miga-base 0.4.2.0 → 0.4.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8d83a4e140647fdcfdd062c0f503e8ad5fefacef870fe5c8c3528e4edeb1e44f
-  data.tar.gz: f8248690dde4d6441658ab6f75181c4786ca7ad6d8d26fa83f195ebdef801c26
+  metadata.gz: f547a13f78444c6d3f7149bb111d3a4444af885ef085fef913c9516fac706215
+  data.tar.gz: 0ae132567bd8e677bfc7e0bafaaeb28138499b1e720302e47f711364f790f020
 SHA512:
-  metadata.gz: 36bd4f0122601175a09f3e61ef81618f8db323b41acda67c927bc9578b86ca1d9da4d714a0a02b91541a320cccbbb5b396da7ebe03c6b7f03b5ccd0880ea5953
-  data.tar.gz: 4874ebeabbebdcd0661ec8b7de879f075fd9847c921319192f3272861ed9f41c5a9954000ef60542164240d2dee8a01a2c752256d32323dc7ded0a5b50b2f099
+  metadata.gz: f174c56c991a3055d347f0450aca196e8c6f4813bb21d18f0bcaca528df40fe76e4ea497ff36d58886817d26fbcb2281459a5866260040de975022e572f6869b
+  data.tar.gz: ff4777abf6dab9bd2800e86533840817a77d01b3724ed51d9a77d0dac4ec1506ca407420b615f5e16fd3548af5b58fd56a3e922a448f2d75052d814cdb504ae3

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

@@ -61,6 +61,10 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
         '--dry',
         'Do not download or save the datasets'
         ){ |v| cli[:dry] = v }
+      opt.on(
+        '--ignore-until STRING',
+        'Ignores all datasets until a name is found (useful for large reruns)'
+        ){ |v| cli[:ignore_until] = v }
       opt.on(
         '--get-metadata',
         'Only download and update metadata for existing datasets'
@@ -177,9 +181,12 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
     # Download entries
     cli.say "Downloading #{ds.size} " + (ds.size == 1 ? 'entry' : 'entries')
     p.do_not_save = true if cli[:save_every] != 1
+    ignore = !cli[:ignore_until].nil?
     ds.each do |name, body|
       d << name
       cli.puts name
+      ignore = false if ignore && name == cli[:ignore_until]
+      next if ignore
       next if p.dataset(name).nil? == cli[:get_md]
       downloaded += 1
       next if cli[:dry]

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 = [0.4, 2, 0]
+  VERSION = [0.4, 3, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2019, 9, 8)
+  VERSION_DATE = Date.new(2019, 9, 10)
 
   ##
   # Reference of MiGA.

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: 0.4.2.0
+  version: 0.4.3.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-09-08 00:00:00.000000000 Z
+date: 2019-09-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -503,7 +503,8 @@ 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