miga-base 0.5.3.0 → 0.5.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d51a2778df35e38e9396c342db79907aa8b63019e33d62f08a745664c01fc14b
-  data.tar.gz: 2e553ce8b5fc59aee8aa74f5262d34175c19bbf52c41efa6817353e8e20dbff5
+  metadata.gz: d7b5a581810fbc79f9808fea7353882960f26f005ff9cc37ccad7483db96f1a4
+  data.tar.gz: dc4d7163c3b6a396e0ca71325d2cb995001b65a467305c918bfc810e161ddae7
 SHA512:
-  metadata.gz: 0c2ebed3117669c8dce789d731dd478a9eaf8dd8ca9a14e89cf1692908264bca6541073407f7d922a3f72e1edd47d5128275a391b5acc798687edb6302d0b66d
-  data.tar.gz: 64f0d0fc5af1bca2a3d2fb3ad3a79fdb31a91c95ef346e2cd2b89cc4342a0189ee7a814adae6b7cf5b80b5ce4a80e99cd1196c71afe1138f769fd0f0d91cf3d7
+  metadata.gz: 71e0e8fa7a6e10ac0396a7e19580e66cd8561979234ffb565c0727e02e9050fd04b94c416d56ce35c8b4c618eeb69fb781d52914df26182c01a295b8481cfad9
+  data.tar.gz: 359ad12300c7a1aa14b3f66a2bef2d875c24ea689ab66f1f16990f35618ec03b3126f849039ffcb5ef0a0f52c328eaa5e81edf0bc862aa78104652a9cf73216a

data/lib/miga/cli/action/run.rb

@@ -12,8 +12,17 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
       cli.opt_object(opt, [:project, :dataset_opt, :result])
       opt.on(
         '-t', '--threads INT', Integer,
-        "Threads to use in the local run (by default: #{cli[:thr]})."
-        ){ |v| cli[:thr] = v }
+        "Threads to use in the local run (by default: #{cli[:thr]})"
+      ) { |v| cli[:thr] = v }
+      opt.on(
+        '-R', '--remote STR',
+        'Description of remote SSH node to launch the job, as "user@hostname"',
+        'By default, the job is executed locally'
+      ) { |v| cli[:remote] = v }
+      opt.on(
+        '-l', '--log PATH',
+        'Path to the output log file to be created. If not set, STDOUT'
+      ) { |v| cli[:log] = v }
     end
   end
 
@@ -21,18 +30,23 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
     virtual_task = false
     miga = MiGA.root_path
     p = cli.load_project
-    cmd = ["PROJECT=#{p.path.shellescape}", 'RUNTYPE=bash',
+    
+    cmd = ["PROJECT=#{p.path.shellescape}",
+      "RUNTYPE=#{cli[:remote] ? 'ssh' : 'bash'}",
       "MIGA=#{miga.shellescape}", "CORES=#{cli[:thr]}"]
-
     obj = cli.load_project_or_dataset
     klass = obj.class
     virtual_task = true if [:p, :d].include? cli[:result]
     cmd << "DATASET=#{obj.name.shellescape}" if obj.is_a? MiGA::Dataset
-
     if klass.RESULT_DIRS[cli[:result]].nil? and not virtual_task
-      raise "Unsupported #{klass.to_s.gsub(/.*::/, '')} result: #{cli[:result]}."
+      raise "Unsupported #{klass.to_s.sub(/.*::/, '')} result: #{cli[:result]}."
     end
     cmd << MiGA.script_path(cli[:result], miga: miga, project: p).shellescape
+    if cli[:remote]
+      cmd.unshift '.', '/etc/profile', ';'
+      cmd = ['ssh', cli[:remote].shellescape, cmd.join(' ').shellescape]
+    end
+    cmd << ['&>', cli[:log].shellescape] if cli[:log]
     pid = spawn cmd.join(' ')
     Process.wait pid
   end

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.5, 3, 0]
+  VERSION = [0.5, 4, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 1, 11)
+  VERSION_DATE = Date.new(2020, 1, 22)
 
   ##
   # Reference of MiGA.

data/scripts/cds.bash

@@ -46,7 +46,7 @@ case "$TYPE" in
         rm "$DATASET".*."$ct"
       fi
     done
-    echo "# Selected table: $BEST_CT"
+    echo "Selected codon table: $BEST_CT"
     ;;
 esac
 

data/scripts/miga.bash

@@ -1,8 +1,9 @@
 #!/bin/bash
 set -e
 #MIGA=${MIGA:-$(cd "$(dirname "$0")/.."; pwd)}
+MIGA_HOME=${MIGA_HOME:-"$HOME"}
 # shellcheck source=/dev/null
-. "$HOME/.miga_rc"
+. "$MIGA_HOME/.miga_rc"
 export PATH="$MIGA/bin:$MIGA/utils/enveomics/Scripts:$PATH"
 SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
 
@@ -15,7 +16,9 @@ for i in $(miga plugins -P "$PROJECT") ; do
 done
 
 if [[ "$SCRIPT" != "d" && "$SCRIPT" != "p" ]] ; then
+  echo '############'
   echo -n "Date: " ; miga date
+  echo "Hostname: $(hostname)"
   echo "MiGA: $MIGA"
   echo "Task: $SCRIPT"
   echo "Project: $PROJECT"
@@ -23,6 +26,7 @@ if [[ "$SCRIPT" != "d" && "$SCRIPT" != "p" ]] ; then
     echo "Dataset: $DATASET"
     miga edit -P "$PROJECT" -D "$DATASET" -m "_step=$SCRIPT"
   fi
+  echo '------------'
 fi
 
 true

data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl

@@ -1 +1 @@
-../../Scripts/FastA.N50.pl
+utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.N50.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl

@@ -1 +1 @@
-../../Scripts/FastA.filterN.pl
+utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.filterN.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl

@@ -1 +1 @@
-../../Scripts/FastA.length.pl
+utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.length.pl

data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl

@@ -1 +1 @@
-../../Scripts/FastA.split.pl
+utils/enveomics/Pipelines/blast.pbs/../../Scripts/FastA.split.pl

data/utils/enveomics/Scripts/lib/enveomics.R

@@ -1 +1 @@
-../../enveomics.R
+utils/enveomics/Scripts/lib/../../enveomics.R

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.5.3.0
+  version: 0.5.4.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-01-11 00:00:00.000000000 Z
+date: 2020-01-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -515,7 +515,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubyforge_project: 
+rubygems_version: 2.7.6
 signing_key: 
 specification_version: 4
 summary: MiGA