miga-base 1.0.5.3 → 1.1.1.0

data/lib/miga/daemon.rb

@@ -231,10 +231,11 @@ class MiGA::Daemon < MiGA::MiGA
   # Construct the command for the given job definition with current
   # daemon settings
   def job_cmd(to_run)
+    what = to_run[:ds].nil? ? :project : :dataset
     vars = {
       'PROJECT' => project.path,
-      'RUNTYPE' => runopts(:type),
-      'CORES' => ppn,
+      'RUNTYPE' => runopts_for(:type, what),
+      'CORES' => ppn(what),
       'MIGA' => MiGA::MiGA.root_path
     }
     vars['DATASET'] = to_run[:ds].name unless to_run[:ds].nil?
@@ -246,13 +247,13 @@ class MiGA::Daemon < MiGA::MiGA
               ),
       vars: vars.map do |k, v|
               runopts(:var).miga_variables(key: k, value: v)
-            end.join(runopts(:varsep)),
-      cpus: ppn,
+            end.join(runopts_for(:varsep, what)),
+      cpus: ppn(what),
       log: File.join(log_dir, "#{to_run[:ds_name]}.log"),
       task_name: to_run[:task_name],
       miga: File.join(MiGA::MiGA.root_path, 'bin/miga').shellescape
     }
-    runopts(:cmd).miga_variables(var_hsh)
+    runopts_for(:cmd, what).miga_variables(var_hsh)
   end
 
   ##

data/lib/miga/dataset/result.rb

@@ -281,7 +281,8 @@ module MiGA::Dataset::Result
       collection: '.ess',
       report: '.ess/log',
       alignments: '.ess/proteins.aln',
-      fastaai_index: '.faix.db.gz'
+      fastaai_index: '.faix.db.gz',
+      fastaai_index_2: '.faix'
     )
   end
 

data/lib/miga/version.rb

@@ -12,15 +12,15 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.0, 5, 3].freeze
+  VERSION = [1.1, 1, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
   VERSION_NAME = 'prima'
 
   ##
-  # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 9, 14)
+  # Date of the current gem relese.
+  VERSION_DATE = Date.new(2021, 10, 29)
 
   ##
   # References of MiGA

data/scripts/essential_genes.bash

@@ -36,19 +36,15 @@ HMM.essential.rb \
   > "${DATASET}.ess/log"
 
 # Index for FastAAI
-NOMULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --no-multi \
+NOMULTI=$(miga ls -P "$PROJECT" -D "$DATASET" --no-multi \
             | wc -l | awk '{print $1}')
 if [[ "$NOMULTI" -eq "1" ]] ; then
-  if [[ "$FAA" == *.gz ]] ; then
-    gzip -cd "$FAA" > "${DATASET}.faix"
-  else
-    cp "$FAA" "${DATASET}.faix"
-  fi
-  FastAAI --qp "${DATASET}.faix" --output "${DATASET}.faix" \
-    --ext ".faix" --index --input-paths --all-vs-all --threads "$CORES"
-  rm "${DATASET}.faix"
-  rm "${DATASET}.faix.hmm"
-  rm "${DATASET}.faix.hmm.filt"
+  echo "$FAA" > "$DATASET"
+  FastAAI build_db --protein_file "$DATASET" \
+    -o "${DATASET}.faix.d" --threads "$CORES"
+  rm "$DATASET"
+  mv "${DATASET}.faix.d/database/FastAAI_database.sqlite.db" "${DATASET}.faix"
+  rm -r "${DATASET}.faix.d"
 fi
 
 # Reduce files

data/scripts/miga.bash

@@ -3,9 +3,7 @@
 ###
 # Setup environment
 set -e
-MIGA_MOD="${MIGA_HOME:-"$HOME"}/.miga_modules"
-[[ -s "$MIGA_MOD" ]] && . "$MIGA_MOD"
-eval "$("$MIGA/bin/miga" env)"
+eval "$("$MIGA/bin/miga-env")"
 SCRIPT=${SCRIPT:-"$(basename "$0" .bash)"}
 
 ###

data/test/common_test.rb

@@ -78,21 +78,21 @@ class CommonTest < Test::Unit::TestCase
 
     # Check advance when missing total
     o = capture_stderr { m.advance('x', 0) }.string
-    assert_match(/\] x *\r/, o)
+    assert_match(%r{\] x *\r}, o)
 
     # Initialize advance
-    o = capture_stderr { m.advance('x', 0, 10) }.string
-    assert_match(/\] x 0\.0% \(0\/10\) *\r/, o)
+    o = capture_stderr { m.advance('x', 0, 1001) }.string
+    assert_match(%r{\] x 0\.0% \(0/1001\) *\r}, o)
 
     # Insufficient data for prediction
     sleep(1)
-    o = capture_stderr { m.advance('x', 1, 10) }.string
-    assert_match(/\] x 10\.0% \(1\/10\) *\r/, o)
+    o = capture_stderr { m.advance('x', 1, 1000) }.string
+    assert_match(%r{\] x 0\.1% \(1/1000\) *\r}, o)
 
     # Predict time
     sleep(1)
-    o = capture_stderr { m.advance('x', 2, 10) }.string
-    assert_match(/\] x 20\.0% \(2\/10\) [7-9]s left *\r/, o)
+    o = capture_stderr { m.advance('x', 2, 1000) }.string
+    assert_match(%r{\] x 0\.2% \(2/1000\) 1\d\.\dm left *\r}, o)
   end
 
   def test_num_suffix