bacterial-annotator 0.8.0 → 0.8.1
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.
- checksums.yaml +4 -4
- data/bin/ba_trnascan +57 -0
- data/bin/bacterial-annotator +1 -0
- metadata +4 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
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---
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SHA1:
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-
metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: 3db94963e7c81c71fd28b372bcdc9cf6271b635b
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4
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data.tar.gz: 077d431814bf5a44e6c74fb000869c11e8b087ab
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SHA512:
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6
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metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: fb06e7960a775911f0a701105f7f49b68862cdb98d6f9fd29d05a5940b476f88495ac721fb32f3b87cce557e44c08fe21c0f59140d6e81da692f729f5bb63c3d
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7
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data.tar.gz: ec3edcb9bcb68880b428d07a0cb33e13d8e12b7132dc244bfd3b2b59fca3d07b600d5a55c7e0b931c6d0aeb6b65e3e791e9d81e44cb57f2e4c2a793452be5ffe
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data/bin/ba_trnascan
ADDED
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@@ -0,0 +1,57 @@
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#!/usr/bin/env ruby
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# -*- coding: utf-8 -*-
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# author: maxime déraspe
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# email: maximilien1er@gmail.com
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# review:
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# date: 18-05-22
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# version: 0.01
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# licence:
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require 'open-uri'
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ROOT_path = File.dirname(__FILE__)
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# trnascan URL = "http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz"
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# infernal URL = "http://eddylab.org/infernal/infernal-1.1.2.tar.gz"
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# Install trnascan on the user system
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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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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
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Dir.chdir("#{ROOT_path}/")
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`tar xvf infernal-1.1.2.tar.gz && rm infernal-1.1.2.tar.gz`
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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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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
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Dir.chdir("#{ROOT_path}/")
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`tar xvf trnascan-se-2.0.0.tar.gz; rm trnascan-se-2.0.0.tar.gz`
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`cd tRNAscan-SE-2.0/ && ./configure --prefix=#{ROOT_path}/tRNAscan-SE-2.0/build && make && make install && cd build/bin && ln -s #{ROOT_path}/infernal-1.1.2/build/bin/ .`
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`cp #{ROOT_path}/tRNAscan-SE-2.0/build/bin/tRNAscan-SE #{ROOT_path}/trnascan.linux`
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File.chmod(0755, "#{ROOT_path}/trnascan.linux")
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rescue
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abort "Problem installing tRNAscan-SE, aborting"
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end
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end
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# Install trnascan if not already install
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if ! File.exists? "#{ROOT_path}/trnascan.linux"
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puts "Installing tRNAscan-SE tRNA finder.."
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puts "See http://lowelab.ucsc.edu/tRNAscan-SE/"
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puts "The Licence is BSD"
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installTrnascan
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puts "Trnascan successfully installed in #{ROOT_path}/trnascan.linux"
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puts ""
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end
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data/bin/bacterial-annotator
CHANGED
metadata
CHANGED
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@@ -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: 0.8.
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version: 0.8.1
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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: 2018-
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date: 2018-05-22 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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@@ -84,6 +84,7 @@ executables:
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- ba_cdhit
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- ba_fasttree
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- ba_mash
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- ba_trnascan
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extensions: []
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extra_rdoc_files: []
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files:
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@@ -96,6 +97,7 @@ files:
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- bin/ba_mash
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- bin/ba_prodigal
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- bin/ba_raxml
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- bin/ba_trnascan
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- bin/bacterial-annotator
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- lib/bacterial-annotator.rb
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- lib/bacterial-annotator/sequence-annotation.rb
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