[med-svn] r9767 - in trunk/packages/sift/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Feb 23 18:22:34 UTC 2012
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) <soonio at gmail.com> Mon, 20 Feb 2012 18:01:12 +0000
+ -- Laszlo Kajan <lkajan at rostlab.org> 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 <debian-med-packaging at lists.alioth.debian.org>
Uploaders: H. Soon Gweon <soonio at gmail.com>, Laszlo Kajan <lkajan at rostlab.org>, Tim Booth <tbooth at ceh.ac.uk>
-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
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