seqtrimnext 2.0.32 → 2.0.33

data/History.txt

@@ -1,3 +1,7 @@
+=== 2.0.33 2011-06-17
+
+Added SEQTRIMNEXT_INIT environment variable
+
 === 2.0.32 2011-06-15
 
 Minor adjustements to work with INGEBIOL

data/bin/seqtrimnext

@@ -63,6 +63,12 @@ require 'seqtrimnext'
 ############ PATHS #######################
 $SEQTRIM_PATH = ROOT_PATH
 
+if ENV['SEQTRIMNEXT_INIT'] && File.exists?(ENV['SEQTRIMNEXT_INIT'])
+  $SEQTRIMNEXT_INIT=File.expand_path(ENV['SEQTRIMNEXT_INIT'])
+else
+  $SEQTRIMNEXT_INIT=File.join($SEQTRIM_PATH,'init_env')
+end
+
 # if there is a BLASTDB environment var, then use it
 if ENV['BLASTDB']# && Dir.exists?(ENV['BLASTDB'])
   $FORMATTED_DB_PATH = ENV['BLASTDB']
@@ -332,6 +338,7 @@ if (!File.exists?(options[:template]))
     exit
   end
 end
+$LOG.info "Using init file: #{$SEQTRIMNEXT_INIT}"
 $LOG.info "Using params file: #{options[:template]}"
 
 # fastq file

data/lib/seqtrimnext/classes/seqtrim.rb

@@ -232,7 +232,7 @@ class Seqtrim
       #execute cd-hit
       if params.get_param('remove_clonality')=='true'
         
-        cmd=get_cd_hit_cmd(cd_hit_input_file,workers,File.join($SEQTRIM_PATH,'init_env'))
+        cmd=get_cd_hit_cmd(cd_hit_input_file,workers,$SEQTRIMNEXT_INIT)
         
         $LOG.info "Executing cd-hit-454: #{cmd}"
         
@@ -301,7 +301,8 @@ class Seqtrim
 				
 				# launch processor server passing the ip, port and all required params
         # server = Server.new(ip,port, workers, SeqtrimWorkManager,custom_worker_file, STDOUT,File.join($SEQTRIM_PATH,'init_env'))
-				server = ScbiMapreduce::Manager.new(ip,port, workers, SeqtrimWorkManager,custom_worker_file, STDOUT,'~/.seqtrimnext')
+        # server = ScbiMapreduce::Manager.new(ip,port, workers, SeqtrimWorkManager,custom_worker_file, STDOUT,'~/.seqtrimnext')
+				server = ScbiMapreduce::Manager.new(ip,port, workers, SeqtrimWorkManager,custom_worker_file, STDOUT,$SEQTRIMNEXT_INIT)
 				server.chunk_size=chunk_size
 				server.start_server
         

data/lib/seqtrimnext.rb

@@ -30,7 +30,7 @@ module Seqtrimnext
   # SEQTRIM_VERSION_STAGE = 'b'
   # SEQTRIM_VERSION = "2.0.0#{SEQTRIM_VERSION_STAGE}#{SEQTRIM_VERSION_REVISION}"
   
-   VERSION = '2.0.32'
+   VERSION = '2.0.33'
   
   SEQTRIM_VERSION = VERSION
   

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 2.0.32
+  version: 2.0.33
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-06-15 00:00:00 Z
+date: 2011-06-17 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray