bio-gemma-wrapper 0.99.5 → 0.99.6
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bin/gemma-wrapper +41 -31
- metadata +6 -6
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 69d74ac5f1a705132d7ddc86bd1182c11fc37cf32062dbb28909f16684a827cb
|
4
|
+
data.tar.gz: 6f912b3c03474c1334a105d6c9471c02d39c205e94b0d07e5281718beec65ee7
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 35fbdf4ccfc482f6898e35b1e46e840db87f34efb35a096206ffef4a131ac8b21a4e6b7893be6ee053a59837eadba6547258d2360d796794c71a60670458943f
|
7
|
+
data.tar.gz: 43f7a7438f475583930e6cf1f50d34206fba7674b3df836791cf7064bd7ca55dddc2cc101f7c5a89d8042645b6dd06245b84d3b38501bc1eab7d18774703a01a
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.99.
|
1
|
+
0.99.6
|
data/bin/gemma-wrapper
CHANGED
@@ -4,7 +4,7 @@
|
|
4
4
|
# Author:: Pjotr Prins
|
5
5
|
# License:: GPL3
|
6
6
|
#
|
7
|
-
# Copyright (C) 2017-
|
7
|
+
# Copyright (C) 2017-2022 Pjotr Prins <pjotr.prins@thebird.nl>
|
8
8
|
|
9
9
|
USAGE = "
|
10
10
|
GEMMA wrapper example:
|
@@ -64,6 +64,7 @@ if not gemma_command
|
|
64
64
|
end
|
65
65
|
end
|
66
66
|
|
67
|
+
hashme = nil
|
67
68
|
|
68
69
|
require 'digest/sha1'
|
69
70
|
require 'fileutils'
|
@@ -214,13 +215,13 @@ end
|
|
214
215
|
# ---- Start banner
|
215
216
|
|
216
217
|
GEMMA_K_VERSION=version
|
217
|
-
GEMMA_K_BANNER = "gemma-wrapper #{version} (Ruby #{RUBY_VERSION}) by Pjotr Prins 2017-
|
218
|
+
GEMMA_K_BANNER = "gemma-wrapper #{version} (Ruby #{RUBY_VERSION}) by Pjotr Prins 2017-2022\n"
|
218
219
|
info.call GEMMA_K_BANNER
|
219
220
|
|
220
221
|
# Check gemma version
|
221
222
|
begin
|
222
223
|
gemma_command2 = options[:gemma_command]
|
223
|
-
info.call "NOTE: gemma-wrapper is soon to be replaced
|
224
|
+
info.call "NOTE: gemma-wrapper is soon to be replaced"
|
224
225
|
|
225
226
|
GEMMA_INFO = `#{gemma_command2}`
|
226
227
|
rescue Errno::ENOENT
|
@@ -279,7 +280,6 @@ raise "Expected GEMMA -a genotype file switch" if anno_idx == nil
|
|
279
280
|
CHROMOSOMES = get_chromosomes(gemma_args[anno_idx+1])
|
280
281
|
|
281
282
|
# ---- Compute HASH on inputs
|
282
|
-
hashme = []
|
283
283
|
geno_idx = gemma_args.index '-g'
|
284
284
|
raise "Expected GEMMA -g genotype file switch" if geno_idx == nil
|
285
285
|
pheno_idx = gemma_args.index '-p'
|
@@ -309,14 +309,15 @@ execute = lambda { |cmd|
|
|
309
309
|
|
310
310
|
compute_hash = lambda do | phenofn = nil |
|
311
311
|
# Compute a HASH on the inputs
|
312
|
-
|
312
|
+
error.call "Hash is empty" if hashme == nil or hashme == []
|
313
|
+
debug.call "Hashing on ",hashme," before phenofn inject"
|
313
314
|
hashes = []
|
314
315
|
hm = if phenofn
|
315
316
|
hashme + ["-p", phenofn]
|
316
317
|
else
|
317
318
|
hashme
|
318
319
|
end
|
319
|
-
debug.call(hm)
|
320
|
+
debug.call("Hashing on ",hm)
|
320
321
|
hm.each do | item |
|
321
322
|
if File.file?(item)
|
322
323
|
hashes << Digest::SHA1.hexdigest(File.read(item))
|
@@ -329,6 +330,18 @@ compute_hash = lambda do | phenofn = nil |
|
|
329
330
|
Digest::SHA1.hexdigest hashes.join(' ')
|
330
331
|
end
|
331
332
|
|
333
|
+
error.call "Do not use the GEMMA -o switch!" if gemma_args.include? '-o'
|
334
|
+
error.call "Do not use the GEMMA -outdir switch!" if gemma_args.include? '-outdir'
|
335
|
+
GEMMA_ARGS_HASH = gemma_args.dup # do not include outdir
|
336
|
+
|
337
|
+
hashme =
|
338
|
+
if DO_COMPUTE_KINSHIP and pheno_idx != nil
|
339
|
+
# Remove the phenotype file from the hash for GRM computation
|
340
|
+
GEMMA_ARGS_HASH[0..pheno_idx-1] + GEMMA_ARGS_HASH[pheno_idx+2..-1]
|
341
|
+
else
|
342
|
+
GEMMA_ARGS_HASH
|
343
|
+
end
|
344
|
+
|
332
345
|
HASH = compute_hash.call()
|
333
346
|
options[:hash] = HASH
|
334
347
|
|
@@ -345,21 +358,10 @@ FileUtils::mkdir_p options[:cache_dir]
|
|
345
358
|
|
346
359
|
Dir.mktmpdir do |tmpdir| # tmpdir for GEMMA output
|
347
360
|
|
348
|
-
error.call "Do not use the GEMMA -o switch!" if gemma_args.include? '-o'
|
349
|
-
error.call "Do not use the GEMMA -outdir switch!" if gemma_args.include? '-outdir'
|
350
|
-
GEMMA_ARGS_HASH = gemma_args.dup # do not include outdir
|
351
361
|
gemma_args << '-outdir'
|
352
362
|
gemma_args << tmpdir
|
353
363
|
GEMMA_ARGS = gemma_args
|
354
364
|
|
355
|
-
hashme =
|
356
|
-
if DO_COMPUTE_KINSHIP and pheno_idx != nil
|
357
|
-
# Remove the phenotype file from the hash for GRM computation
|
358
|
-
GEMMA_ARGS_HASH[0..pheno_idx-1] + GEMMA_ARGS_HASH[pheno_idx+2..-1]
|
359
|
-
else
|
360
|
-
GEMMA_ARGS_HASH
|
361
|
-
end
|
362
|
-
|
363
365
|
debug.call "Options: ",options,"\n" if !options[:quiet]
|
364
366
|
|
365
367
|
invoke_gemma = lambda do |extra_args, cache_hit = false, chr = "full", permutation = 1|
|
@@ -560,22 +562,30 @@ end
|
|
560
562
|
# ---- Invoke parallel
|
561
563
|
if options[:parallel]
|
562
564
|
# parallel_cmds = ["echo 1","sleep 1 && echo 2", "false", "echo 3"]
|
563
|
-
|
564
|
-
|
565
|
-
|
566
|
-
|
567
|
-
|
568
|
-
|
569
|
-
|
570
|
-
err = execute.call(cmd+"|parallel -j #{jobs} --resume --joblog #{joblog}")
|
571
|
-
break if err == 0
|
565
|
+
|
566
|
+
Tempfile.open("commands.txt") do |f|
|
567
|
+
cmdfn = f.path
|
568
|
+
File.open(cmdfn,"w") do |f|
|
569
|
+
parallel_cmds.each do |c|
|
570
|
+
f.puts(c)
|
571
|
+
end
|
572
572
|
end
|
573
|
+
cmd = "cat \"#{cmdfn}\""
|
574
|
+
err = execute.call(cmd+"|parallel --joblog #{joblog}") # first try optimistically to run all jobs in parallel
|
573
575
|
if err != 0
|
574
|
-
|
575
|
-
|
576
|
-
|
577
|
-
|
578
|
-
|
576
|
+
[16,8,4,1].each do |jobs|
|
577
|
+
info.call("Failed to complete parallel run -- retrying with smaller RAM footprint!")
|
578
|
+
err = execute.call(cmd+"|parallel -j #{jobs} --resume --joblog #{joblog}")
|
579
|
+
break if err == 0
|
580
|
+
end
|
581
|
+
if err != 0
|
582
|
+
info.call("Parallel run failed!")
|
583
|
+
debug.call("Job log is: ",File.read(joblog))
|
584
|
+
# Remove remaining files
|
585
|
+
FileUtils.mv joblog, joblog+".bak", verbose: false, force: true
|
586
|
+
FileUtils.rm_rf("#{tmpdir}/*", secure: true)
|
587
|
+
exit err
|
588
|
+
end
|
579
589
|
end
|
580
590
|
end
|
581
591
|
info.call("Run successful!")
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio-gemma-wrapper
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.99.
|
4
|
+
version: 0.99.6
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Pjotr Prins
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2022-01-22 00:00:00.000000000 Z
|
12
12
|
dependencies: []
|
13
13
|
description: GEMMA wrapper adds LOCO and permutation support. Also runs in parallel
|
14
14
|
and caches K between runs with LOCO support
|
@@ -29,7 +29,7 @@ homepage: https://github.com/genetics-statistics/gemma-wrapper
|
|
29
29
|
licenses:
|
30
30
|
- GPL3
|
31
31
|
metadata: {}
|
32
|
-
post_install_message:
|
32
|
+
post_install_message:
|
33
33
|
rdoc_options: []
|
34
34
|
require_paths:
|
35
35
|
- lib
|
@@ -44,8 +44,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
44
44
|
- !ruby/object:Gem::Version
|
45
45
|
version: '0'
|
46
46
|
requirements: []
|
47
|
-
rubygems_version: 3.
|
48
|
-
signing_key:
|
47
|
+
rubygems_version: 3.2.22
|
48
|
+
signing_key:
|
49
49
|
specification_version: 4
|
50
50
|
summary: GEMMA with LOCO and permutations
|
51
51
|
test_files: []
|