqs_chosen_via_median_info.csh 2012-02-23 18:08:31.187044489 +0100 -+++ sift-4.0.3b/bin/seqs_chosen_via_median_info.csh 2012-02-23 18:08:32.643044533 +0100 +--- sift-4.0.3b.orig/bin/seqs_chosen_via_median_info.csh 2010-03-08 19:00:42.000000000 +0100 ++++ sift-4.0.3b/bin/seqs_chosen_via_median_info.csh 2012-02-23 18:57:19.475044542 +0100 @@ -1,7 +1,8 @@ -#!/bin/csh +#!/bin/csh -e @@ -228,8 +233,8 @@ - Index: sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh =================================================================== ---- sift-4.0.3b.orig/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-23 18:08:31.211044477 +0100 -+++ sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-23 18:08:32.655044434 +0100 +--- sift-4.0.3b.orig/bin/SIFT_for_submitting_fasta_seq.csh 2010-03-08 19:09:47.000000000 +0100 ++++ sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-23 18:57:19.483044535 +0100 @@ -1,4 +1,4 @@ -#!/bin/csh +#!/bin/csh -e @@ -289,8 +294,8 @@ exit Index: sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh =================================================================== ---- sift-4.0.3b.orig/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 18:08:31.239044641 +0100 -+++ sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 18:08:32.659044484 +0100 +--- sift-4.0.3b.orig/bin/SIFT_for_submitting_NCBI_gi_id.csh 2010-03-08 19:08:31.000000000 +0100 ++++ sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 18:57:19.487044671 +0100 @@ -1,4 +1,4 @@ -#!/bin/csh +#!/bin/csh -e @@ -379,8 +384,8 @@ Index: sift-4.0.3b/src/Alignment.c =================================================================== ---- sift-4.0.3b.orig/src/Alignment.c 2012-02-23 18:08:31.743044444 +0100 -+++ sift-4.0.3b/src/Alignment.c 2012-02-23 18:08:32.671044520 +0100 +--- sift-4.0.3b.orig/src/Alignment.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/Alignment.c 2012-02-23 18:57:19.499044525 +0100 @@ -17,7 +17,7 @@ #define _ALIGNMENT_C_ #include "PN_convert.c" @@ -487,8 +492,8 @@ Index: sift-4.0.3b/src/blocklist.c =================================================================== ---- sift-4.0.3b.orig/src/blocklist.c 2012-02-23 18:08:31.771044464 +0100 -+++ sift-4.0.3b/src/blocklist.c 2012-02-23 18:08:32.679044523 +0100 +--- sift-4.0.3b.orig/src/blocklist.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/blocklist.c 2012-02-23 18:57:19.507044729 +0100 @@ -9,7 +9,7 @@ #include <string.h> #include "blocklist.h" @@ -500,8 +505,8 @@ routines for a list of blocks Index: sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c =================================================================== ---- sift-4.0.3b.orig/src/choose_seqs_via_psiblastseedmedian.c 2012-02-23 18:08:31.799044500 +0100 -+++ sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c 2012-02-23 18:08:32.691044443 +0100 +--- sift-4.0.3b.orig/src/choose_seqs_via_psiblastseedmedian.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c 2012-02-23 18:57:19.515044579 +0100 @@ -1,6 +1,6 @@ /* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */ /* Use, modification or distribution of these programs is subject to */ @@ -861,8 +866,8 @@ Index: sift-4.0.3b/src/clump_output_alignedseq.c =================================================================== ---- sift-4.0.3b.orig/src/clump_output_alignedseq.c 2012-02-23 18:08:31.827044512 +0100 -+++ sift-4.0.3b/src/clump_output_alignedseq.c 2012-02-23 18:08:32.695044441 +0100 +--- sift-4.0.3b.orig/src/clump_output_alignedseq.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/clump_output_alignedseq.c 2012-02-23 18:57:19.519044624 +0100 @@ -25,7 +25,7 @@ #include "Clumping.c" @@ -892,8 +897,8 @@ Index: sift-4.0.3b/src/consensus_to_seq.c =================================================================== ---- sift-4.0.3b.orig/src/consensus_to_seq.c 2012-02-23 18:08:31.855044444 +0100 -+++ sift-4.0.3b/src/consensus_to_seq.c 2012-02-23 18:08:32.702877577 +0100 +--- sift-4.0.3b.orig/src/consensus_to_seq.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/consensus_to_seq.c 2012-02-23 18:57:19.527044570 +0100 @@ -120,7 +120,7 @@ else { @@ -923,8 +928,8 @@ { Index: sift-4.0.3b/src/info_on_seqs.c =================================================================== ---- sift-4.0.3b.orig/src/info_on_seqs.c 2012-02-23 18:08:31.883044476 +0100 -+++ sift-4.0.3b/src/info_on_seqs.c 2012-02-23 18:08:32.711044390 +0100 +--- sift-4.0.3b.orig/src/info_on_seqs.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/info_on_seqs.c 2012-02-23 18:57:19.531044519 +0100 @@ -11,7 +11,7 @@ #include "Psiblast.c" /* #include "Information.c */ @@ -1013,7 +1018,7 @@ Index: sift-4.0.3b/src/Makefile =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 -+++ sift-4.0.3b/src/Makefile 2012-02-23 18:08:32.715044504 +0100 ++++ sift-4.0.3b/src/Makefile 2012-02-23 18:57:19.535044487 +0100 @@ -0,0 +1,42 @@ +include-prefix := $(prefix) +lib-prefix := $(prefix) @@ -1059,8 +1064,8 @@ +# vim:ai: Index: sift-4.0.3b/src/Matrix_Info.c =================================================================== ---- sift-4.0.3b.orig/src/Matrix_Info.c 2012-02-23 18:08:31.926985528 +0100 -+++ sift-4.0.3b/src/Matrix_Info.c 2012-02-23 18:08:32.722914533 +0100 +--- sift-4.0.3b.orig/src/Matrix_Info.c 2009-11-23 19:13:33.000000000 +0100 ++++ sift-4.0.3b/src/Matrix_Info.c 2012-02-23 18:57:19.550918309 +0100 @@ -384,7 +384,7 @@ int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant, pos_error_fp, pos_total; @@ -1196,8 +1201,8 @@ stringp = strtok (line, " \r\n\t"); Index: sift-4.0.3b/src/PN_blocks.c =================================================================== ---- sift-4.0.3b.orig/src/PN_blocks.c 2012-02-23 18:08:31.954905856 +0100 -+++ sift-4.0.3b/src/PN_blocks.c 2012-02-23 18:08:32.735044571 +0100 +--- sift-4.0.3b.orig/src/PN_blocks.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/PN_blocks.c 2012-02-23 18:57:19.558918350 +0100 @@ -671,7 +671,7 @@ Block* newblock; Residue* residue_pointer; @@ -1209,8 +1214,8 @@ for (i=0; i < block->width; i++) { Index: sift-4.0.3b/src/PN_convert.c =================================================================== ---- sift-4.0.3b.orig/src/PN_convert.c 2012-02-23 18:08:31.994973526 +0100 -+++ sift-4.0.3b/src/PN_convert.c 2012-02-23 18:08:32.751044530 +0100 +--- sift-4.0.3b.orig/src/PN_convert.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/PN_convert.c 2012-02-23 18:57:19.566886394 +0100 @@ -1,6 +1,6 @@ /* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */ /* Use, modification or distribution of these programs is subject to */ @@ -2268,8 +2273,8 @@ Index: sift-4.0.3b/src/Protdist.c =================================================================== ---- sift-4.0.3b.orig/src/Protdist.c 2012-02-23 18:08:32.023044444 +0100 -+++ sift-4.0.3b/src/Protdist.c 2012-02-23 18:08:32.763044644 +0100 +--- sift-4.0.3b.orig/src/Protdist.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/Protdist.c 2012-02-23 18:57:19.575044563 +0100 @@ -124,7 +124,7 @@ { double max_dist; @@ -2281,8 +2286,8 @@ Index: sift-4.0.3b/src/Psiblast.c =================================================================== ---- sift-4.0.3b.orig/src/Psiblast.c 2012-02-23 18:08:32.055044535 +0100 -+++ sift-4.0.3b/src/Psiblast.c 2012-02-23 18:08:32.771044516 +0100 +--- sift-4.0.3b.orig/src/Psiblast.c 2009-11-23 19:13:33.000000000 +0100 ++++ sift-4.0.3b/src/Psiblast.c 2012-02-23 18:57:19.586919315 +0100 @@ -1,6 +1,6 @@ /* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */ /* Use, modification or distribution of these programs is subject to */ @@ -2486,8 +2491,8 @@ #endif Index: sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c =================================================================== ---- sift-4.0.3b.orig/src/psiblast_res_to_fasta_dbpairwise.c 2012-02-23 18:08:32.083044617 +0100 -+++ sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c 2012-02-23 18:08:32.779044561 +0100 +--- sift-4.0.3b.orig/src/psiblast_res_to_fasta_dbpairwise.c 2009-11-23 19:13:33.000000000 +0100 ++++ sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c 2012-02-23 18:57:19.647044663 +0100 @@ -32,8 +32,8 @@ #include "Protdist.c" #include "Psiblast.c" @@ -2575,8 +2580,8 @@ } Index: sift-4.0.3b/src/seqs_from_psiblast_res.c =================================================================== ---- sift-4.0.3b.orig/src/seqs_from_psiblast_res.c 2012-02-23 18:08:32.111044382 +0100 -+++ sift-4.0.3b/src/seqs_from_psiblast_res.c 2012-02-23 18:08:32.783044514 +0100 +--- sift-4.0.3b.orig/src/seqs_from_psiblast_res.c 2009-11-23 19:13:33.000000000 +0100 ++++ sift-4.0.3b/src/seqs_from_psiblast_res.c 2012-02-23 18:57:19.651044467 +0100 @@ -23,7 +23,7 @@ #include "stringhash.c" #include "Psiblast.c" @@ -2613,7 +2618,7 @@ Index: sift-4.0.3b/src/sift_blimps.h =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 -+++ sift-4.0.3b/src/sift_blimps.h 2012-02-23 18:08:32.787044550 +0100 ++++ sift-4.0.3b/src/sift_blimps.h 2012-02-23 18:57:19.659044510 +0100 @@ -0,0 +1,12 @@ +#ifndef SIFT_BLIMPS_H +#define SIFT_BLIMPS_H @@ -2629,8 +2634,8 @@ +#endif Index: sift-4.0.3b/src/SortList.c =================================================================== ---- sift-4.0.3b.orig/src/SortList.c 2012-02-23 18:08:32.155044442 +0100 -+++ sift-4.0.3b/src/SortList.c 2012-02-23 18:08:32.798931158 +0100 +--- sift-4.0.3b.orig/src/SortList.c 2009-11-23 19:13:33.000000000 +0100 ++++ sift-4.0.3b/src/SortList.c 2012-02-23 18:57:19.666926854 +0100 @@ -13,7 +13,7 @@ lowest_scoring_aa (Matrix* matrix, int pos) { @@ -2643,7 +2648,7 @@ Index: sift-4.0.3b/SIFT_for_submitting_fasta_seq.csh.pod =================================================================== --- /dev/null 1970-01-01 00:00:00.000000000 +0000 -+++ sift-4.0.3b/SIFT_for_submitting_fasta_seq.csh.pod 2012-02-23 18:44:17.694990539 +0100 ++++ sift-4.0.3b/SIFT_for_submitting_fasta_seq.csh.pod 2012-02-23 18:57:19.675044442 +0100 @@ -0,0 +1,55 @@ +=head1 NAME + @@ -2702,8 +2707,8 @@ +L<info_on_seqs> Index: sift-4.0.3b/bin/Classify_SNPs_Indels.pl =================================================================== ---- sift-4.0.3b.orig/bin/Classify_SNPs_Indels.pl 2012-02-23 18:08:31.267044551 +0100 -+++ sift-4.0.3b/bin/Classify_SNPs_Indels.pl 2012-02-23 18:08:32.819044418 +0100 +--- sift-4.0.3b.orig/bin/Classify_SNPs_Indels.pl 2010-03-08 18:54:49.000000000 +0100 ++++ sift-4.0.3b/bin/Classify_SNPs_Indels.pl 2012-02-23 18:57:19.687004191 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2712,8 +2717,8 @@ Index: sift-4.0.3b/bin/SIFT_intersect_cds.pl =================================================================== ---- sift-4.0.3b.orig/bin/SIFT_intersect_cds.pl 2012-02-23 18:08:31.295044427 +0100 -+++ sift-4.0.3b/bin/SIFT_intersect_cds.pl 2012-02-23 18:08:32.827044531 +0100 +--- sift-4.0.3b.orig/bin/SIFT_intersect_cds.pl 2010-03-08 19:10:08.000000000 +0100 ++++ sift-4.0.3b/bin/SIFT_intersect_cds.pl 2012-02-23 18:57:19.695044575 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2722,8 +2727,8 @@ use File::Basename; Index: sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl =================================================================== ---- sift-4.0.3b.orig/bin/SNPClassifier/Classify_SNPs.pl 2012-02-23 18:08:31.322941731 +0100 -+++ sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl 2012-02-23 18:08:32.835044435 +0100 +--- sift-4.0.3b.orig/bin/SNPClassifier/Classify_SNPs.pl 2009-11-23 19:13:30.000000000 +0100 ++++ sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl 2012-02-23 18:57:19.703044603 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2732,8 +2737,8 @@ # # Index: sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl =================================================================== ---- sift-4.0.3b.orig/bin/SNPClassifier/Extract_Coding_Info.pl 2012-02-23 18:08:31.354993527 +0100 -+++ sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl 2012-02-23 18:08:32.839005136 +0100 +--- sift-4.0.3b.orig/bin/SNPClassifier/Extract_Coding_Info.pl 2009-11-23 19:13:30.000000000 +0100 ++++ sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl 2012-02-23 18:57:19.711041186 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2742,8 +2747,8 @@ # # Index: sift-4.0.3b/bin/detect_indel.pl =================================================================== ---- sift-4.0.3b.orig/bin/detect_indel.pl 2012-02-23 18:08:31.383044520 +0100 -+++ sift-4.0.3b/bin/detect_indel.pl 2012-02-23 18:08:32.843044391 +0100 +--- sift-4.0.3b.orig/bin/detect_indel.pl 2010-03-08 19:08:09.000000000 +0100 ++++ sift-4.0.3b/bin/detect_indel.pl 2012-02-23 18:57:19.715044412 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/perl -w @@ -2752,8 +2757,8 @@ # This program is licensed to you under the Fred Index: sift-4.0.3b/bin/detect_repeat.pl =================================================================== ---- sift-4.0.3b.orig/bin/detect_repeat.pl 2012-02-23 18:08:31.411044488 +0100 -+++ sift-4.0.3b/bin/detect_repeat.pl 2012-02-23 18:08:32.850889637 +0100 +--- sift-4.0.3b.orig/bin/detect_repeat.pl 2010-03-08 19:12:09.000000000 +0100 ++++ sift-4.0.3b/bin/detect_repeat.pl 2012-02-23 18:57:19.723044449 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2762,8 +2767,8 @@ # Hutchinos Cancer Research Center (FHCRC) Index: sift-4.0.3b/bin/get_sequences.pl =================================================================== ---- sift-4.0.3b.orig/bin/get_sequences.pl 2012-02-23 18:08:31.439044517 +0100 -+++ sift-4.0.3b/bin/get_sequences.pl 2012-02-23 18:08:32.854922592 +0100 +--- sift-4.0.3b.orig/bin/get_sequences.pl 2010-03-08 18:57:38.000000000 +0100 ++++ sift-4.0.3b/bin/get_sequences.pl 2012-02-23 18:57:19.727044469 +0100 @@ -1,4 +1,4 @@ -#! /opt/local/bin/perl5 -w +#!/usr/bin/perl -w @@ -2772,8 +2777,8 @@ # Index: sift-4.0.3b/bin/indelfile_to_gff.pl =================================================================== ---- sift-4.0.3b.orig/bin/indelfile_to_gff.pl 2012-02-23 18:08:31.547044394 +0100 -+++ sift-4.0.3b/bin/indelfile_to_gff.pl 2012-02-23 18:08:32.863044512 +0100 +--- sift-4.0.3b.orig/bin/indelfile_to_gff.pl 2010-03-08 19:12:29.000000000 +0100 ++++ sift-4.0.3b/bin/indelfile_to_gff.pl 2012-02-23 18:57:19.731044505 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2782,8 +2787,8 @@ # NONCOMMERICAL LICENSE. A copy of the license may be found at Index: sift-4.0.3b/bin/map_coords_to_bin.pl =================================================================== ---- sift-4.0.3b.orig/bin/map_coords_to_bin.pl 2012-02-23 18:08:31.575044504 +0100 -+++ sift-4.0.3b/bin/map_coords_to_bin.pl 2012-02-23 18:08:32.867044562 +0100 +--- sift-4.0.3b.orig/bin/map_coords_to_bin.pl 2010-03-08 19:12:47.000000000 +0100 ++++ sift-4.0.3b/bin/map_coords_to_bin.pl 2012-02-23 18:57:19.739044482 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2792,8 +2797,8 @@ # Hutchinos Cancer Research Center (FHCRC) Index: sift-4.0.3b/bin/map_coords_to_bin_indels.pl =================================================================== ---- sift-4.0.3b.orig/bin/map_coords_to_bin_indels.pl 2012-02-23 18:08:31.603044446 +0100 -+++ sift-4.0.3b/bin/map_coords_to_bin_indels.pl 2012-02-23 18:08:32.874995674 +0100 +--- sift-4.0.3b.orig/bin/map_coords_to_bin_indels.pl 2010-03-08 19:13:11.000000000 +0100 ++++ sift-4.0.3b/bin/map_coords_to_bin_indels.pl 2012-02-23 18:57:19.747044533 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2802,8 +2807,8 @@ # This program is licensed to you under the Fred Index: sift-4.0.3b/bin/model_transcript.pl =================================================================== ---- sift-4.0.3b.orig/bin/model_transcript.pl 2012-02-23 18:08:31.631044520 +0100 -+++ sift-4.0.3b/bin/model_transcript.pl 2012-02-23 18:08:32.879044530 +0100 +--- sift-4.0.3b.orig/bin/model_transcript.pl 2010-03-08 19:12:57.000000000 +0100 ++++ sift-4.0.3b/bin/model_transcript.pl 2012-02-23 18:57:19.751044465 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/perl -w @@ -2812,8 +2817,8 @@ my $SIFT_HOME = $ENV{'SIFT_HOME'}; Index: sift-4.0.3b/bin/reformat_chrfile.pl =================================================================== ---- sift-4.0.3b.orig/bin/reformat_chrfile.pl 2012-02-23 18:08:31.659044469 +0100 -+++ sift-4.0.3b/bin/reformat_chrfile.pl 2012-02-23 18:08:32.887044468 +0100 +--- sift-4.0.3b.orig/bin/reformat_chrfile.pl 2010-03-08 19:00:22.000000000 +0100 ++++ sift-4.0.3b/bin/reformat_chrfile.pl 2012-02-23 18:57:19.755044452 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2822,8 +2827,8 @@ # Hutchinos Cancer Research Center (FHCRC) Index: sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl =================================================================== ---- sift-4.0.3b.orig/bin/sift_feed_to_chr_coords_batch.pl 2012-02-23 18:08:31.687044484 +0100 -+++ sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl 2012-02-23 18:08:32.891044403 +0100 +--- sift-4.0.3b.orig/bin/sift_feed_to_chr_coords_batch.pl 2010-03-08 19:00:53.000000000 +0100 ++++ sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl 2012-02-23 18:57:19.763044525 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2832,8 +2837,8 @@ Index: sift-4.0.3b/bin/snv_db_engine.pl =================================================================== ---- sift-4.0.3b.orig/bin/snv_db_engine.pl 2012-02-23 18:08:31.715044519 +0100 -+++ sift-4.0.3b/bin/snv_db_engine.pl 2012-02-23 18:08:32.899028510 +0100 +--- sift-4.0.3b.orig/bin/snv_db_engine.pl 2010-02-20 02:32:17.000000000 +0100 ++++ sift-4.0.3b/bin/snv_db_engine.pl 2012-02-23 18:57:19.771044564 +0100 @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl @@ -2842,8 +2847,8 @@ # Index: sift-4.0.3b/src/Clumping.c =================================================================== ---- sift-4.0.3b.orig/src/Clumping.c 2012-02-23 18:08:32.183044439 +0100 -+++ sift-4.0.3b/src/Clumping.c 2012-02-23 18:08:32.907044423 +0100 +--- sift-4.0.3b.orig/src/Clumping.c 2009-11-23 19:13:34.000000000 +0100 ++++ sift-4.0.3b/src/Clumping.c 2012-02-23 18:57:19.779044548 +0100 @@ -183,7 +183,7 @@ printf ("Clumped %d sequences into %d clusters\n", nseq, iclus); /* keep this print because get # of clustersin awk statement */ @@ -2862,3 +2867,54 @@ return no_of_clumps; } /* end of cluster */ +Index: sift-4.0.3b/info_on_seqs.pod +=================================================================== +--- /dev/null 1970-01-01 00:00:00.000000000 +0000 ++++ sift-4.0.3b/info_on_seqs.pod 2012-02-23 19:04:55.246919579 +0100 +@@ -0,0 +1,46 @@ ++=head1 NAME ++ ++info_on_seqs - perform final step of SIFT prediction ++ ++=head1 SYNOPSIS ++ ++info_on_seqs <FASTA_FILE> <SUBSTITUTIONS_FILE> <OUTPUT> ++ ++=head1 DESCRIPTION ++ ++You should use L<SIFT_for_submitting_fasta_seq.csh> instead of this program unless you know what you are doing. ++ ++This program prepares the final SIFT prediction. In addition to the command line arguments, it expects certain files present I<next to> the FASTA_FILE. ++ ++=head1 OPTIONS ++ ++=over ++ ++=item <FASTA_FILE> ++ ++Protein sequence in fasta format. ++ ++=item <SUBSTITUTIONS_FILE> ++ ++File of substitutions to be predicted. See /usr/share/doc/sift/examples/lacI.subst for an example of the format. If you give '-', scores for all mutations of the entire protein sequence are printed. ++ ++=item <OUTPUT> ++ ++Output file. ++ ++=back ++ ++=head1 AUTHOR ++ ++Pauline Ng ++ ++=head1 COPYRIGHT AND LICENSE ++ ++(C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center ++ ++Noncommercial license. See /usr/share/doc/sift/copyright for details. ++ ++=head1 SEE ALSO ++ ++L<SIFT_for_submitting_fasta_seq.csh> ++ Modified: trunk/packages/sift/trunk/debian/rules =================================================================== --- trunk/packages/sift/trunk/debian/rules 2012-02-23 17:54:29 UTC (rev 9766) +++ trunk/packages/sift/trunk/debian/rules 2012-02-23 18:22:34 UTC (rev 9767) @@ -3,7 +3,7 @@ # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 -DESTDIR:=$(PWD)/debian/sift +DESTDIR:=$(CURDIR)/debian/sift VERSION:=4.0.3b prefix:=/usr _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
