[med-svn] r9759 - trunk/packages/sift/trunk/debian/patches
H. Soon Gweon
soonio-guest at alioth.debian.org
Thu Feb 23 12:42:33 UTC 2012
Author: soonio-guest
Date: 2012-02-23 12:42:33 +0000 (Thu, 23 Feb 2012)
New Revision: 9759
Modified:
trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
trunk/packages/sift/trunk/debian/patches/series
Log:
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 10:15:16 UTC (rev 9758)
+++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-23 12:42:33 UTC (rev 9759)
@@ -1,7 +1,5 @@
-Index: sift-4.0.3b/bin/SIFT_exome_nssnvs.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_exome_nssnvs.pl 2012-02-22 19:00:37.858982104 +0100
-+++ sift-4.0.3b/bin/SIFT_exome_nssnvs.pl 2012-02-22 19:00:38.858982216 +0100
+--- a/bin/SIFT_exome_nssnvs.pl
++++ b/bin/SIFT_exome_nssnvs.pl
@@ -1,4 +1,8 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -12,10 +10,8 @@
use List::Util qw[min max];
use File::Copy;
use Getopt::Std;
-Index: sift-4.0.3b/bin/SIFT_exome_indels.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_exome_indels.pl 2012-02-22 19:00:37.886982165 +0100
-+++ sift-4.0.3b/bin/SIFT_exome_indels.pl 2012-02-22 19:00:38.862982166 +0100
+--- a/bin/SIFT_exome_indels.pl
++++ b/bin/SIFT_exome_indels.pl
@@ -1,4 +1,6 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -33,20 +29,16 @@
$SIFT_HOME = $ENV{'SIFT_HOME'};
use vars qw($opt_i $opt_c $opt_d $opt_o);
getopts("i:c:d:o:");
-Index: sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl
-===================================================================
---- sift-4.0.3b.orig/bin/perlscripts/get_BLINK_seq.pl 2012-02-22 19:00:37.918982062 +0100
-+++ sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl 2012-02-22 19:00:38.874982046 +0100
+--- a/bin/perlscripts/get_BLINK_seq.pl
++++ b/bin/perlscripts/get_BLINK_seq.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
#use strict;
use LWP::Simple;
use LWP::UserAgent;
-Index: sift-4.0.3b/bin/seqs_chosen_via_median_info.csh
-===================================================================
---- sift-4.0.3b.orig/bin/seqs_chosen_via_median_info.csh 2012-02-22 19:00:37.946982117 +0100
-+++ sift-4.0.3b/bin/seqs_chosen_via_median_info.csh 2012-02-22 19:00:38.878982030 +0100
+--- a/bin/seqs_chosen_via_median_info.csh
++++ b/bin/seqs_chosen_via_median_info.csh
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -187,10 +179,8 @@
exit (0)
-Index: sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-22 19:00:37.974982205 +0100
-+++ sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-22 19:00:38.886982043 +0100
+--- a/bin/SIFT_for_submitting_fasta_seq.csh
++++ b/bin/SIFT_for_submitting_fasta_seq.csh
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -244,10 +234,8 @@
+echo "Output in ($PWD/)$tmpsift"
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 2012-02-22 19:00:38.006982068 +0100
-+++ sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-22 19:00:38.890982033 +0100
+--- a/bin/SIFT_for_submitting_NCBI_gi_id.csh
++++ b/bin/SIFT_for_submitting_NCBI_gi_id.csh
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -336,10 +324,8 @@
exit
-Index: sift-4.0.3b/src/Alignment.c
-===================================================================
---- sift-4.0.3b.orig/src/Alignment.c 2012-02-22 19:00:38.034982113 +0100
-+++ sift-4.0.3b/src/Alignment.c 2012-02-22 19:00:38.902982054 +0100
+--- a/src/Alignment.c
++++ b/src/Alignment.c
@@ -17,7 +17,7 @@
#define _ALIGNMENT_C_
#include "PN_convert.c"
@@ -440,10 +426,8 @@
return no_of_clumps;
} /* end of cluster */
-Index: sift-4.0.3b/src/blocklist.c
-===================================================================
---- sift-4.0.3b.orig/src/blocklist.c 2012-02-22 19:00:38.058982070 +0100
-+++ sift-4.0.3b/src/blocklist.c 2012-02-22 19:00:38.906982119 +0100
+--- a/src/blocklist.c
++++ b/src/blocklist.c
@@ -9,7 +9,7 @@
#include <string.h>
#include "blocklist.h"
@@ -453,10 +437,8 @@
/*======================================================================
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 2012-02-22 19:00:38.086982313 +0100
-+++ sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c 2012-02-22 19:00:38.910982060 +0100
+--- a/src/choose_seqs_via_psiblastseedmedian.c
++++ b/src/choose_seqs_via_psiblastseedmedian.c
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -814,10 +796,8 @@
{
FILE* fp;
-Index: sift-4.0.3b/src/clump_output_alignedseq.c
-===================================================================
---- sift-4.0.3b.orig/src/clump_output_alignedseq.c 2012-02-22 19:00:38.114982284 +0100
-+++ sift-4.0.3b/src/clump_output_alignedseq.c 2012-02-22 19:00:38.918982082 +0100
+--- a/src/clump_output_alignedseq.c
++++ b/src/clump_output_alignedseq.c
@@ -25,7 +25,7 @@
#include "Clumping.c"
@@ -845,10 +825,8 @@
}
-Index: sift-4.0.3b/src/consensus_to_seq.c
-===================================================================
---- sift-4.0.3b.orig/src/consensus_to_seq.c 2012-02-22 19:00:38.142982305 +0100
-+++ sift-4.0.3b/src/consensus_to_seq.c 2012-02-22 19:00:38.922982104 +0100
+--- a/src/consensus_to_seq.c
++++ b/src/consensus_to_seq.c
@@ -120,7 +120,7 @@
else
{
@@ -876,10 +854,8 @@
}
if ( (*outfp = fopen (outfilename, "w")) == NULL)
{
-Index: sift-4.0.3b/src/info_on_seqs.c
-===================================================================
---- sift-4.0.3b.orig/src/info_on_seqs.c 2012-02-22 19:00:38.170982073 +0100
-+++ sift-4.0.3b/src/info_on_seqs.c 2012-02-22 19:00:38.930982180 +0100
+--- a/src/info_on_seqs.c
++++ b/src/info_on_seqs.c
@@ -11,7 +11,7 @@
#include "Psiblast.c"
/* #include "Information.c */
@@ -965,10 +941,8 @@
}
strcpy (errorfilename, outfilename);
-Index: sift-4.0.3b/src/Makefile
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ sift-4.0.3b/src/Makefile 2012-02-22 19:00:38.934982116 +0100
+--- /dev/null
++++ b/src/Makefile
@@ -0,0 +1,42 @@
+include-prefix := $(prefix)
+lib-prefix := $(prefix)
@@ -1012,10 +986,8 @@
+include deps.mk
+
+# vim:ai:
-Index: sift-4.0.3b/src/Matrix_Info.c
-===================================================================
---- sift-4.0.3b.orig/src/Matrix_Info.c 2012-02-22 19:00:38.218982174 +0100
-+++ sift-4.0.3b/src/Matrix_Info.c 2012-02-22 19:00:38.950982088 +0100
+--- a/src/Matrix_Info.c
++++ b/src/Matrix_Info.c
@@ -384,7 +384,7 @@
int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant,
pos_error_fp, pos_total;
@@ -1149,10 +1121,8 @@
while (fgets (line, LARGE_BUFF_LENGTH, infofp) != NULL) {
word1[0] = '\0'; word2[0] = '\0';
stringp = strtok (line, " \r\n\t");
-Index: sift-4.0.3b/src/PN_blocks.c
-===================================================================
---- sift-4.0.3b.orig/src/PN_blocks.c 2012-02-22 19:00:38.246982103 +0100
-+++ sift-4.0.3b/src/PN_blocks.c 2012-02-22 19:00:38.962982072 +0100
+--- a/src/PN_blocks.c
++++ b/src/PN_blocks.c
@@ -671,7 +671,7 @@
Block* newblock;
Residue* residue_pointer;
@@ -1162,10 +1132,8 @@
non_X_length = 0;
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 2012-02-22 19:00:38.274982085 +0100
-+++ sift-4.0.3b/src/PN_convert.c 2012-02-22 19:00:38.970982120 +0100
+--- a/src/PN_convert.c
++++ b/src/PN_convert.c
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2221,10 +2189,8 @@
}
-Index: sift-4.0.3b/src/Protdist.c
-===================================================================
---- sift-4.0.3b.orig/src/Protdist.c 2012-02-22 19:00:38.302982197 +0100
-+++ sift-4.0.3b/src/Protdist.c 2012-02-22 19:00:38.982982146 +0100
+--- a/src/Protdist.c
++++ b/src/Protdist.c
@@ -124,7 +124,7 @@
{
double max_dist;
@@ -2234,10 +2200,8 @@
max_dist = 0;
-Index: sift-4.0.3b/src/Psiblast.c
-===================================================================
---- sift-4.0.3b.orig/src/Psiblast.c 2012-02-22 19:00:38.330982123 +0100
-+++ sift-4.0.3b/src/Psiblast.c 2012-02-22 19:00:38.990982065 +0100
+--- a/src/Psiblast.c
++++ b/src/Psiblast.c
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2439,10 +2403,8 @@
} /* end get_top_seq */
#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 2012-02-22 19:00:38.358982082 +0100
-+++ sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c 2012-02-22 19:00:38.994982229 +0100
+--- a/src/psiblast_res_to_fasta_dbpairwise.c
++++ b/src/psiblast_res_to_fasta_dbpairwise.c
@@ -32,8 +32,8 @@
#include "Protdist.c"
#include "Psiblast.c"
@@ -2528,10 +2490,8 @@
fprintf (errorfp, "couldn't open %s in processing PSIBLAST results\n", filename);
exit (-1);
}
-Index: sift-4.0.3b/src/seqs_from_psiblast_res.c
-===================================================================
---- sift-4.0.3b.orig/src/seqs_from_psiblast_res.c 2012-02-22 19:00:38.386982373 +0100
-+++ sift-4.0.3b/src/seqs_from_psiblast_res.c 2012-02-22 19:00:39.002982155 +0100
+--- a/src/seqs_from_psiblast_res.c
++++ b/src/seqs_from_psiblast_res.c
@@ -23,7 +23,7 @@
#include "stringhash.c"
#include "Psiblast.c"
@@ -2565,10 +2525,8 @@
}
if ((*seqfp = fopen (seqfilename, "r")) == NULL)
-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 2012-02-22 19:00:39.010982010 +0100
+--- /dev/null
++++ b/src/sift_blimps.h
@@ -0,0 +1,12 @@
+#ifndef SIFT_BLIMPS_H
+#define SIFT_BLIMPS_H
@@ -2582,10 +2540,8 @@
+}
+
+#endif
-Index: sift-4.0.3b/src/SortList.c
-===================================================================
---- sift-4.0.3b.orig/src/SortList.c 2012-02-22 19:00:38.434982061 +0100
-+++ sift-4.0.3b/src/SortList.c 2012-02-22 19:00:39.018982004 +0100
+--- a/src/SortList.c
++++ b/src/SortList.c
@@ -13,7 +13,7 @@
lowest_scoring_aa (Matrix* matrix, int pos)
{
@@ -2595,10 +2551,8 @@
double min;
min = 10000;
-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 2012-02-22 19:00:39.030982082 +0100
+--- /dev/null
++++ b/SIFT_for_submitting_fasta_seq.csh.pod
@@ -0,0 +1,47 @@
+=head1 NAME
+
@@ -2647,140 +2601,112 @@
+(C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center
+
+Noncommercial license. See /usr/share/doc/sift/copyright for details.
-Index: sift-4.0.3b/bin/Classify_SNPs_Indels.pl
-===================================================================
---- sift-4.0.3b.orig/bin/Classify_SNPs_Indels.pl 2012-02-22 19:03:06.990896077 +0100
-+++ sift-4.0.3b/bin/Classify_SNPs_Indels.pl 2012-02-22 19:03:14.254917862 +0100
+--- a/bin/Classify_SNPs_Indels.pl
++++ b/bin/Classify_SNPs_Indels.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
$SIFT_HOME = $ENV{'SIFT_HOME'};
$bin = "$SIFT_HOME/bin";
-Index: sift-4.0.3b/bin/SIFT_intersect_cds.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SIFT_intersect_cds.pl 2012-02-22 19:03:07.031044471 +0100
-+++ sift-4.0.3b/bin/SIFT_intersect_cds.pl 2012-02-22 19:03:17.591044446 +0100
+--- a/bin/SIFT_intersect_cds.pl
++++ b/bin/SIFT_intersect_cds.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
$| = 1;
use Getopt::Std;
use File::Basename;
-Index: sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SNPClassifier/Classify_SNPs.pl 2012-02-22 19:03:07.071044526 +0100
-+++ sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl 2012-02-22 19:03:20.783044586 +0100
+--- a/bin/SNPClassifier/Classify_SNPs.pl
++++ b/bin/SNPClassifier/Classify_SNPs.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
###############################################################################
# #
-Index: sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl
-===================================================================
---- sift-4.0.3b.orig/bin/SNPClassifier/Extract_Coding_Info.pl 2012-02-22 19:03:07.111044554 +0100
-+++ sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl 2012-02-22 19:03:23.655044475 +0100
+--- a/bin/SNPClassifier/Extract_Coding_Info.pl
++++ b/bin/SNPClassifier/Extract_Coding_Info.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
###############################################################################
# #
-Index: sift-4.0.3b/bin/detect_indel.pl
-===================================================================
---- sift-4.0.3b.orig/bin/detect_indel.pl 2012-02-22 19:03:07.151044633 +0100
-+++ sift-4.0.3b/bin/detect_indel.pl 2012-02-22 19:03:27.259044551 +0100
+--- a/bin/detect_indel.pl
++++ b/bin/detect_indel.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
# 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 2012-02-22 19:03:07.191044540 +0100
-+++ sift-4.0.3b/bin/detect_repeat.pl 2012-02-22 19:03:30.531044561 +0100
+--- a/bin/detect_repeat.pl
++++ b/bin/detect_repeat.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
-Index: sift-4.0.3b/bin/get_sequences.pl
-===================================================================
---- sift-4.0.3b.orig/bin/get_sequences.pl 2012-02-22 19:03:07.231044538 +0100
-+++ sift-4.0.3b/bin/get_sequences.pl 2012-02-22 19:03:39.311044572 +0100
+--- a/bin/get_sequences.pl
++++ b/bin/get_sequences.pl
@@ -1,4 +1,4 @@
-#! /opt/local/bin/perl5 -w
+#!/usr/bin/perl -w
#####################################################################
#
-Index: sift-4.0.3b/bin/indelfile_to_gff.pl
-===================================================================
---- sift-4.0.3b.orig/bin/indelfile_to_gff.pl 2012-02-22 19:03:07.271044539 +0100
-+++ sift-4.0.3b/bin/indelfile_to_gff.pl 2012-02-22 19:03:42.495044498 +0100
+--- a/bin/indelfile_to_gff.pl
++++ b/bin/indelfile_to_gff.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
# 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 2012-02-22 19:03:07.351044410 +0100
-+++ sift-4.0.3b/bin/map_coords_to_bin.pl 2012-02-22 19:03:48.566952010 +0100
+--- a/bin/map_coords_to_bin.pl
++++ b/bin/map_coords_to_bin.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# 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 2012-02-22 19:03:07.311044483 +0100
-+++ sift-4.0.3b/bin/map_coords_to_bin_indels.pl 2012-02-22 19:03:45.650957846 +0100
+--- a/bin/map_coords_to_bin_indels.pl
++++ b/bin/map_coords_to_bin_indels.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# 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 2012-02-22 19:03:07.387044539 +0100
-+++ sift-4.0.3b/bin/model_transcript.pl 2012-02-22 19:03:52.035044606 +0100
+--- a/bin/model_transcript.pl
++++ b/bin/model_transcript.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use DBI;
my $SIFT_HOME = $ENV{'SIFT_HOME'};
-Index: sift-4.0.3b/bin/reformat_chrfile.pl
-===================================================================
---- sift-4.0.3b.orig/bin/reformat_chrfile.pl 2012-02-22 19:03:07.427044485 +0100
-+++ sift-4.0.3b/bin/reformat_chrfile.pl 2012-02-22 19:03:55.835042109 +0100
+--- a/bin/reformat_chrfile.pl
++++ b/bin/reformat_chrfile.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
# 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 2012-02-22 19:03:07.467044605 +0100
-+++ sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl 2012-02-22 19:04:00.695044421 +0100
+--- a/bin/sift_feed_to_chr_coords_batch.pl
++++ b/bin/sift_feed_to_chr_coords_batch.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
my $SIFT_HOME = $ENV{'SIFT_HOME'};
my $bin = "$SIFT_HOME/bin";
-Index: sift-4.0.3b/bin/snv_db_engine.pl
-===================================================================
---- sift-4.0.3b.orig/bin/snv_db_engine.pl 2012-02-22 19:03:07.507044529 +0100
-+++ sift-4.0.3b/bin/snv_db_engine.pl 2012-02-22 19:04:04.095044531 +0100
+--- a/bin/snv_db_engine.pl
++++ b/bin/snv_db_engine.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
Modified: trunk/packages/sift/trunk/debian/patches/series
===================================================================
--- trunk/packages/sift/trunk/debian/patches/series 2012-02-23 10:15:16 UTC (rev 9758)
+++ trunk/packages/sift/trunk/debian/patches/series 2012-02-23 12:42:33 UTC (rev 9759)
@@ -1 +1,2 @@
fix_perl_interpreter_and_lib_path
+fix_perl_path
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