From bb9c48c7f173322f333f39b9ec4d2dd76bd7ce4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <afsverissimo@gmail.com>
Date: Thu, 20 Oct 2016 18:51:47 +0100
Subject: [PATCH] defaults to 2 process and corrects some validations

---
 config/config_blast.rb  | 6 +++---
 config/default.yml      | 7 ++++++-
 test/blastn/config.yml  | 2 ++
 test/tblastn/config.yml | 2 ++
 test/tblastx/config.yml | 2 ++
 user.yml                | 2 +-
 6 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/config/config_blast.rb b/config/config_blast.rb
index e993248..3f53e98 100644
--- a/config/config_blast.rb
+++ b/config/config_blast.rb
@@ -273,9 +273,9 @@ def validate_config
                                  'db_and_queries', String,
                                  'Should be the query parent directory')
       if !@store.query.key?('folders') || !@store.query.folders.is_a?(Array)
-        log_required_sub.call('folders', 'query.list', '\n    - (folder name)')
-      else @store.query.folders.size == 0
-        log_required_sub.call('folders', 'query.list', '\n    - (at least one folder name)')
+        log_required_sub.call('folders', 'query.folders', '\n    - (folder name)')
+      elsif @store.query.folders.size == 0
+        log_required_sub.call('folders', 'query.folders', '\n    - (at least one folder name)')
       end
     end
     #
diff --git a/config/default.yml b/config/default.yml
index 50a41fe..80b93e3 100644
--- a/config/default.yml
+++ b/config/default.yml
@@ -35,8 +35,13 @@ prune_identical:
 #
 #
 # output directory options:
-#  - dir: output directory's name
 #  - ext: extension for blast files
+#  - dir: corresponds to the directory's name and path where will be stored the results. By default, it is set to “output".
+#  - extension: extension for blast files, by default “.out”.
+#  - intermediate: corresponds to the directory’s name where will be saved all the intermediate files generated by MassBlast.
+#  - blast_results: corresponds to the directory’s name where will be saved all the Blast results generated by Blast+.
+#  - fastas: corresponds to the directory’s name where will be saved all the fasta files generated by MassBlast.
+#
 output:
   dir: output
   extension: .out
diff --git a/test/blastn/config.yml b/test/blastn/config.yml
index 4f62337..661087c 100644
--- a/test/blastn/config.yml
+++ b/test/blastn/config.yml
@@ -26,6 +26,8 @@ use_threads: 1
 debug:
   file: ../../output/log.blastn_rspec.txt
   show_stdout_if_file: false
+
+annotation_dir: ../../db_and_queries/annotation
 #
 #
 # Opts are engine specific, the default in user.yml
diff --git a/test/tblastn/config.yml b/test/tblastn/config.yml
index 58ed9e3..4117c95 100644
--- a/test/tblastn/config.yml
+++ b/test/tblastn/config.yml
@@ -26,6 +26,8 @@ use_threads: 1
 debug:
   file: ../../output/log.tblastn_rspec.txt
   show_stdout_if_file: false
+
+annotation_dir: ../../db_and_queries/annotation
 #
 #
 # Opts are engine specific, the default in user.yml
diff --git a/test/tblastx/config.yml b/test/tblastx/config.yml
index d03931a..fa46a95 100644
--- a/test/tblastx/config.yml
+++ b/test/tblastx/config.yml
@@ -26,6 +26,8 @@ use_threads: 1
 debug:
   file: ../../output/log.tblastx_rspec.txt
   show_stdout_if_file: false
+
+annotation_dir: ../../db_and_queries/annotation
 #
 #
 # Opts are engine specific, the default in user.yml
diff --git a/user.yml b/user.yml
index ac46b34..aad0a78 100644
--- a/user.yml
+++ b/user.yml
@@ -16,7 +16,7 @@ separate_db: true
 #
 # number of threads to use
 #  only valid with separate_db option
-use_threads: 1
+use_threads: 2
 #
 # path to debugging file, change it in respect to user.yml
 debug: