seqtrimnext 2.0.32 → 2.0.33
Sign up to get free protection for your applications and to get access to all the features.
- data/History.txt +4 -0
- data/bin/seqtrimnext +7 -0
- data/lib/seqtrimnext/classes/seqtrim.rb +3 -2
- data/lib/seqtrimnext.rb +1 -1
- metadata +2 -2
data/History.txt
CHANGED
data/bin/seqtrimnext
CHANGED
@@ -63,6 +63,12 @@ require 'seqtrimnext'
|
|
63
63
|
############ PATHS #######################
|
64
64
|
$SEQTRIM_PATH = ROOT_PATH
|
65
65
|
|
66
|
+
if ENV['SEQTRIMNEXT_INIT'] && File.exists?(ENV['SEQTRIMNEXT_INIT'])
|
67
|
+
$SEQTRIMNEXT_INIT=File.expand_path(ENV['SEQTRIMNEXT_INIT'])
|
68
|
+
else
|
69
|
+
$SEQTRIMNEXT_INIT=File.join($SEQTRIM_PATH,'init_env')
|
70
|
+
end
|
71
|
+
|
66
72
|
# if there is a BLASTDB environment var, then use it
|
67
73
|
if ENV['BLASTDB']# && Dir.exists?(ENV['BLASTDB'])
|
68
74
|
$FORMATTED_DB_PATH = ENV['BLASTDB']
|
@@ -332,6 +338,7 @@ if (!File.exists?(options[:template]))
|
|
332
338
|
exit
|
333
339
|
end
|
334
340
|
end
|
341
|
+
$LOG.info "Using init file: #{$SEQTRIMNEXT_INIT}"
|
335
342
|
$LOG.info "Using params file: #{options[:template]}"
|
336
343
|
|
337
344
|
# fastq file
|
@@ -232,7 +232,7 @@ class Seqtrim
|
|
232
232
|
#execute cd-hit
|
233
233
|
if params.get_param('remove_clonality')=='true'
|
234
234
|
|
235
|
-
cmd=get_cd_hit_cmd(cd_hit_input_file,workers
|
235
|
+
cmd=get_cd_hit_cmd(cd_hit_input_file,workers,$SEQTRIMNEXT_INIT)
|
236
236
|
|
237
237
|
$LOG.info "Executing cd-hit-454: #{cmd}"
|
238
238
|
|
@@ -301,7 +301,8 @@ class Seqtrim
|
|
301
301
|
|
302
302
|
# launch processor server passing the ip, port and all required params
|
303
303
|
# server = Server.new(ip,port, workers, SeqtrimWorkManager,custom_worker_file, STDOUT,File.join($SEQTRIM_PATH,'init_env'))
|
304
|
-
|
304
|
+
# server = ScbiMapreduce::Manager.new(ip,port, workers, SeqtrimWorkManager,custom_worker_file, STDOUT,'~/.seqtrimnext')
|
305
|
+
server = ScbiMapreduce::Manager.new(ip,port, workers, SeqtrimWorkManager,custom_worker_file, STDOUT,$SEQTRIMNEXT_INIT)
|
305
306
|
server.chunk_size=chunk_size
|
306
307
|
server.start_server
|
307
308
|
|
data/lib/seqtrimnext.rb
CHANGED
metadata
CHANGED
@@ -2,7 +2,7 @@
|
|
2
2
|
name: seqtrimnext
|
3
3
|
version: !ruby/object:Gem::Version
|
4
4
|
prerelease:
|
5
|
-
version: 2.0.
|
5
|
+
version: 2.0.33
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
8
8
|
- Dario Guerrero & Almudena Bocinos
|
@@ -10,7 +10,7 @@ autorequire:
|
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
12
|
|
13
|
-
date: 2011-06-
|
13
|
+
date: 2011-06-17 00:00:00 Z
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
16
16
|
name: narray
|