bio-gemma-wrapper 0.99.5 → 0.99.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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+  metadata.gz: 69d74ac5f1a705132d7ddc86bd1182c11fc37cf32062dbb28909f16684a827cb
+  data.tar.gz: 6f912b3c03474c1334a105d6c9471c02d39c205e94b0d07e5281718beec65ee7
 SHA512:
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+  data.tar.gz: 43f7a7438f475583930e6cf1f50d34206fba7674b3df836791cf7064bd7ca55dddc2cc101f7c5a89d8042645b6dd06245b84d3b38501bc1eab7d18774703a01a

data/VERSION

@@ -1 +1 @@
-0.99.5
+0.99.6

data/bin/gemma-wrapper

@@ -4,7 +4,7 @@
 # Author:: Pjotr Prins
 # License:: GPL3
 #
-# Copyright (C) 2017-2021 Pjotr Prins <pjotr.prins@thebird.nl>
+# Copyright (C) 2017-2022 Pjotr Prins <pjotr.prins@thebird.nl>
 
 USAGE = "
 GEMMA wrapper example:
@@ -64,6 +64,7 @@ if not gemma_command
   end
 end
 
+hashme = nil
 
 require 'digest/sha1'
 require 'fileutils'
@@ -214,13 +215,13 @@ end
 # ---- Start banner
 
 GEMMA_K_VERSION=version
-GEMMA_K_BANNER = "gemma-wrapper #{version} (Ruby #{RUBY_VERSION}) by Pjotr Prins 2017-2021\n"
+GEMMA_K_BANNER = "gemma-wrapper #{version} (Ruby #{RUBY_VERSION}) by Pjotr Prins 2017-2022\n"
 info.call GEMMA_K_BANNER
 
 # Check gemma version
 begin
   gemma_command2 = options[:gemma_command]
-  info.call "NOTE: gemma-wrapper is soon to be replaced by gemma2/lib"
+  info.call "NOTE: gemma-wrapper is soon to be replaced"
 
   GEMMA_INFO = `#{gemma_command2}`
 rescue Errno::ENOENT
@@ -279,7 +280,6 @@ raise "Expected GEMMA -a genotype file switch" if anno_idx == nil
 CHROMOSOMES = get_chromosomes(gemma_args[anno_idx+1])
 
 # ---- Compute HASH on inputs
-hashme = []
 geno_idx = gemma_args.index '-g'
 raise "Expected GEMMA -g genotype file switch" if geno_idx == nil
 pheno_idx = gemma_args.index '-p'
@@ -309,14 +309,15 @@ execute = lambda { |cmd|
 
 compute_hash = lambda do | phenofn = nil |
   # Compute a HASH on the inputs
-  debug.call "Hashing on ",hashme,"\n"
+  error.call "Hash is empty" if hashme == nil or hashme == []
+  debug.call "Hashing on ",hashme," before phenofn inject"
   hashes = []
   hm = if phenofn
          hashme + ["-p", phenofn]
        else
          hashme
        end
-  debug.call(hm)
+  debug.call("Hashing on ",hm)
   hm.each do | item |
     if File.file?(item)
       hashes << Digest::SHA1.hexdigest(File.read(item))
@@ -329,6 +330,18 @@ compute_hash = lambda do | phenofn = nil |
   Digest::SHA1.hexdigest hashes.join(' ')
 end
 
+error.call "Do not use the GEMMA -o switch!" if gemma_args.include? '-o'
+error.call "Do not use the GEMMA -outdir switch!" if gemma_args.include? '-outdir'
+GEMMA_ARGS_HASH = gemma_args.dup # do not include outdir
+
+hashme =
+  if DO_COMPUTE_KINSHIP and pheno_idx != nil
+    # Remove the phenotype file from the hash for GRM computation
+    GEMMA_ARGS_HASH[0..pheno_idx-1] + GEMMA_ARGS_HASH[pheno_idx+2..-1]
+  else
+    GEMMA_ARGS_HASH
+  end
+
 HASH = compute_hash.call()
 options[:hash] = HASH
 
@@ -345,21 +358,10 @@ FileUtils::mkdir_p options[:cache_dir]
 
 Dir.mktmpdir do |tmpdir| # tmpdir for GEMMA output
 
-error.call "Do not use the GEMMA -o switch!" if gemma_args.include? '-o'
-error.call "Do not use the GEMMA -outdir switch!" if gemma_args.include? '-outdir'
-GEMMA_ARGS_HASH = gemma_args.dup # do not include outdir
 gemma_args << '-outdir'
 gemma_args << tmpdir
 GEMMA_ARGS = gemma_args
 
-hashme =
-  if DO_COMPUTE_KINSHIP and pheno_idx != nil
-    # Remove the phenotype file from the hash for GRM computation
-    GEMMA_ARGS_HASH[0..pheno_idx-1] + GEMMA_ARGS_HASH[pheno_idx+2..-1]
-  else
-    GEMMA_ARGS_HASH
-  end
-
 debug.call "Options: ",options,"\n" if !options[:quiet]
 
 invoke_gemma = lambda do |extra_args, cache_hit = false, chr = "full", permutation = 1|
@@ -560,22 +562,30 @@ end
 # ---- Invoke parallel
 if options[:parallel]
   # parallel_cmds = ["echo 1","sleep 1 && echo 2", "false", "echo 3"]
-  cmd = parallel_cmds.join("\\n")
-
-  cmd = "echo -e \"#{cmd}\""
-  err = execute.call(cmd+"|parallel --joblog #{joblog}") # first try optimistically to run all jobs in parallel
-  if err != 0
-    [16,8,4,1].each do |jobs|
-      info.call("Failed to complete parallel run -- retrying with smaller RAM footprint!")
-      err = execute.call(cmd+"|parallel -j #{jobs} --resume --joblog #{joblog}")
-      break if err == 0
+
+  Tempfile.open("commands.txt") do |f|
+    cmdfn = f.path
+    File.open(cmdfn,"w") do |f|
+      parallel_cmds.each do |c|
+        f.puts(c)
+      end
     end
+    cmd = "cat \"#{cmdfn}\""
+    err = execute.call(cmd+"|parallel --joblog #{joblog}") # first try optimistically to run all jobs in parallel
     if err != 0
-      info.call("Run failed!")
-      # Remove remaining files
-      FileUtils.rm_rf("#{tmpdir}/*", secure: true)
-      FileUtils.mv joblog, joblog+".bak", verbose: false, force: true
-      exit err
+      [16,8,4,1].each do |jobs|
+        info.call("Failed to complete parallel run -- retrying with smaller RAM footprint!")
+        err = execute.call(cmd+"|parallel -j #{jobs} --resume --joblog #{joblog}")
+        break if err == 0
+      end
+      if err != 0
+        info.call("Parallel run failed!")
+        debug.call("Job log is: ",File.read(joblog))
+        # Remove remaining files
+        FileUtils.mv joblog, joblog+".bak", verbose: false, force: true
+        FileUtils.rm_rf("#{tmpdir}/*", secure: true)
+        exit err
+      end
     end
   end
   info.call("Run successful!")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gemma-wrapper
 version: !ruby/object:Gem::Version
-  version: 0.99.5
+  version: 0.99.6
 platform: ruby
 authors:
 - Pjotr Prins
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-11-26 00:00:00.000000000 Z
+date: 2022-01-22 00:00:00.000000000 Z
 dependencies: []
 description: GEMMA wrapper adds LOCO and permutation support. Also runs in parallel
   and caches K between runs with LOCO support
@@ -29,7 +29,7 @@ homepage: https://github.com/genetics-statistics/gemma-wrapper
 licenses:
 - GPL3
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -44,8 +44,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
-signing_key: 
+rubygems_version: 3.2.22
+signing_key:
 specification_version: 4
 summary: GEMMA with LOCO and permutations
 test_files: []