[med-svn] r9765 - in trunk/packages/sift/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Feb 23 16:49:39 UTC 2012
Author: lkajan-guest
Date: 2012-02-23 16:49:39 +0000 (Thu, 23 Feb 2012)
New Revision: 9765
Added:
trunk/packages/sift/trunk/debian/examples
trunk/packages/sift/trunk/debian/manpages
Modified:
trunk/packages/sift/trunk/debian/links
trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
trunk/packages/sift/trunk/debian/rules
Log:
SIFT_for_submitting_fasta_seq.csh is functional
Added: trunk/packages/sift/trunk/debian/examples
===================================================================
--- trunk/packages/sift/trunk/debian/examples (rev 0)
+++ trunk/packages/sift/trunk/debian/examples 2012-02-23 16:49:39 UTC (rev 9765)
@@ -0,0 +1,5 @@
+test/lacI.SIFTprediction
+test/lacI.alignedfasta
+test/lacI.fasta
+test/lacI.fasta.query.out
+test/lacI.subst
Modified: trunk/packages/sift/trunk/debian/links
===================================================================
--- trunk/packages/sift/trunk/debian/links 2012-02-23 14:24:40 UTC (rev 9764)
+++ trunk/packages/sift/trunk/debian/links 2012-02-23 16:49:39 UTC (rev 9765)
@@ -1,2 +1,4 @@
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
+usr/share/man/man1/SIFT_for_submitting_fasta_seq.csh.1.gz usr/share/man/man1/sift_for_submitting_fasta_seq.csh.1.gz
Added: trunk/packages/sift/trunk/debian/manpages
===================================================================
--- trunk/packages/sift/trunk/debian/manpages (rev 0)
+++ trunk/packages/sift/trunk/debian/manpages 2012-02-23 16:49:39 UTC (rev 9765)
@@ -0,0 +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 14:24:40 UTC (rev 9764)
+++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path 2012-02-23 16:49:39 UTC (rev 9765)
@@ -1,5 +1,7 @@
---- a/bin/SIFT_exome_nssnvs.pl
-+++ b/bin/SIFT_exome_nssnvs.pl
+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
@@ -1,4 +1,8 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -10,8 +12,28 @@
use List::Util qw[min max];
use File::Copy;
use Getopt::Std;
---- a/bin/SIFT_exome_indels.pl
-+++ b/bin/SIFT_exome_indels.pl
+@@ -12,7 +16,7 @@
+
+ $| = 1;
+ system("umask 006");
+-$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.2/';
++$ENV{'SIFT_HOME'} = '/usr/lib/sift/';
+ my $SIFT_HOME = $ENV{'SIFT_HOME'};
+ use vars qw($opt_i $opt_d $opt_o $opt_A $opt_B $opt_C $opt_D $opt_E $opt_F $opt_G $opt_H $opt_I $opt_J $opt_K $opt_L);
+ getopts("i:d:o:A:B:C:D:E:F:G:H:I:J:K:L:");
+@@ -62,7 +66,7 @@
+ my $oo12 = defined($opt_L) ? 1:0;
+ my $pid = $$;
+ my $bin = "$SIFT_HOME/bin";
+-my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";
++my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";
+ my $Variation_db_dir = $opt_d;
+ mkdir $tmp;
+ my $num_coords_per_split = 1000;
+Index: sift-4.0.3b/bin/SIFT_exome_indels.pl
+===================================================================
+--- sift-4.0.3b.orig/bin/SIFT_exome_indels.pl 2012-02-23 17:36:50.543044482 +0100
++++ sift-4.0.3b/bin/SIFT_exome_indels.pl 2012-02-23 17:36:51.974984816 +0100
@@ -1,4 +1,6 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
@@ -25,27 +47,44 @@
use File::Copy;
use Getopt::Std;
-$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.1';
-+$ENV{'SIFT_HOME'} = '/usr/share/sift';
++$ENV{'SIFT_HOME'} = '/usr/lib/sift';
$SIFT_HOME = $ENV{'SIFT_HOME'};
use vars qw($opt_i $opt_c $opt_d $opt_o);
getopts("i:c:d:o:");
---- a/bin/perlscripts/get_BLINK_seq.pl
-+++ b/bin/perlscripts/get_BLINK_seq.pl
+@@ -38,7 +40,7 @@
+ system("umask 006");
+ my $bin = "$SIFT_HOME/bin";
+ my $pid = $$;
+-my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";
++my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";
+ require "$bin/SIFT_subroutines.pm";
+ mkdir $tmp;
+ 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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
#use strict;
use LWP::Simple;
use LWP::UserAgent;
---- a/bin/seqs_chosen_via_median_info.csh
-+++ b/bin/seqs_chosen_via_median_info.csh
-@@ -1,4 +1,4 @@
+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
+@@ -1,7 +1,8 @@
-#!/bin/csh
+#!/bin/csh -e
# seqs_chosen_via_median_info.csh
# Arg1 = protein sequence in fasta format
# Arg2 = blastpgp database
-@@ -9,11 +9,8 @@
++# Arg3 = blastpgp processors (-a)
+
+ # This program is licensed to you under the Fred
+ # Hutchinos Cancer Research Center (FHCRC)
+@@ -9,14 +10,16 @@
# http://blocks.fhcrc.org/sift/license.html and should be attached
# to this software
@@ -59,7 +98,15 @@
set seq_database = $2
set median_threshold = 2.75;
-@@ -24,22 +21,24 @@
++if ( $3 == "" ) then
++ set blastprocessors = 1
++else
++ set blastprocessors = $3
++endif
+
+ # Cleanup query sequence. NCBI stuff is intolerant of format
+ # deviations.
+@@ -24,22 +27,24 @@
set tail = $1:t
set pid = $tail:r
echo tail is $tail
@@ -88,7 +135,7 @@
# b option, # of alignments to show (else it is 250)
# m option, type of alignment 0-pairwise, 6-flat master slave w/out identites
-@@ -47,10 +46,18 @@
+@@ -47,10 +52,18 @@
# make error file & remove only if PSI-BLAST is finished within time allotted
# not filtering query because Jorja says new statistics take care of that
@@ -98,18 +145,18 @@
-$NCBI/blastpgp -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399
+if ( $?SIFT_DEBUG ) then
-+ echo "if ! ( -e "/tmp/savethis.out" ) blastpgp -d $seq_database -i $query -o /tmp/savethis.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399"
-+ if ! ( -e "/tmp/savethis.out" ) blastpgp -d $seq_database -i $query -o /tmp/savethis.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399;
++ echo "if ! ( -e "/tmp/savethis.out" ) blastpgp -a $blastprocessors -d $seq_database -i $query -o /tmp/savethis.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399"
++ if ! ( -e "/tmp/savethis.out" ) blastpgp -a $blastprocessors -d $seq_database -i $query -o /tmp/savethis.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399;
+ echo "cp -a /tmp/savethis.out $query.out"
+ cp -a /tmp/savethis.out $query.out
+else
-+ echo "blastpgp -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399"
-+ blastpgp -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399
++ echo "blastpgp -a $blastprocessors -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399"
++ blastpgp -a $blastprocessors -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399
+endif
if ($status != 0) then
echo "exiting because stauts not equal to 0"
-@@ -59,45 +66,52 @@
+@@ -59,45 +72,50 @@
unlimit cputime
# finished within 10 minutes, remove error file
@@ -122,23 +169,23 @@
# get the psiblast alignment of all the sequences found.
-$bindir/psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered
-+echo "psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered"
-+psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered
++echo "__SIFT_BINDIR__/psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered"
++ __SIFT_BINDIR__/psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered
if ($status != 0) then
exit (-1)
endif
-$bindir/clump_output_alignedseq $query.globalX $tmpdir/$pid.clumped .9 0 >& /dev/null
-+echo "clump_output_alignedseq $query.globalX $TMPDIR/$pid.clumped .9 0 >& /dev/null"
-+clump_output_alignedseq $query.globalX $TMPDIR/$pid.clumped .9 0 >& /dev/null
++echo "__SIFT_BINDIR__/clump_output_alignedseq $query.globalX $TMPDIR/$pid.clumped .9 0 >& /dev/null"
++ __SIFT_BINDIR__/clump_output_alignedseq $query.globalX $TMPDIR/$pid.clumped .9 0 >& /dev/null
-echo "choose seqs time limit exceeded." > $tmpdir/$pid.time.error
+echo "choose seqs time limit exceeded." > $TMPDIR/$pid.time.error
limit cputime 30m
-$bindir/choose_seqs_via_psiblastseedmedian $query.unfiltered $tmpdir/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold >& /dev/null
-+echo "choose_seqs_via_psiblastseedmedian $query.unfiltered $TMPDIR/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold"
-+ choose_seqs_via_psiblastseedmedian $query.unfiltered $TMPDIR/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold
++echo "__SIFT_BINDIR__/choose_seqs_via_psiblastseedmedian $query.unfiltered $TMPDIR/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold"
++ __SIFT_BINDIR__/choose_seqs_via_psiblastseedmedian $query.unfiltered $TMPDIR/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold
if ($status != 0) then
echo "exiting because stauts not equal to 0"
@@ -149,13 +196,13 @@
+rm -f $TMPDIR/$pid.time.error
-$bindir/consensus_to_seq $query.selectedclumped $tmpdir/$pid.clumped.consensuskey $tmpdir/$pid.selected >& /dev/null
-+echo "consensus_to_seq $query.selectedclumped $TMPDIR/$pid.clumped.consensuskey $TMPDIR/$pid.selected >& /dev/null"
-+consensus_to_seq $query.selectedclumped $TMPDIR/$pid.clumped.consensuskey $TMPDIR/$pid.selected >& /dev/null
++echo "__SIFT_BINDIR__/consensus_to_seq $query.selectedclumped $TMPDIR/$pid.clumped.consensuskey $TMPDIR/$pid.selected >& /dev/null"
++ __SIFT_BINDIR__/consensus_to_seq $query.selectedclumped $TMPDIR/$pid.clumped.consensuskey $TMPDIR/$pid.selected >& /dev/null
-$bindir/seqs_from_psiblast_res $query.out $tmpdir/$pid.selected $iterations $query.unfiltered $tmpdir/$pid.alignedfasta $pid
-+echo "seqs_from_psiblast_res $query.out $TMPDIR/$pid.selected $iterations $query.unfiltered $TMPDIR/$pid.alignedfasta $pid"
-+seqs_from_psiblast_res $query.out $TMPDIR/$pid.selected $iterations $query.unfiltered $TMPDIR/$pid.alignedfasta $pid
++echo "__SIFT_BINDIR__/seqs_from_psiblast_res $query.out $TMPDIR/$pid.selected $iterations $query.unfiltered $TMPDIR/$pid.alignedfasta $pid"
++ __SIFT_BINDIR__/seqs_from_psiblast_res $query.out $TMPDIR/$pid.selected $iterations $query.unfiltered $TMPDIR/$pid.alignedfasta $pid
- rm $tmpdir/$pid.clumped*
- rm $query.selectedclumped*
@@ -177,17 +224,23 @@
+ rm -f $query
+ rm -f $query.unfiltered
exit (0)
-
-
---- a/bin/SIFT_for_submitting_fasta_seq.csh
-+++ b/bin/SIFT_for_submitting_fasta_seq.csh
+-
+-
+Index: sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh
+===================================================================
+--- sift-4.0.3b.orig/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-23 17:36:50.631044452 +0100
++++ sift-4.0.3b/bin/SIFT_for_submitting_fasta_seq.csh 2012-02-23 17:36:51.995044466 +0100
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
# SIFT.csh
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
-@@ -13,27 +13,35 @@
+@@ -10,30 +10,37 @@
+ # Argument 1: the protein sequence file in fasta format
+ # Argument 2: the pathname to the protein sequence database
+ # Argument 3: the substitution file (file containing amino acid substitutions to be predicted on.
++# Argument 4: blast processors
### Set these for your installation
# Location of blastpgp
@@ -197,16 +250,16 @@
# Location of BLIMPS
-setenv BLIMPS_DIR /opt/www/sift/sift3.0/blimps/
+-
+-# Location of SIFT
+-setenv SIFT_DIR /opt/www/sift/sift3.0
+setenv BLIMPS_DIR __MAKE_PREFIX__/share/sift/blimps
- # Location of SIFT
--setenv SIFT_DIR /opt/www/sift/sift3.0
-+setenv SIFT_DIR __MAKE_PREFIX__/lib/sift/
-
# SIFT's output files are written here
-set tmpdir = /opt/www/sift/sift3.0/tmp
+setenv TMPDIR `mktemp -d` || exit 1
+
++setenv SIFT_BINDIR __SIFT_BINDIR__
+setenv SIFT_SCRIPTDIR __SIFT_SCRIPTDIR__
+setenv BLASTMAT __MAKE_PREFIX__/share/ncbi/data
+
@@ -228,21 +281,23 @@
+
+echo "$SIFT_SCRIPTDIR/seqs_chosen_via_median_info.csh $1 $2 $4"
+$SIFT_SCRIPTDIR/seqs_chosen_via_median_info.csh $1 $2 $4
-+echo "sift_info_on_seqs $tmpfasta $3 $tmpsift"
-+sift_info_on_seqs $tmpfasta $3 $tmpsift
++echo "$SIFT_SCRIPTDIR/sift_info_on_seqs $tmpfasta $3 $tmpsift"
++$SIFT_SCRIPTDIR/sift_info_on_seqs $tmpfasta $3 $tmpsift
+rm -rf $TMPDIR
+echo "Output in ($PWD/)$tmpsift"
exit
---- a/bin/SIFT_for_submitting_NCBI_gi_id.csh
-+++ b/bin/SIFT_for_submitting_NCBI_gi_id.csh
+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
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -e
# SIFT.csh
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
-@@ -6,53 +6,59 @@
+@@ -6,53 +6,56 @@
# http://blocks.fhcrc.org/sift/license.html and should be attached
# to this software
@@ -263,24 +318,22 @@
# Location of BLIMPS
-setenv BLIMPS_DIR ../blimps
-+setenv BLIMPS_DIR __MAKE_PREFIX__/share/sift/blimps
-
+-
-# Location of SIFT
-setenv SIFT_DIR ../
-+# Location of SIFT
-+setenv SIFT_DIR __MAKE_PREFIX__/lib/sift/
++setenv BLIMPS_DIR __MAKE_PREFIX__/share/sift/blimps
# SIFT's output files are written here
-set tmpdir = ../tmp
+setenv TMPDIR `mktemp -d` || exit 1
-
--### Shouldn't need to make any more changes, look for output in $tmpdir
--set bindir = $SIFT_DIR/bin
++
+setenv SIFT_SCRIPTDIR __SIFT_SCRIPTDIR__
+setenv BLASTMAT __MAKE_PREFIX__/share/ncbi/data
+
+if ( -e "$HOME/.siftrc" ) source "$HOME/.siftrc";
-+
+
+-### Shouldn't need to make any more changes, look for output in $tmpdir
+-set bindir = $SIFT_DIR/bin
+### Shouldn't need to make any more changes, look for output in $tmpdir
set gi = $1
set polymorphism_file = $2
@@ -324,8 +377,10 @@
exit
---- a/src/Alignment.c
-+++ b/src/Alignment.c
+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
@@ -17,7 +17,7 @@
#define _ALIGNMENT_C_
#include "PN_convert.c"
@@ -426,8 +481,10 @@
return no_of_clumps;
} /* end of cluster */
---- a/src/blocklist.c
-+++ b/src/blocklist.c
+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
@@ -9,7 +9,7 @@
#include <string.h>
#include "blocklist.h"
@@ -437,8 +494,10 @@
/*======================================================================
routines for a list of blocks
---- a/src/choose_seqs_via_psiblastseedmedian.c
-+++ b/src/choose_seqs_via_psiblastseedmedian.c
+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
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -796,8 +855,10 @@
{
FILE* fp;
---- a/src/clump_output_alignedseq.c
-+++ b/src/clump_output_alignedseq.c
+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
@@ -25,7 +25,7 @@
#include "Clumping.c"
@@ -825,8 +886,10 @@
}
---- a/src/consensus_to_seq.c
-+++ b/src/consensus_to_seq.c
+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
@@ -120,7 +120,7 @@
else
{
@@ -854,8 +917,10 @@
}
if ( (*outfp = fopen (outfilename, "w")) == NULL)
{
---- a/src/info_on_seqs.c
-+++ b/src/info_on_seqs.c
+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
@@ -11,7 +11,7 @@
#include "Psiblast.c"
/* #include "Information.c */
@@ -941,8 +1006,10 @@
}
strcpy (errorfilename, outfilename);
---- /dev/null
-+++ b/src/Makefile
+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
@@ -0,0 +1,42 @@
+include-prefix := $(prefix)
+lib-prefix := $(prefix)
@@ -966,15 +1033,15 @@
+ rm -rf *.o $(BIN)
+
+install:
-+ mkdir -p $(DESTDIR)$(prefix)/lib/sift && \
++ mkdir -p $(DESTDIR)$(prefix)/lib/sift/bin && \
+ cp -a \
+ choose_seqs_via_psiblastseedmedian \
+ clump_output_alignedseq \
+ consensus_to_seq \
+ psiblast_res_to_fasta_dbpairwise \
+ seqs_from_psiblast_res \
-+ $(DESTDIR)$(prefix)/lib/sift/ && \
-+ cp -a info_on_seqs $(DESTDIR)$(prefix)/lib/sift/sift_info_on_seqs
++ $(DESTDIR)$(prefix)/lib/sift/bin/ && \
++ cp -a info_on_seqs $(DESTDIR)$(prefix)/lib/sift/bin/sift_info_on_seqs
+
+help:
+
@@ -986,8 +1053,10 @@
+include deps.mk
+
+# vim:ai:
---- a/src/Matrix_Info.c
-+++ b/src/Matrix_Info.c
+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
@@ -384,7 +384,7 @@
int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant,
pos_error_fp, pos_total;
@@ -1121,8 +1190,10 @@
while (fgets (line, LARGE_BUFF_LENGTH, infofp) != NULL) {
word1[0] = '\0'; word2[0] = '\0';
stringp = strtok (line, " \r\n\t");
---- a/src/PN_blocks.c
-+++ b/src/PN_blocks.c
+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
@@ -671,7 +671,7 @@
Block* newblock;
Residue* residue_pointer;
@@ -1132,8 +1203,10 @@
non_X_length = 0;
for (i=0; i < block->width; i++) {
---- a/src/PN_convert.c
-+++ b/src/PN_convert.c
+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
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2189,8 +2262,10 @@
}
---- a/src/Protdist.c
-+++ b/src/Protdist.c
+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
@@ -124,7 +124,7 @@
{
double max_dist;
@@ -2200,8 +2275,10 @@
max_dist = 0;
---- a/src/Psiblast.c
-+++ b/src/Psiblast.c
+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
@@ -1,6 +1,6 @@
/* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
@@ -2403,8 +2480,10 @@
} /* end get_top_seq */
#endif
---- a/src/psiblast_res_to_fasta_dbpairwise.c
-+++ b/src/psiblast_res_to_fasta_dbpairwise.c
+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
@@ -32,8 +32,8 @@
#include "Protdist.c"
#include "Psiblast.c"
@@ -2490,8 +2569,10 @@
fprintf (errorfp, "couldn't open %s in processing PSIBLAST results\n", filename);
exit (-1);
}
---- a/src/seqs_from_psiblast_res.c
-+++ b/src/seqs_from_psiblast_res.c
+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
@@ -23,7 +23,7 @@
#include "stringhash.c"
#include "Psiblast.c"
@@ -2525,8 +2606,10 @@
}
if ((*seqfp = fopen (seqfilename, "r")) == NULL)
---- /dev/null
-+++ b/src/sift_blimps.h
+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
@@ -0,0 +1,12 @@
+#ifndef SIFT_BLIMPS_H
+#define SIFT_BLIMPS_H
@@ -2540,8 +2623,10 @@
+}
+
+#endif
---- a/src/SortList.c
-+++ b/src/SortList.c
+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
@@ -13,7 +13,7 @@
lowest_scoring_aa (Matrix* matrix, int pos)
{
@@ -2551,8 +2636,10 @@
double min;
min = 10000;
---- /dev/null
-+++ b/SIFT_for_submitting_fasta_seq.csh.pod
+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 @@
+=head1 NAME
+
@@ -2560,7 +2647,7 @@
+
+=head1 SYNOPSIS
+
-+SIFT_for_submitting_fasta_seq.csh <FASTA_FILE> <BLAST_DB> [SUBSTITUTIONS_FILE]
++SIFT_for_submitting_fasta_seq.csh <FASTA_FILE> <BLAST_DB> [SUBSTITUTIONS_FILE] [BLAST_PROCESSORS]
+
+=head1 DESCRIPTION
+
@@ -2590,7 +2677,7 @@
+
+=head1 EXAMPLES
+
-+C<SIFT_for_submitting_fasta_seq.csh /usr/share/doc/sift/test/lacI.fasta [BLAST_DB] /usr/share/doc/sift/test/lacI.subst>
++ SIFT_for_submitting_fasta_seq.csh /usr/share/doc/sift/examples/lacI.fasta [BLAST_DB] /usr/share/doc/sift/examples/lacI.subst
+
+=head1 AUTHOR
+
@@ -2601,155 +2688,143 @@
+(C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center
+
+Noncommercial license. See /usr/share/doc/sift/copyright for details.
---- a/bin/Classify_SNPs_Indels.pl
-+++ b/bin/Classify_SNPs_Indels.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
$SIFT_HOME = $ENV{'SIFT_HOME'};
$bin = "$SIFT_HOME/bin";
---- a/bin/SIFT_intersect_cds.pl
-+++ b/bin/SIFT_intersect_cds.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
$| = 1;
use Getopt::Std;
use File::Basename;
---- a/bin/SNPClassifier/Classify_SNPs.pl
-+++ b/bin/SNPClassifier/Classify_SNPs.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
###############################################################################
# #
---- a/bin/SNPClassifier/Extract_Coding_Info.pl
-+++ b/bin/SNPClassifier/Extract_Coding_Info.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
###############################################################################
# #
---- a/bin/detect_indel.pl
-+++ b/bin/detect_indel.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
# This program is licensed to you under the Fred
---- a/bin/detect_repeat.pl
-+++ b/bin/detect_repeat.pl
+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
@@ -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)
---- a/bin/get_sequences.pl
-+++ b/bin/get_sequences.pl
+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
@@ -1,4 +1,4 @@
-#! /opt/local/bin/perl5 -w
+#!/usr/bin/perl -w
#####################################################################
#
---- a/bin/indelfile_to_gff.pl
-+++ b/bin/indelfile_to_gff.pl
+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
@@ -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
---- a/bin/map_coords_to_bin.pl
-+++ b/bin/map_coords_to_bin.pl
+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
@@ -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)
---- a/bin/map_coords_to_bin_indels.pl
-+++ b/bin/map_coords_to_bin_indels.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# This program is licensed to you under the Fred
---- a/bin/model_transcript.pl
-+++ b/bin/model_transcript.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use DBI;
my $SIFT_HOME = $ENV{'SIFT_HOME'};
---- a/bin/reformat_chrfile.pl
-+++ b/bin/reformat_chrfile.pl
+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
@@ -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)
---- a/bin/sift_feed_to_chr_coords_batch.pl
-+++ b/bin/sift_feed_to_chr_coords_batch.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
my $SIFT_HOME = $ENV{'SIFT_HOME'};
my $bin = "$SIFT_HOME/bin";
---- a/bin/snv_db_engine.pl
-+++ b/bin/snv_db_engine.pl
+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
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
use Class::Struct;
#
---- a/bin/SIFT_exome_indels.pl
-+++ b/bin/SIFT_exome_indels.pl
-@@ -14,7 +14,7 @@
- use Tie::IxHash;
- use File::Copy;
- use Getopt::Std;
--$ENV{'SIFT_HOME'} = '/usr/share/sift';
-+$ENV{'SIFT_HOME'} = '/usr/lib/sift';
- $SIFT_HOME = $ENV{'SIFT_HOME'};
- use vars qw($opt_i $opt_c $opt_d $opt_o);
- getopts("i:c:d:o:");
-@@ -40,7 +40,7 @@
- system("umask 006");
- my $bin = "$SIFT_HOME/bin";
- my $pid = $$;
--my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";
-+my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";
- require "$bin/SIFT_subroutines.pm";
- mkdir $tmp;
- chmod 0777, $tmp;
---- a/bin/SIFT_exome_nssnvs.pl
-+++ b/bin/SIFT_exome_nssnvs.pl
-@@ -16,7 +16,7 @@
-
- $| = 1;
- system("umask 006");
--$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.2/';
-+$ENV{'SIFT_HOME'} = '/usr/lib/sift/';
- my $SIFT_HOME = $ENV{'SIFT_HOME'};
- use vars qw($opt_i $opt_d $opt_o $opt_A $opt_B $opt_C $opt_D $opt_E $opt_F $opt_G $opt_H $opt_I $opt_J $opt_K $opt_L);
- getopts("i:d:o:A:B:C:D:E:F:G:H:I:J:K:L:");
-@@ -66,7 +66,7 @@
- my $oo12 = defined($opt_L) ? 1:0;
- my $pid = $$;
- my $bin = "$SIFT_HOME/bin";
--my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";
-+my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";
- my $Variation_db_dir = $opt_d;
- mkdir $tmp;
- my $num_coords_per_split = 1000;
Modified: trunk/packages/sift/trunk/debian/rules
===================================================================
--- trunk/packages/sift/trunk/debian/rules 2012-02-23 14:24:40 UTC (rev 9764)
+++ trunk/packages/sift/trunk/debian/rules 2012-02-23 16:49:39 UTC (rev 9765)
@@ -3,11 +3,12 @@
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
-DESTDIR:=debian/sift
+DESTDIR:=$(PWD)/debian/sift
VERSION:=4.0.3b
prefix:=/usr
-SIFT_SCRIPTDIR := $(DESTDIR)$(prefix)/lib/sift/bin
+SIFT_BINDIR := $(prefix)/lib/sift/bin
+SIFT_SCRIPTDIR := $(prefix)/lib/sift/bin
parallel := 1
$(eval $(DEB_BUILD_OPTIONS))
@@ -40,12 +41,13 @@
override_dh_install:
dh_install -X.svn bin $(prefix)/lib/sift/
+ dh_install -X.svn 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;' $(DESTDIR)$(prefix)/lib/sift/bin/$$f; \
+ sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
done;
for f in seqs_chosen_via_median_info.csh 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;' $(SIFT_SCRIPTDIR)/$$f; \
+ sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
done;
chmod +x $(DESTDIR)$(prefix)/lib/sift/bin/perlscripts/separate_query_from_rest_of_seqs.pl
# look out: DNA_PROT_SUBROUTINES.pl is really a module(should be pm)!
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