[med-svn] r9766 - in trunk/packages/sift/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Feb 23 17:54:29 UTC 2012
Author: lkajan-guest
Date: 2012-02-23 17:54:29 +0000 (Thu, 23 Feb 2012)
New Revision: 9766
Modified:
trunk/packages/sift/trunk/debian/links
trunk/packages/sift/trunk/debian/manpages
trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
trunk/packages/sift/trunk/debian/rules
Log:
added info_on_seqs to /usr/bin via symlink; added manpage for info_on_seqs
Modified: trunk/packages/sift/trunk/debian/links
===================================================================
--- trunk/packages/sift/trunk/debian/links 2012-02-23 16:49:39 UTC (rev 9765)
+++ trunk/packages/sift/trunk/debian/links 2012-02-23 17:54:29 UTC (rev 9766)
@@ -1,3 +1,4 @@
+usr/lib/sift/bin/info_on_seqs usr/bin/info_on_seqs
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_for_submitting_fasta_seq.csh
usr/lib/sift/bin/SIFT_for_submitting_fasta_seq.csh usr/bin/sift_for_submitting_fasta_seq.csh
Modified: trunk/packages/sift/trunk/debian/manpages
===================================================================
--- trunk/packages/sift/trunk/debian/manpages 2012-02-23 16:49:39 UTC (rev 9765)
+++ trunk/packages/sift/trunk/debian/manpages 2012-02-23 17:54:29 UTC (rev 9766)
@@ -1 +1,2 @@
+info_on_seqs.1
SIFT_for_submitting_fasta_seq.csh.1
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 16:49:39 UTC (rev 9765)
+++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-23 17:54:29 UTC (rev 9766)
@@ -1,7 +1,7 @@
Index: sift-4.0.3b/bin/SIFT_exome_nssnvs.pl
===================================================================
---- sift-4.0.3b.orig/bin/SIFT_exome_nssnvs.pl 2012-02-23 17:36:50.514902927 +0100
-+++ sift-4.0.3b/bin/SIFT_exome_nssnvs.pl 2012-02-23 17:36:51.971041259 +0100
+--- 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
@@ -1,4 +1,8 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -32,8 +32,8 @@
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 17:36:50.543044482 +0100
-+++ sift-4.0.3b/bin/SIFT_exome_indels.pl 2012-02-23 17:36:51.974984816 +0100
+--- 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
@@ -1,4 +1,6 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -62,8 +62,8 @@
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 17:36:50.575044513 +0100
-+++ sift-4.0.3b/bin/perlscripts/get_BLINK_seq.pl 2012-02-23 17:36:51.986885573 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -72,8 +72,8 @@
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 17:36:50.603044463 +0100
-+++ sift-4.0.3b/bin/seqs_chosen_via_median_info.csh 2012-02-23 17:36:51.991044657 +0100
+--- 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
@@ -1,7 +1,8 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -228,8 +228,8 @@
-
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 17:36:50.631044452 +0100
-+++ sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-23 17:36:51.995044466 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -280,17 +280,17 @@
+set tmpsift = $tail_of_root.SIFTprediction
+
+echo "$SIFT_SCRIPTDIR/seqs_chosen_via_median_info.csh $1 $2 $4"
-+$SIFT_SCRIPTDIR/seqs_chosen_via_median_info.csh $1 $2 $4
-+echo "$SIFT_SCRIPTDIR/sift_info_on_seqs $tmpfasta $3 $tmpsift"
-+$SIFT_SCRIPTDIR/sift_info_on_seqs $tmpfasta $3 $tmpsift
++ $SIFT_SCRIPTDIR/seqs_chosen_via_median_info.csh $1 $2 $4
++echo "$SIFT_SCRIPTDIR/info_on_seqs $tmpfasta $3 $tmpsift"
++ $SIFT_SCRIPTDIR/info_on_seqs $tmpfasta $3 $tmpsift
+rm -rf $TMPDIR
+echo "Output in ($PWD/)$tmpsift"
exit
Index: sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh
===================================================================
---- sift-4.0.3b.orig/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 17:36:50.659044477 +0100
-+++ sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 17:36:52.003044559 +0100
+--- sift-4.0.3b.orig/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 18:08:31.239044641 +0100
++++ sift-4.0.3b/bin/SIFT_for_submitting_NCBI_gi_id.csh 2012-02-23 18:08:32.659044484 +0100
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
@@ -371,7 +371,7 @@
-# final scoring
-$bindir/info_on_seqs $alignedseqs $polymorphism_file $outfile
+# final scoring
-+sift_info_on_seqs $alignedseqs $polymorphism_file $outfile
++info_on_seqs $alignedseqs $polymorphism_file $outfile
+rm -rf $TMPDIR
+echo "Output in ($PWD/)$outfile"
@@ -379,8 +379,8 @@
Index: sift-4.0.3b/src/Alignment.c
===================================================================
---- sift-4.0.3b.orig/src/Alignment.c 2012-02-23 17:36:51.111044492 +0100
-+++ sift-4.0.3b/src/Alignment.c 2012-02-23 17:36:52.015044565 +0100
+--- 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
@@ -17,7 +17,7 @@
#define _ALIGNMENT_C_
#include "PN_convert.c"
@@ -472,19 +472,23 @@
exit (-1);
}
strptr = strtok (line, " \t\r\n"); /* this should be Query */
-@@ -2110,7 +2117,7 @@
- printf ("Clumped %d sequences into %d clusters\n", nseq, i2);
+@@ -2107,10 +2114,10 @@
+ }
+
+
+- printf ("Clumped %d sequences into %d clusters\n", nseq, i2);
++ printf("Clumped %d sequences into %d clusters\n", nseq, i2);
/* keep this print because get # of clustersin awk statement */
free(pairs);
-printf ("exiting clump\n");
-+fprintf (stderr, "exiting clump\n");
++fprintf (stderr, "%s:%d exiting clump\n", __FILE__, __LINE__);
return no_of_clumps;
} /* end of cluster */
Index: sift-4.0.3b/src/blocklist.c
===================================================================
---- sift-4.0.3b.orig/src/blocklist.c 2012-02-23 17:36:51.139044522 +0100
-+++ sift-4.0.3b/src/blocklist.c 2012-02-23 17:36:52.019044417 +0100
+--- 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
@@ -9,7 +9,7 @@
#include <string.h>
#include "blocklist.h"
@@ -496,8 +500,8 @@
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 17:36:51.167044477 +0100
-+++ sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c 2012-02-23 17:36:52.027044493 +0100
+--- 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
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -857,8 +861,8 @@
Index: sift-4.0.3b/src/clump_output_alignedseq.c
===================================================================
---- sift-4.0.3b.orig/src/clump_output_alignedseq.c 2012-02-23 17:36:51.191044438 +0100
-+++ sift-4.0.3b/src/clump_output_alignedseq.c 2012-02-23 17:36:52.035015422 +0100
+--- 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
@@ -25,7 +25,7 @@
#include "Clumping.c"
@@ -888,8 +892,8 @@
Index: sift-4.0.3b/src/consensus_to_seq.c
===================================================================
---- sift-4.0.3b.orig/src/consensus_to_seq.c 2012-02-23 17:36:51.235044417 +0100
-+++ sift-4.0.3b/src/consensus_to_seq.c 2012-02-23 17:36:52.038951551 +0100
+--- 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
@@ -120,7 +120,7 @@
else
{
@@ -919,8 +923,8 @@
{
Index: sift-4.0.3b/src/info_on_seqs.c
===================================================================
---- sift-4.0.3b.orig/src/info_on_seqs.c 2012-02-23 17:36:51.263044435 +0100
-+++ sift-4.0.3b/src/info_on_seqs.c 2012-02-23 17:36:52.046893259 +0100
+--- 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
@@ -11,7 +11,7 @@
#include "Psiblast.c"
/* #include "Information.c */
@@ -1009,7 +1013,7 @@
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 17:36:52.051031845 +0100
++++ sift-4.0.3b/src/Makefile 2012-02-23 18:08:32.715044504 +0100
@@ -0,0 +1,42 @@
+include-prefix := $(prefix)
+lib-prefix := $(prefix)
@@ -1038,10 +1042,10 @@
+ choose_seqs_via_psiblastseedmedian \
+ clump_output_alignedseq \
+ consensus_to_seq \
++ info_on_seqs \
+ psiblast_res_to_fasta_dbpairwise \
+ seqs_from_psiblast_res \
-+ $(DESTDIR)$(prefix)/lib/sift/bin/ && \
-+ cp -a info_on_seqs $(DESTDIR)$(prefix)/lib/sift/bin/sift_info_on_seqs
++ $(DESTDIR)$(prefix)/lib/sift/bin/
+
+help:
+
@@ -1055,8 +1059,8 @@
+# vim:ai:
Index: sift-4.0.3b/src/Matrix_Info.c
===================================================================
---- sift-4.0.3b.orig/src/Matrix_Info.c 2012-02-23 17:36:51.307044530 +0100
-+++ sift-4.0.3b/src/Matrix_Info.c 2012-02-23 17:36:52.066895455 +0100
+--- 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
@@ -384,7 +384,7 @@
int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant,
pos_error_fp, pos_total;
@@ -1192,8 +1196,8 @@
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 17:36:51.334965879 +0100
-+++ sift-4.0.3b/src/PN_blocks.c 2012-02-23 17:36:52.079044467 +0100
+--- 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
@@ -671,7 +671,7 @@
Block* newblock;
Residue* residue_pointer;
@@ -1205,8 +1209,8 @@
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 17:36:51.363044523 +0100
-+++ sift-4.0.3b/src/PN_convert.c 2012-02-23 17:36:52.086926773 +0100
+--- 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
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2264,8 +2268,8 @@
Index: sift-4.0.3b/src/Protdist.c
===================================================================
---- sift-4.0.3b.orig/src/Protdist.c 2012-02-23 17:36:51.391044376 +0100
-+++ sift-4.0.3b/src/Protdist.c 2012-02-23 17:36:52.095020421 +0100
+--- 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
@@ -124,7 +124,7 @@
{
double max_dist;
@@ -2277,8 +2281,8 @@
Index: sift-4.0.3b/src/Psiblast.c
===================================================================
---- sift-4.0.3b.orig/src/Psiblast.c 2012-02-23 17:36:51.419044488 +0100
-+++ sift-4.0.3b/src/Psiblast.c 2012-02-23 17:36:52.107044599 +0100
+--- 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
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2482,8 +2486,8 @@
#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 17:36:51.447044436 +0100
-+++ sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c 2012-02-23 17:36:52.111044477 +0100
+--- 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
@@ -32,8 +32,8 @@
#include "Protdist.c"
#include "Psiblast.c"
@@ -2571,8 +2575,8 @@
}
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 17:36:51.475044426 +0100
-+++ sift-4.0.3b/src/seqs_from_psiblast_res.c 2012-02-23 17:36:52.119041156 +0100
+--- 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
@@ -23,7 +23,7 @@
#include "stringhash.c"
#include "Psiblast.c"
@@ -2609,7 +2613,7 @@
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 17:36:52.123044424 +0100
++++ sift-4.0.3b/src/sift_blimps.h 2012-02-23 18:08:32.787044550 +0100
@@ -0,0 +1,12 @@
+#ifndef SIFT_BLIMPS_H
+#define SIFT_BLIMPS_H
@@ -2625,8 +2629,8 @@
+#endif
Index: sift-4.0.3b/src/SortList.c
===================================================================
---- sift-4.0.3b.orig/src/SortList.c 2012-02-23 17:36:51.523044476 +0100
-+++ sift-4.0.3b/src/SortList.c 2012-02-23 17:36:52.134926539 +0100
+--- 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
@@ -13,7 +13,7 @@
lowest_scoring_aa (Matrix* matrix, int pos)
{
@@ -2639,15 +2643,15 @@
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 17:36:52.147044479 +0100
-@@ -0,0 +1,47 @@
++++ sift-4.0.3b/SIFT_for_submitting_fasta_seq.csh.pod 2012-02-23 18:44:17.694990539 +0100
+@@ -0,0 +1,55 @@
+=head1 NAME
+
+SIFT_for_submitting_fasta_seq.csh - predict effect of an amino acid substitution on protein function
+
+=head1 SYNOPSIS
+
-+SIFT_for_submitting_fasta_seq.csh <FASTA_FILE> <BLAST_DB> [SUBSTITUTIONS_FILE] [BLAST_PROCESSORS]
++SIFT_for_submitting_fasta_seq.csh <FASTA_FILE> <BLAST_DB> <SUBSTITUTIONS_FILE> [BLAST_PROCESSORS]
+
+=head1 DESCRIPTION
+
@@ -2663,16 +2667,20 @@
+
+=item <FASTA_FILE>
+
-+protein sequence in fasta format
++Protein sequence in fasta format.
+
+=item <BLAST_DB>
+
+Protein database to search. These sequences are assumed to be functional.
+
-+=item [SUBSTITUTIONS_FILE]
++=item <SUBSTITUTIONS_FILE>
+
-+File of substitutions to be predicted on (optional). See /usr/share/doc/sift/test/lacI.subst for an example of the format. This file is optional. Alternatively, you can print scores for the entire protein sequence.
++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 [BLAST_PROCESSORS]
++
++Number of processors/cores to use when running blast via the B<-a> argument.
++
+=back
+
+=head1 EXAMPLES
@@ -2688,10 +2696,14 @@
+(C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center
+
+Noncommercial license. See /usr/share/doc/sift/copyright for details.
++
++=head1 SEE ALSO
++
++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 17:36:50.683044426 +0100
-+++ sift-4.0.3b/bin/Classify_SNPs_Indels.pl 2012-02-23 17:36:52.163044486 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2700,8 +2712,8 @@
Index: sift-4.0.3b/bin/SIFT_intersect_cds.pl
===================================================================
---- sift-4.0.3b.orig/bin/SIFT_intersect_cds.pl 2012-02-23 17:36:50.711044504 +0100
-+++ sift-4.0.3b/bin/SIFT_intersect_cds.pl 2012-02-23 17:36:52.175044428 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2710,8 +2722,8 @@
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 17:36:50.767044415 +0100
-+++ sift-4.0.3b/bin/SNPClassifier/Classify_SNPs.pl 2012-02-23 17:36:52.183044530 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2720,8 +2732,8 @@
# #
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 17:36:50.799044468 +0100
-+++ sift-4.0.3b/bin/SNPClassifier/Extract_Coding_Info.pl 2012-02-23 17:36:52.186988904 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2730,8 +2742,8 @@
# #
Index: sift-4.0.3b/bin/detect_indel.pl
===================================================================
---- sift-4.0.3b.orig/bin/detect_indel.pl 2012-02-23 17:36:50.826909467 +0100
-+++ sift-4.0.3b/bin/detect_indel.pl 2012-02-23 17:36:52.191044612 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
@@ -2740,8 +2752,8 @@
# 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 17:36:50.855044447 +0100
-+++ sift-4.0.3b/bin/detect_repeat.pl 2012-02-23 17:36:52.199044390 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2750,8 +2762,8 @@
# 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 17:36:50.883044478 +0100
-+++ sift-4.0.3b/bin/get_sequences.pl 2012-02-23 17:36:52.203044601 +0100
+--- 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
@@ -1,4 +1,4 @@
-#! /opt/local/bin/perl5 -w
+#!/usr/bin/perl -w
@@ -2760,8 +2772,8 @@
#
Index: sift-4.0.3b/bin/indelfile_to_gff.pl
===================================================================
---- sift-4.0.3b.orig/bin/indelfile_to_gff.pl 2012-02-23 17:36:50.911044433 +0100
-+++ sift-4.0.3b/bin/indelfile_to_gff.pl 2012-02-23 17:36:52.211044464 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2770,8 +2782,8 @@
# 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 17:36:50.939044471 +0100
-+++ sift-4.0.3b/bin/map_coords_to_bin.pl 2012-02-23 17:36:52.215044694 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2780,8 +2792,8 @@
# 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 17:36:50.967044498 +0100
-+++ sift-4.0.3b/bin/map_coords_to_bin_indels.pl 2012-02-23 17:36:52.223044480 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2790,8 +2802,8 @@
# 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 17:36:50.995044391 +0100
-+++ sift-4.0.3b/bin/model_transcript.pl 2012-02-23 17:36:52.227044599 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
@@ -2800,8 +2812,8 @@
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 17:36:51.023044480 +0100
-+++ sift-4.0.3b/bin/reformat_chrfile.pl 2012-02-23 17:36:52.235044437 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2810,8 +2822,8 @@
# 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 17:36:51.051044533 +0100
-+++ sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl 2012-02-23 17:36:52.239044600 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -2820,11 +2832,33 @@
Index: sift-4.0.3b/bin/snv_db_engine.pl
===================================================================
---- sift-4.0.3b.orig/bin/snv_db_engine.pl 2012-02-23 17:36:51.083044500 +0100
-+++ sift-4.0.3b/bin/snv_db_engine.pl 2012-02-23 17:36:52.247044554 +0100
+--- 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
use Class::Struct;
#
+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
+@@ -183,7 +183,7 @@
+ printf ("Clumped %d sequences into %d clusters\n", nseq, iclus);
+ /* keep this print because get # of clustersin awk statement */
+ free(pairs);
+-printf ("exiting clump\n");
++fprintf( stderr, "%s:%d exiting clump\n", __FILE__, __LINE__);
+ return clusters_of_seqs;
+ } /* end of cluster */
+
+@@ -440,7 +440,7 @@
+ printf ("Clumped %d sequences into %d clusters\n", nseq, i2);
+ /* keep this print because get # of clustersin awk statement */
+ free(pairs);
+-printf ("exiting clump\n");
++fprintf( stderr, "%s:%d exiting clump\n", __FILE__, __LINE__);
+ return no_of_clumps;
+ } /* end of cluster */
+
Modified: trunk/packages/sift/trunk/debian/rules
===================================================================
--- trunk/packages/sift/trunk/debian/rules 2012-02-23 16:49:39 UTC (rev 9765)
+++ trunk/packages/sift/trunk/debian/rules 2012-02-23 17:54:29 UTC (rev 9766)
@@ -16,7 +16,7 @@
%:
dh --with quilt $@
-MAN1:=SIFT_for_submitting_fasta_seq.csh.1
+MAN1:=info_on_seqs.1 SIFT_for_submitting_fasta_seq.csh.1
.PHONY: man
man: $(MAN1)
@@ -40,8 +40,8 @@
make -C src DESTDIR=$(DESTDIR) prefix=$(prefix) install
override_dh_install:
- dh_install -X.svn bin $(prefix)/lib/sift/
- dh_install -X.svn blimps/docs $(prefix)/share/sift/blimps/
+ dh_install -X.svn -X.swp bin $(prefix)/lib/sift/
+ dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/
#Links are created by debian/links
for f in SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \
sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
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