bacterial-annotator 1.0.0 → 1.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1dad9c41b499dc463758390648f19af38b55a660e0ac408303fca0383bbf9463
-  data.tar.gz: 3d58da07ceced3fabba23a685d8f7b25e0bddc511cd690a5e6b4e24666ad3c89
+  metadata.gz: 7355a51394c598b6f53b033eb6889918961a6a6f85004f64887852adc76e2a6a
+  data.tar.gz: cfbaa022c31eedbd16d2f66127d3c7c652fc8fe512f63e416c132aaadf3bb029
 SHA512:
-  metadata.gz: d860ebf490024dad6ec9a28c8b68a21cc8447b347236cff9938ebc372244fdcc3f414bb9f2280fa58bded32e221a5614d6b5d1e9e681837d8f8948c4a20dc3c2
-  data.tar.gz: 7ad1c1444c156679632129799120b303055e90316baceb2c17f3441afa58298aeaf7840f1bdc5989bb2931452cd76a26e723ed54a602d41f73efc781b23f5215
+  metadata.gz: 65a929fffcdabfaba9771fbc50a02205773e6f59bea6acfb98f12bdf6b4ff0e26e4be0ec1a5521cb51f68e21276d6555de4ce900872823e3c90987c00c17afd1
+  data.tar.gz: ad1f6f48a49a9319184ae02c612f294cd735b7fc28f0721b7f4b30aabf57de31a184b87527927593b7ae4bbe814024dbbeccbfa91135b69f5052021039fe0882

data/bin/ba_cdhit

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installcdhit
 
   begin
-    resp = open("https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz")
+    resp = URI.open("https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz")
     open("#{ROOT_path}/cdhit-4.6.8.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_diamond

@@ -14,9 +14,8 @@ ROOT_path = File.dirname(__FILE__)
 
 # Install diamond on the user system
 def installDiamond
-
   begin
-    resp = open("https://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz")
+    resp = URI.open("https://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz")
     open("#{ROOT_path}/diamond-linux64.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_fasta36

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installFasta36
 
   begin
-    resp = open("https://github.com/wrpearson/fasta36/releases/download/fasta-v36.3.8g/fasta-36.3.8g-linux64.tar.gz")
+    resp = URI.open("https://github.com/wrpearson/fasta36/releases/download/fasta-v36.3.8g/fasta-36.3.8g-linux64.tar.gz")
     open("#{ROOT_path}/fasta-36.3.8g-linux64.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_fasttree

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installFastTree
 
   begin
-    resp = open("http://www.microbesonline.org/fasttree/FastTreeMP")
+    resp = URI.open("http://www.microbesonline.org/fasttree/FastTreeMP")
     open("#{ROOT_path}/fasttree.linux", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_mafft

@@ -15,7 +15,7 @@ ROOT_path = File.dirname(__FILE__)
 def installMafft
 
   begin
-    resp = open("https://mafft.cbrc.jp/alignment/software/mafft-7.222-without-extensions-src.tgz")
+    resp = URI.open("https://mafft.cbrc.jp/alignment/software/mafft-7.222-without-extensions-src.tgz")
     open("#{ROOT_path}/mafft-7.222-without-extensions-src.tgz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_mash

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installMash
 
   begin
-    resp = open("https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar")
+    resp = URI.open("https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar")
     open("#{ROOT_path}/mash.tar", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_prodigal

@@ -16,7 +16,7 @@ ROOT_path = File.dirname(__FILE__)
 def installProdigal
 
   begin
-    resp = open("https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz")
+    resp = URI.open("https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz")
     open("#{ROOT_path}/v2.6.2.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_raxml

@@ -15,7 +15,7 @@ ROOT_path = File.dirname(__FILE__)
 def installRaxml
 
   begin
-    resp = open("https://github.com/stamatak/standard-RAxML/archive/v8.2.11.zip")
+    resp = URI.open("https://github.com/stamatak/standard-RAxML/archive/v8.2.11.zip")
     open("#{ROOT_path}/master.zip", "wb") do |file|
       file.write(resp.read)
     end

data/bin/ba_trnascan

@@ -18,7 +18,7 @@ def installTrnascan
   begin
 
     # infernal as dependencies
-    resp = open("http://eddylab.org/infernal/infernal-1.1.2.tar.gz")
+    resp = URI.open("http://eddylab.org/infernal/infernal-1.1.2.tar.gz")
     open("#{ROOT_path}/infernal-1.1.2.tar.gz", "wb") do |file|
       file.write(resp.read)
     end
@@ -27,7 +27,7 @@ def installTrnascan
     `cd infernal-1.1.2 && ./configure --prefix=#{ROOT_path}/infernal-1.1.2/build && make && make install`
 
     # trnascan-se
-    resp = open("http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz")
+    resp = URI.open("http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz")
     open("#{ROOT_path}/trnascan-se-2.0.0.tar.gz", "wb") do |file|
       file.write(resp.read)
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-01-13 00:00:00.000000000 Z
+date: 2025-01-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -125,7 +125,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.6
+rubygems_version: 3.3.3
 signing_key:
 specification_version: 4
 summary: Bacterial Annotator