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Update spine to 0.3.2 #12175

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merged 4 commits into from
Aug 29, 2019
Merged

Update spine to 0.3.2 #12175

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4a56255
Update spine to 0.3.2
epruesse Nov 18, 2018
f50e5e1
Update meta.yaml
dpryan79 Aug 29, 2019
0d243e9
Merge branch 'master' into bump/spine
dpryan79 Aug 29, 2019
4c6b938
update patch
dpryan79 Aug 29, 2019
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10 changes: 5 additions & 5 deletions recipes/spine/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "spine" %}
{% set version = "0.2.2" %}
{% set hash = "b39b51ae645d4835c7fe8cee755dc0a149a4aba9cb82e596b9a6fe18373e6bd1" %}
{% set version = "0.3.2" %}
{% set hash = "3781141ee283f499efcd3329d33dcc4a610a326cc4e6435ef32c7f6feb68ba40" %}

package:
name: {{ name|lower }}
Expand All @@ -13,14 +13,14 @@ source:
- spine.patch

build:
number: 1
number: 0
noarch: generic

requirements:
build:
host:
- perl
- perl-module-build
- perl-file-which

run:
- perl
- perl-file-which
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28 changes: 18 additions & 10 deletions recipes/spine/spine.patch
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Original file line number Diff line number Diff line change
@@ -1,19 +1,27 @@
--- spine.pl 2017-07-24 21:23:08.000000000 +0300
+++ spine.pl 2017-07-24 21:26:33.000000000 +0300
@@ -250,9 +250,9 @@
diff --git a/spine.pl b/spine.pl
index 554fdc4..950d9e7 100644
--- a/spine.pl
+++ b/spine.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/opt/anaconda1anaconda2anaconda3/bin/perl

my $version = "0.3.2";
## Changes from v0.3.1 -> v0.3.2
@@ -301,9 +301,9 @@ my $home_dir = abs_path($0); #get the absolute path to spine.pl
$home_dir =~ s/\/[^\/]*$//; #strip off "/spine.pl"
unless ($web){
print STDERR "home_dir = $home_dir\n";
- die "ERROR: Can't find the required file \"nucmer_multi.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir/scripts) and has not been renamed.\n" unless (-e "$home_dir/scripts/nucmer_multi.pl");
- die "ERROR: Can't find the required file \"nucmer_backbone.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir/scripts) and has not been renamed.\n" unless (-e "$home_dir/scripts/nucmer_backbone.pl");
- my $nbb_vers = `perl $home_dir/scripts/nucmer_backbone.pl -V`;
+ die "ERROR: Can't find the required file \"nucmer_multi.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir) and has not been renamed.\n" unless (-e "$home_dir/nucmer_multi.pl");
+ die "ERROR: Can't find the required file \"nucmer_multi.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir) and has not been renamed.\n" unless (-e "$home_dir/scripts/nucmer_multi.pl");
+ die "ERROR: Can't find the required file \"nucmer_backbone.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir) and has not been renamed.\n" unless (-e "$home_dir/nucmer_backbone.pl");
+ my $nbb_vers = `perl $home_dir/nucmer_backbone.pl -V`;
chomp $nbb_vers;
my $min_nbb_vers = 0.3;
my $min_nbb_vers = 0.4;
my $wrong_vers = "unknown";
@@ -269,8 +269,8 @@
@@ -320,8 +320,8 @@ unless ($web){
}
}
die "ERROR: Minimum version of scripts/nucmer_backbone.pl is $min_nbb_vers (detected version is $wrong_vers)\n" if $wrong_vers;
Expand All @@ -24,7 +32,7 @@
chomp ($nm_vers);
my $min_nm_vers = 0.3;
$wrong_vers = "unknown";
@@ -287,7 +287,7 @@
@@ -338,7 +338,7 @@ unless ($web){
}
}
die "ERROR: Minimum version of scripts/nucmer_multi.pl is $min_nm_vers (detected version is $wrong_vers)\n" if $wrong_vers;
Expand All @@ -33,7 +41,7 @@
}

#read in file of files
@@ -462,7 +462,7 @@
@@ -568,7 +568,7 @@ my $return;
local $opt_o = $pref;
local $opt_n = $nuc_loc;
local $opt_w = 1 if $web;
Expand All @@ -42,10 +50,10 @@
}
unless ($return){
die "ERROR: Couldn't run nucmer_multi.pl: $@\n" if $@;
@@ -506,7 +506,7 @@
local $opt_r = $out_opt_r;
@@ -614,7 +614,7 @@ print STDERR "out_pan = $out_pan\n" if $out_pan and !$web;
local $opt_g = $out_opt_g;
local $opt_w = 1 if $web;
local $opt_z = $version;
- $return = do "$home_dir/scripts/nucmer_backbone.pl";
+ $return = do "$home_dir/nucmer_backbone.pl";
}
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