bacterial-annotator 1.0.0 → 1.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (11) hide show
  1. checksums.yaml +4 -4
  2. data/bin/ba_cdhit +1 -1
  3. data/bin/ba_diamond +1 -2
  4. data/bin/ba_fasta36 +1 -1
  5. data/bin/ba_fasttree +1 -1
  6. data/bin/ba_mafft +1 -1
  7. data/bin/ba_mash +1 -1
  8. data/bin/ba_prodigal +1 -1
  9. data/bin/ba_raxml +1 -1
  10. data/bin/ba_trnascan +2 -2
  11. metadata +3 -3
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA256:
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- metadata.gz: 1dad9c41b499dc463758390648f19af38b55a660e0ac408303fca0383bbf9463
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- data.tar.gz: 3d58da07ceced3fabba23a685d8f7b25e0bddc511cd690a5e6b4e24666ad3c89
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+ metadata.gz: 7355a51394c598b6f53b033eb6889918961a6a6f85004f64887852adc76e2a6a
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+ data.tar.gz: cfbaa022c31eedbd16d2f66127d3c7c652fc8fe512f63e416c132aaadf3bb029
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  SHA512:
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- metadata.gz: d860ebf490024dad6ec9a28c8b68a21cc8447b347236cff9938ebc372244fdcc3f414bb9f2280fa58bded32e221a5614d6b5d1e9e681837d8f8948c4a20dc3c2
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- data.tar.gz: 7ad1c1444c156679632129799120b303055e90316baceb2c17f3441afa58298aeaf7840f1bdc5989bb2931452cd76a26e723ed54a602d41f73efc781b23f5215
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+ metadata.gz: 65a929fffcdabfaba9771fbc50a02205773e6f59bea6acfb98f12bdf6b4ff0e26e4be0ec1a5521cb51f68e21276d6555de4ce900872823e3c90987c00c17afd1
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+ data.tar.gz: ad1f6f48a49a9319184ae02c612f294cd735b7fc28f0721b7f4b30aabf57de31a184b87527927593b7ae4bbe814024dbbeccbfa91135b69f5052021039fe0882
data/bin/ba_cdhit CHANGED
@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
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  def installcdhit
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  begin
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- resp = open("https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz")
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+ resp = URI.open("https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz")
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  open("#{ROOT_path}/cdhit-4.6.8.tar.gz", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_diamond CHANGED
@@ -14,9 +14,8 @@ ROOT_path = File.dirname(__FILE__)
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  # Install diamond on the user system
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  def installDiamond
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-
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  begin
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- resp = open("https://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz")
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+ resp = URI.open("https://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz")
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  open("#{ROOT_path}/diamond-linux64.tar.gz", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_fasta36 CHANGED
@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
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  def installFasta36
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  begin
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- resp = open("https://github.com/wrpearson/fasta36/releases/download/fasta-v36.3.8g/fasta-36.3.8g-linux64.tar.gz")
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+ resp = URI.open("https://github.com/wrpearson/fasta36/releases/download/fasta-v36.3.8g/fasta-36.3.8g-linux64.tar.gz")
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  open("#{ROOT_path}/fasta-36.3.8g-linux64.tar.gz", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_fasttree CHANGED
@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
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  def installFastTree
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  begin
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- resp = open("http://www.microbesonline.org/fasttree/FastTreeMP")
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+ resp = URI.open("http://www.microbesonline.org/fasttree/FastTreeMP")
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  open("#{ROOT_path}/fasttree.linux", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_mafft CHANGED
@@ -15,7 +15,7 @@ ROOT_path = File.dirname(__FILE__)
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  def installMafft
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  begin
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- resp = open("https://mafft.cbrc.jp/alignment/software/mafft-7.222-without-extensions-src.tgz")
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+ resp = URI.open("https://mafft.cbrc.jp/alignment/software/mafft-7.222-without-extensions-src.tgz")
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  open("#{ROOT_path}/mafft-7.222-without-extensions-src.tgz", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_mash CHANGED
@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
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  def installMash
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  begin
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- resp = open("https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar")
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+ resp = URI.open("https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar")
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  open("#{ROOT_path}/mash.tar", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_prodigal CHANGED
@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
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  def installProdigal
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  begin
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- resp = open("https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz")
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+ resp = URI.open("https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz")
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  open("#{ROOT_path}/v2.6.2.tar.gz", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_raxml CHANGED
@@ -15,7 +15,7 @@ ROOT_path = File.dirname(__FILE__)
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  def installRaxml
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  begin
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- resp = open("https://github.com/stamatak/standard-RAxML/archive/v8.2.11.zip")
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+ resp = URI.open("https://github.com/stamatak/standard-RAxML/archive/v8.2.11.zip")
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  open("#{ROOT_path}/master.zip", "wb") do |file|
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  file.write(resp.read)
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  end
data/bin/ba_trnascan CHANGED
@@ -18,7 +18,7 @@ def installTrnascan
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  begin
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  # infernal as dependencies
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- resp = open("http://eddylab.org/infernal/infernal-1.1.2.tar.gz")
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+ resp = URI.open("http://eddylab.org/infernal/infernal-1.1.2.tar.gz")
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  open("#{ROOT_path}/infernal-1.1.2.tar.gz", "wb") do |file|
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  file.write(resp.read)
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  end
@@ -27,7 +27,7 @@ def installTrnascan
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  `cd infernal-1.1.2 && ./configure --prefix=#{ROOT_path}/infernal-1.1.2/build && make && make install`
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  # trnascan-se
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- resp = open("http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz")
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+ resp = URI.open("http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz")
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  open("#{ROOT_path}/trnascan-se-2.0.0.tar.gz", "wb") do |file|
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  file.write(resp.read)
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: bacterial-annotator
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  version: !ruby/object:Gem::Version
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- version: 1.0.0
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+ version: 1.0.1
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  platform: ruby
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  authors:
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  - Maxime Deraspe
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2024-01-13 00:00:00.000000000 Z
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+ date: 2025-01-06 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio
@@ -125,7 +125,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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- rubygems_version: 3.1.6
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+ rubygems_version: 3.3.3
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  signing_key:
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  specification_version: 4
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  summary: Bacterial Annotator