bio-gemma-wrapper 0.99.1 → 0.99.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9ddfd904e74beebe0de1b97732d872fce171732965a835b101b9cc9be815bb05
-  data.tar.gz: 2dae1c019da23f2f87216694d641fc1eb852aa7800557bd10cfb08cb3425e844
+  metadata.gz: e27a8a3abb00b758095df5956b3854674faf5ff681a93bc028df273c40125c0d
+  data.tar.gz: e9675dbb0ea0f087dd21774635d38f3cda11b46a88b36c77dd308086fd0ec5f2
 SHA512:
-  metadata.gz: 38454a3f12dab85bef711051e73e20a015fe6b6d9c71bafada2197b9aef1aa0eabe3f3709cb0dc9d0c39f4cc454c15bc4d3aea5d06140ccde72fa13aa6285f51
-  data.tar.gz: 28e77a6995893245c501e602d488b5e0c504549fa91d8c94f902591b87b4454fe9b7923667dfacae2ab1dac7f6f7d814df1ec036b2b4f616dfd4b84c549d35d1
+  metadata.gz: 81cf5440fa531d5a831efa787800c8bea230d47cddc666a31fff066551ff347708a41ddf1368c0d3946c7ba9faef8e5882e398ad340850253c53961cce96f662
+  data.tar.gz: 582ae78c48a1eb8eeca01172eaeaba9d5ca23e69601967e334f8c218e3a4dd74b297861b01ce49b1357798b49a96c12e737100dcacec7fc34b70da1fc9c75f0d

data/VERSION

@@ -1 +1 @@
-0.99.1
+0.99.2

data/bin/gemma-wrapper

@@ -41,7 +41,7 @@ Gemma gets used from the path. You can override by setting
 "
 # These are used for testing compatibility with the gemma tool
 GEMMA_V_MAJOR = 98
-GEMMA_V_MINOR = 1
+GEMMA_V_MINOR = 4
 
 basepath = File.dirname(File.dirname(__FILE__))
 $: << File.join(basepath,'lib')
@@ -239,6 +239,8 @@ DO_COMPUTE_GWA = !DO_COMPUTE_KINSHIP
 # ---- Set up parallel
 if options[:parallel]
   begin
+    skip_cite = `echo "will cite" |parallel --citation`
+    debug.call(skip_cite)
     PARALLEL_INFO = `parallel --help`
   rescue Errno::ENOENT
     error.call "<parallel> command not found"
@@ -256,7 +258,6 @@ if DO_COMPUTE_GWA and options[:permute_phenotypes]
   raise "Did not expect GEMMA -p phenotype whith permutations (only use --permutate-phenotypes)" if pheno_idx
 end
 
-
 execute = lambda { |cmd|
   info.call("Executing: #{cmd}")
   err = 0
@@ -276,14 +277,6 @@ execute = lambda { |cmd|
   err
 }
 
-hashme =
-  if DO_COMPUTE_KINSHIP and pheno_idx != nil
-    # Remove the phenotype file from the hash for GRM computation
-    gemma_args[0..pheno_idx-1] + gemma_args[pheno_idx+2..-1]
-  else
-    gemma_args
-  end
-
 compute_hash = lambda do | phenofn = nil |
   # Compute a HASH on the inputs
   debug.call "Hashing on ",hashme,"\n"
@@ -302,6 +295,7 @@ compute_hash = lambda do | phenofn = nil |
       hashes << item
     end
   end
+  debug.call(hashes)
   Digest::SHA1.hexdigest hashes.join(' ')
 end
 
@@ -311,12 +305,23 @@ options[:hash] = HASH
 # Create cache dir
 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 << options[:cache_dir]
+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|
@@ -326,7 +331,7 @@ invoke_gemma = lambda do |extra_args, cache_hit = false, chr = "full", permutati
   if options[:slurm]
     info.call cmd
     hashi = HASH
-    prefix = options[:cache_dir]+'/'+hashi
+    prefix = tmpdir+'/'+hashi
     scriptfn  = prefix+".#{chr}.#{permutation}-pbs.sh"
     script = "#!/bin/bash
 #SBATCH --job-name=gemma-#{scriptfn}
@@ -371,6 +376,7 @@ srun #{cmd}
   end
 end
 
+# Takes the hash value and checks whether the (output) file exists
 # returns datafn, logfn, cache_hit
 cache = lambda do | chr, ext, h=HASH, permutation=0 |
   inject = (chr==nil ? "" : ".#{chr}" )+ext
@@ -517,3 +523,17 @@ if options[:parallel]
   info.call("Run successful!")
 end
 json_out.call
+
+# copy all output files to the cache_dir. If a file exists only emit a warning
+Dir.glob("*.txt", base: tmpdir) do | fn |
+  source = tmpdir + "/" + fn
+  dest = options[:cache_dir] + "/" + fn
+  if not File.exist?(dest) or options[:force]
+    info.call "Move #{source} to #{dest}"
+    FileUtils.mv source, dest, verbose: false
+  else
+    warning.call "File #{dest} already exists. Not overwriting"
+  end
+end
+
+end # tmpdir

data/gemma-wrapper.gemspec

@@ -2,7 +2,7 @@ Gem::Specification.new do |s|
   s.name        = 'bio-gemma-wrapper'
   s.version     = File.read('VERSION')
   s.summary     = "GEMMA with LOCO and permutations"
-  s.description = "GEMMA wrapper adds LOCO and permutation support. Also caches K between runs with LOCO support"
+  s.description = "GEMMA wrapper adds LOCO and permutation support. Also runs in parallel and caches K between runs with LOCO support"
   s.authors     = ["Pjotr Prins"]
   s.email       = 'pjotr.public01@thebird.nl'
   s.files       = ["bin/gemma-wrapper",

metadata

@@ -1,17 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: bio-gemma-wrapper
 version: !ruby/object:Gem::Version
-  version: 0.99.1
+  version: 0.99.2
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-07-11 00:00:00.000000000 Z
+date: 2021-08-08 00:00:00.000000000 Z
 dependencies: []
-description: GEMMA wrapper adds LOCO and permutation support. Also caches K between
-  runs with LOCO support
+description: GEMMA wrapper adds LOCO and permutation support. Also runs in parallel
+  and caches K between runs with LOCO support
 email: pjotr.public01@thebird.nl
 executables:
 - gemma-wrapper
@@ -43,8 +43,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.6.2
+rubygems_version: 3.2.5
 signing_key: 
 specification_version: 4
 summary: GEMMA with LOCO and permutations