| line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
|
1
|
1
|
|
|
1
|
|
197267
|
use alienfile; |
|
|
1
|
|
|
|
|
2
|
|
|
|
1
|
|
|
|
|
6
|
|
|
2
|
1
|
|
|
1
|
|
135
|
use strict; |
|
|
1
|
|
|
|
|
2
|
|
|
|
1
|
|
|
|
|
12
|
|
|
3
|
1
|
|
|
1
|
|
3
|
use warnings; |
|
|
1
|
|
|
|
|
2
|
|
|
|
1
|
|
|
|
|
27
|
|
|
4
|
1
|
|
|
1
|
|
417
|
use Data::Dump qw(dump); |
|
|
1
|
|
|
|
|
4596
|
|
|
|
1
|
|
|
|
|
437
|
|
|
5
|
|
|
|
|
|
|
configure sub { |
|
6
|
|
|
|
|
|
|
|
|
7
|
|
|
|
|
|
|
## find out of pipx is actually installed |
|
8
|
|
|
|
|
|
|
my $is_pipx_installed; |
|
9
|
|
|
|
|
|
|
my $cmd = `pipx --version`; |
|
10
|
|
|
|
|
|
|
$is_pipx_installed = $cmd =~ /[0..9]+/; |
|
11
|
|
|
|
|
|
|
|
|
12
|
|
|
|
|
|
|
## if pipx is not installed, install it using OS appropriate package managers |
|
13
|
|
|
|
|
|
|
unless ($is_pipx_installed) { |
|
14
|
|
|
|
|
|
|
my $os = $^O; |
|
15
|
|
|
|
|
|
|
my %os_mapping = ( |
|
16
|
|
|
|
|
|
|
'darwin' => { |
|
17
|
|
|
|
|
|
|
install => 'brew install pipx', |
|
18
|
|
|
|
|
|
|
setpath => 'pipx ensurepath', |
|
19
|
|
|
|
|
|
|
upgrade => 'brew update && brew upgrade pipx', |
|
20
|
|
|
|
|
|
|
}, |
|
21
|
|
|
|
|
|
|
'linux' => { |
|
22
|
|
|
|
|
|
|
install => 'sudo apt install pipx', |
|
23
|
|
|
|
|
|
|
setpath => 'pipx ensurepath', |
|
24
|
|
|
|
|
|
|
upgrade => '', |
|
25
|
|
|
|
|
|
|
}, |
|
26
|
|
|
|
|
|
|
'MSWin32' => { |
|
27
|
|
|
|
|
|
|
install => 'scoop install pipx', |
|
28
|
|
|
|
|
|
|
setpath => 'pipx ensurepath', |
|
29
|
|
|
|
|
|
|
upgrade => 'scoop update pipx', |
|
30
|
|
|
|
|
|
|
}, |
|
31
|
|
|
|
|
|
|
); |
|
32
|
|
|
|
|
|
|
unless ( exists $os_mapping{$os} ) { |
|
33
|
|
|
|
|
|
|
my @valid_oses = keys %os_mapping; |
|
34
|
|
|
|
|
|
|
die "Unsupported os : $os, must be one of @valid_oses"; |
|
35
|
|
|
|
|
|
|
} |
|
36
|
|
|
|
|
|
|
|
|
37
|
|
|
|
|
|
|
## adjust the linux install steps based on version |
|
38
|
|
|
|
|
|
|
if ( $os eq 'linux' ) { |
|
39
|
|
|
|
|
|
|
my @os_details = `cat /etc/os-release`; |
|
40
|
|
|
|
|
|
|
chomp @os_details; |
|
41
|
|
|
|
|
|
|
my %os_details = map { split /=/, $_ } @os_details; |
|
42
|
|
|
|
|
|
|
$os_details{VERSION_ID} =~ s/\"//g; |
|
43
|
|
|
|
|
|
|
if ( $os_details{VERSION_ID} <= 22.04 ) { |
|
44
|
|
|
|
|
|
|
$os_mapping{linux} = { |
|
45
|
|
|
|
|
|
|
install => 'python3 -m pip install --user pipx', |
|
46
|
|
|
|
|
|
|
setpath => 'python3 -m pipx ensurepath', |
|
47
|
|
|
|
|
|
|
upgrade => 'python3 -m pip install --user --upgrade pipx', |
|
48
|
|
|
|
|
|
|
}; |
|
49
|
|
|
|
|
|
|
} |
|
50
|
|
|
|
|
|
|
} |
|
51
|
|
|
|
|
|
|
|
|
52
|
|
|
|
|
|
|
system $os_mapping{$os}->{install}; |
|
53
|
|
|
|
|
|
|
system $os_mapping{$os}->{setpath}; |
|
54
|
|
|
|
|
|
|
system $os_mapping{$os}->{upgrade}; |
|
55
|
|
|
|
|
|
|
} |
|
56
|
|
|
|
|
|
|
}; |
|
57
|
|
|
|
|
|
|
## dummy probe to force a system install |
|
58
|
|
|
|
|
|
|
probe sub { |
|
59
|
|
|
|
|
|
|
'system'; |
|
60
|
|
|
|
|
|
|
}; |
|
61
|
|
|
|
|
|
|
|
|
62
|
|
|
|
|
|
|
sys sub { |
|
63
|
|
|
|
|
|
|
|
|
64
|
|
|
|
|
|
|
##find out if cutadapt is actually installed |
|
65
|
|
|
|
|
|
|
my $cmd = `pipx environment`; |
|
66
|
|
|
|
|
|
|
$cmd = `cutadapt --help`; |
|
67
|
|
|
|
|
|
|
my $is_cutadapt_installed = $cmd =~ /\Acutadapt\s+version\s+[0-9.]+/; |
|
68
|
|
|
|
|
|
|
|
|
69
|
|
|
|
|
|
|
## if cutadapt is not installed, install it via pipx |
|
70
|
|
|
|
|
|
|
unless ($is_cutadapt_installed) { |
|
71
|
|
|
|
|
|
|
system 'pipx install cutadapt'; |
|
72
|
|
|
|
|
|
|
} |
|
73
|
|
|
|
|
|
|
|
|
74
|
|
|
|
|
|
|
}; |
|
75
|
|
|
|
|
|
|
|
|
76
|
|
|
|
|
|
|
gather sub { |
|
77
|
|
|
|
|
|
|
my ($build) = @_; |
|
78
|
|
|
|
|
|
|
$build->runtime_prop->{command}= 'cutadapt'; |
|
79
|
|
|
|
|
|
|
}; |
|
80
|
|
|
|
|
|
|
1; |