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comparison Roary/lib/Bio/Roary/External/CheckTools.pm @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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1 package Bio::Roary::External::CheckTools;
2
3 # ABSTRACT: Check external executables are available and are the correct version
4
5 =head1 SYNOPSIS
6 Functionality borrowed from PROKKA by Torsten Seemann.
7 Check external executables are available and are the correct version
8
9 use Bio::Roary::External::CheckTools;
10
11 my $obj = Bio::Roary::External::CheckTools->new();
12 $obj->check_all_tools;
13
14 =cut
15
16 use Moose;
17 use File::Spec;
18 use Log::Log4perl qw(:easy);
19 has 'logger' => ( is => 'ro', lazy => 1, builder => '_build_logger' );
20
21 sub _build_logger {
22 my ($self) = @_;
23 Log::Log4perl->easy_init($DEBUG);
24 my $logger = get_logger();
25 return $logger;
26 }
27
28 my $BIDEC = '(\d+\.\d+)'; # pattern of NN.NN for versions that can be compared
29
30 my %tools = (
31 'parallel' => {
32 GETVER => "parallel --version | grep '^GNU parallel 2'",
33 REGEXP => qr/GNU parallel (\d+)/,
34 MINVER => "20130422",
35 NEEDED => 1,
36 },
37 'blastp' => {
38 GETVER => "blastp -version",
39 REGEXP => qr/blastp:\s+(\d+\.\d+\.\d+)/,
40 NEEDED => 1,
41 },
42 'makeblastdb' => {
43 GETVER => "makeblastdb -version",
44 REGEXP => qr/makeblastdb:\s+(\d+\.\d+\.\d+)/,
45 NEEDED => 1,
46 },
47 'mcl' => {
48 GETVER => "mcl --version | head -n 1",
49 REGEXP => qr/(\d+\-\d+)/,
50 NEEDED => 1,
51 },
52 'bedtools' => {
53 GETVER => "bedtools --version",
54 REGEXP => qr/bedtools v($BIDEC)/,
55 MINVER => "2.1",
56 NEEDED => 1,
57 },
58 'mafft' => {
59 GETVER => "mafft --version < /dev/null 2>&1",
60 REGEXP => qr/(\d+\.\d+)/,
61 NEEDED => 1,
62 },
63 'kraken' => {
64 GETVER => "kraken -v | head -n 1",
65 REGEXP => qr/(\d+\.\d+\.*\d*.*)/,
66 NEEDED => 0,
67 },
68 'kraken-report' => {
69 GETVER => "kraken-report -v | head -n 1",
70 REGEXP => qr/(\d+\.\d+\.*\d*.*)/,
71 NEEDED => 0,
72 },
73 'Rscript' => {
74 GETVER => "Rscript --version 2>&1 | head -n 1",
75 REGEXP => qr/R scripting front-end version ($BIDEC)/,
76 MINVER => "3",
77 NEEDED => 0,
78 },
79 'prank' => {
80 GETVER => "prank | grep -m 1 ^prank",
81 REGEXP => qr/prank v.(\d+)/,
82 NEEDED => 0,
83 },
84
85 # now just the standard unix tools we need
86 'grep' => { NEEDED => 1 },
87 'sed' => { NEEDED => 1 },
88 'awk' => { NEEDED => 1 },
89
90 );
91
92 my %cdhit_tools = (
93 'cdhit' => {
94 GETVER => "cdhit -h | grep 'CD-HIT version'",
95 REGEXP => qr/version\s+($BIDEC)/i,
96 MINVER => "4.6",
97 },
98 'cd-hit' => {
99 GETVER => "cd-hit -h | grep 'CD-HIT version'",
100 REGEXP => qr/version\s+($BIDEC)/i,
101 MINVER => "4.6",
102 }
103 );
104
105 my %fasttree_tools = (
106 'fasttree' => {
107 GETVER => "fasttree 2>&1 | head -n 1",
108 REGEXP => qr/Usage for FastTree version ($BIDEC)/,
109 },
110 'FastTree' => {
111 GETVER => "FastTree 2>&1 | head -n 1",
112 REGEXP => qr/Usage for FastTree version ($BIDEC)/,
113 }
114 );
115
116 sub which_tool_exec {
117 my ( $self, $alt_tools ) = @_;
118 for my $toolname ( sort keys %{$alt_tools} ) {
119 my $fp = $self->find_exe($toolname);
120 return $toolname if $fp;
121 }
122 $self->logger->error( "Required tool missing. Can't find one of " . join( '/', keys %{$alt_tools} ) . " in your \$PATH." );
123 return undef;
124 }
125
126 sub check_tool {
127 my ( $self, $toolname ) = @_;
128 my $t = $tools{$toolname};
129 my $fp = $self->find_exe($toolname);
130 $self->logger->error("ERROR: Can't find required '$toolname' in your \$PATH") if !$fp and $t->{NEEDED};
131 $self->logger->error("Optional tool '$toolname' not found in your \$PATH") if !$fp and !$t->{NEEDED};
132
133 if ($fp) {
134 $t->{HAVE} = $fp;
135 $self->logger->warn("Looking for '$toolname' - found $fp");
136 if ( $t->{GETVER} ) {
137 my ($s) = qx($t->{GETVER});
138 if ( defined $s ) {
139 $s =~ $t->{REGEXP};
140 $t->{VERSION} = $1 if defined $1;
141 $self->logger->warn("Determined $toolname version is $t->{VERSION}");
142 if ( defined $t->{MINVER} and $t->{VERSION} < $t->{MINVER} ) {
143 $self->logger->error("Roary needs $toolname $t->{MINVER} or higher. Please upgrade and try again.");
144 }
145 if ( defined $t->{MAXVER} and $t->{VERSION} > $t->{MAXVER} ) {
146 $self->logger->error(
147 "Roary needs a version of $toolname between $t->{MINVER} and $t->{MAXVER}. Please downgrade and try again.");
148 }
149 }
150 else {
151 $self->logger->error( "Could not determine version of $toolname - please install version ", $t->{MINVER}, " or higher" )
152 ; # FIXME: or less <= MAXVER if given
153 }
154 }
155 }
156 }
157
158 sub check_all_tools {
159 my ($self) = @_;
160 $ENV{"GREP_OPTIONS"} = ''; # --colour => version grep fails (Issue #117)
161 for my $toolname ( sort keys %tools ) {
162 $self->check_tool($toolname);
163 }
164
165 my $cdhit = $self->which_tool_exec( \%cdhit_tools );
166 if ($cdhit) {
167 $tools{$cdhit} = $cdhit_tools{$cdhit};
168 $self->check_tool($cdhit);
169 }
170
171 my $fasttree = $self->which_tool_exec( \%fasttree_tools );
172 if ($fasttree) {
173 $tools{$fasttree} = $fasttree_tools{$fasttree};
174 $self->check_tool($fasttree);
175 }
176
177 return $self;
178 }
179
180 sub find_exe {
181 my ( $self, $bin ) = @_;
182 for my $dir ( File::Spec->path ) {
183 my $exe = File::Spec->catfile( $dir, $bin );
184 return $exe if -x $exe;
185 }
186 return;
187 }
188
189 no Moose;
190 __PACKAGE__->meta->make_immutable;
191
192 1;