rbbt-util 5.25.14 → 5.25.15
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +2 -1
- data/lib/rbbt/resource/util.rb +20 -7
- data/share/install/software/lib/install_helpers +2 -1
- metadata +2 -3
- data/share/install/software/HTSLIB +0 -6
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 84ee8220e10055644029255ec78f3650d9cbb43c
|
4
|
+
data.tar.gz: 7709e99accf8b271dd67b684643490f29b629aa6
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5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 6d9b3a82a19ddf6a305816aa0c1c74c5bb4c25285fa229defb0dc7f3d6c03a95302f594d132123b33e7fa2fe800f630015173fcb86f0ce8d76e72fab703de5d7
|
7
|
+
data.tar.gz: 189622da3a2235075c903abe9d6a06ec2f307697083b8626e1ed35c34c2a22b0f7a6d9ee3786bb2f54d8e3f996e901dd78a1424490f0f1fde3e2f965529a74c4
|
data/lib/rbbt/hpc.rb
CHANGED
@@ -263,7 +263,8 @@ EOF
|
|
263
263
|
if File.exists?(fout)
|
264
264
|
return
|
265
265
|
elsif dry_run
|
266
|
-
STDERR.puts Log.color(:magenta, "To execute run: sbatch '#{workdir}/command.slurm'")
|
266
|
+
STDERR.puts Log.color(:magenta, "To execute run: ") + Log.color(:blue, "sbatch '#{workdir}/command.slurm'")
|
267
|
+
STDERR.puts Log.color(:magenta, "To monitor progress run (needs local rbbt): ") + Log.color(:blue, "rbbt mn --tail -w '#{workdir}'")
|
267
268
|
raise Marenostrum::SBATCH, workdir
|
268
269
|
else
|
269
270
|
Open.rm fsync
|
data/lib/rbbt/resource/util.rb
CHANGED
@@ -33,6 +33,7 @@ module Resource
|
|
33
33
|
def set_software_env(software_dir)
|
34
34
|
software_dir.find_all.each do |software_dir|
|
35
35
|
next unless software_dir.exists?
|
36
|
+
software_dir = File.expand_path(software_dir)
|
36
37
|
bin_dir = File.join(software_dir, 'bin')
|
37
38
|
opt_dir = File.join(software_dir, 'opt')
|
38
39
|
|
@@ -50,28 +51,40 @@ module Resource
|
|
50
51
|
end
|
51
52
|
|
52
53
|
Open.read(File.join opt_dir, '.c-paths').split(/\n/).each do |line|
|
53
|
-
|
54
|
+
dir = line.chomp
|
55
|
+
dir = File.join(opt_dir, dir) unless dir[0] == "/"
|
56
|
+
Misc.env_add('C_INCLULDE_PATH',dir)
|
54
57
|
end if File.exist? File.join(opt_dir, '.c-paths')
|
55
58
|
|
56
59
|
Open.read(File.join opt_dir, '.ld-paths').split(/\n/).each do |line|
|
57
|
-
|
58
|
-
|
60
|
+
dir = line.chomp
|
61
|
+
dir = File.join(opt_dir, dir) unless dir[0] == "/"
|
62
|
+
Misc.env_add('LD_LIBRARY_PATH',dir)
|
63
|
+
Misc.env_add('LD_RUN_PATH',dir)
|
59
64
|
end if File.exist? File.join(opt_dir, '.ld-paths')
|
60
65
|
|
61
66
|
Open.read(File.join opt_dir, '.pkgconfig-paths').split(/\n/).each do |line|
|
62
|
-
|
67
|
+
dir = line.chomp
|
68
|
+
dir = File.join(opt_dir, dir) unless dir[0] == "/"
|
69
|
+
Misc.env_add('PKG_CONFIG_PATH',dir)
|
63
70
|
end if File.exist? File.join(opt_dir, '.pkgconfig-paths')
|
64
71
|
|
65
72
|
Open.read(File.join opt_dir, '.aclocal-paths').split(/\n/).each do |line|
|
66
|
-
|
73
|
+
dir = line.chomp
|
74
|
+
dir = File.join(opt_dir, dir) unless dir[0] == "/"
|
75
|
+
Misc.env_add('ACLOCAL_FLAGS', "-I #{dir}", ' ')
|
67
76
|
end if File.exist? File.join(opt_dir, '.aclocal-paths')
|
68
77
|
|
69
78
|
Open.read(File.join opt_dir, '.java-classpaths').split(/\n/).each do |line|
|
70
|
-
|
79
|
+
dir = line.chomp
|
80
|
+
dir = File.join(opt_dir, dir) unless dir[0] == "/"
|
81
|
+
Misc.env_add('CLASSPATH', "#{dir}")
|
71
82
|
end if File.exist? File.join(opt_dir, '.java-classpaths')
|
72
83
|
|
73
84
|
Dir.glob(File.join opt_dir, 'jars', '*').each do |file|
|
74
|
-
|
85
|
+
dir = line.chomp
|
86
|
+
dir = File.join(opt_dir, dir) unless dir[0] == "/"
|
87
|
+
Misc.env_add('CLASSPATH', "#{dir}")
|
75
88
|
end
|
76
89
|
|
77
90
|
if File.exist?(File.join(opt_dir, '.post_install')) and File.directory?(File.join(opt_dir, '.post_install'))
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.25.
|
4
|
+
version: 5.25.15
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2019-01-
|
11
|
+
date: 2019-01-09 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -333,7 +333,6 @@ files:
|
|
333
333
|
- share/color/color_names
|
334
334
|
- share/color/diverging_colors.hex
|
335
335
|
- share/config.ru
|
336
|
-
- share/install/software/HTSLIB
|
337
336
|
- share/install/software/lib/install_helpers
|
338
337
|
- share/rbbt_commands/alias
|
339
338
|
- share/rbbt_commands/app/install
|