genevalidatorapp 2.1.2 → 2.1.3
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- checksums.yaml +4 -4
- data/.travis.yml +14 -4
- data/lib/genevalidatorapp/exceptions.rb +16 -6
- data/lib/genevalidatorapp/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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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: 750d842e8248a3e7998399088e76e7feedbbe670b034fb628f187c8b6a4ae540
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4
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+
data.tar.gz: de9835d6c0bfb2da7ffb9125d65c4bf829cb64d09e6be26af76109ec781a59c4
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5
5
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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: 457a297ebd41a808d81e9c3122bc2aa407a42ba211a95c1a710aaa32b0e6652dc4ea234ef67aaf09353d31a5b8666b791f1d2400239478bbb104bb48edd455ba
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7
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+
data.tar.gz: 1675b6ba5484c879189be7d49f1491b1177216f70cdc4204de1db24b35c335f254fd28af1191a342f6312946734a86de25f4fda16392b44a5ea88b9112d175d3
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data/.travis.yml
CHANGED
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@@ -5,7 +5,17 @@ rvm:
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5
5
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- "2.4.4"
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6
6
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- "2.5.1"
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7
7
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before_install:
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8
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-
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9
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-
-
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10
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-
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11
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-
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8
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# Install MAFFT
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9
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- mkdir dependencies
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10
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- mkdir dependencies/mafft
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11
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- curl -L --fail https://mafft.cbrc.jp/alignment/software/mafft-7.397-linux.tgz | tar -xzf - --strip-components=1 -C dependencies/mafft
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12
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+
- MAFFT_DIR="$PWD/dependencies/mafft/mafftdir"
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13
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- MAFFT_BINARIES="${MAFFT_DIR}/libexec"; export MAFFT_BINARIES;
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14
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# BLAST
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15
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- mkdir dependencies/blast
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16
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- curl -L --fail https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz | tar -xzf - --strip-components=1 -C dependencies/blast
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17
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+
- BLAST_BIN="$PWD/dependencies/blast/bin"
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18
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- export PATH=${MAFFT_DIR}/bin:${BLAST_BIN}:$PATH
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19
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# add GV as a dependency
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20
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- echo "gem 'genevalidator'" >> Gemfile
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21
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script: bundle exec rake test
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@@ -81,9 +81,19 @@ MSG
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81
81
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end
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82
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end
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83
83
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84
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+
## MAFFT NOT INSTALLED OR NOT COMPATIBLE ##
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85
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+
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86
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# Raised if GV could not locate MAFFT binaries on
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87
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# user's system.
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88
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+
class MAFFT_NOT_INSTALLED < StandardError
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89
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def to_s
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90
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'Could not locate MAFFT binaries.'
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91
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end
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92
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end
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93
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+
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84
94
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## BLAST NOT INSTALLED OR NOT COMPATIBLE ##
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85
95
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86
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-
# Raised if
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96
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# Raised if GV could not locate NCBI BLAST+ installation on
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87
97
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# user's system.
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88
98
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class BLAST_NOT_INSTALLED < StandardError
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89
99
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def to_s
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@@ -91,7 +101,7 @@ MSG
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91
101
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end
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92
102
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end
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93
103
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94
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-
# Raised if
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104
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# Raised if GV could not successfully execute 'blastp -version'
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95
105
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# on user's system (see #141).
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96
106
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class BLAST_NOT_EXECUTABLE < StandardError
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97
107
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def to_s
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@@ -99,8 +109,8 @@ MSG
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99
109
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end
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100
110
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end
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101
111
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102
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-
# Raised if
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103
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-
# system but not meeting
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112
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+
# Raised if GV determined NCBI BLAST+ present on the user's
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113
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# system but not meeting GV's minimum version requirement.
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104
114
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class BLAST_NOT_COMPATIBLE < StandardError
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105
115
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def initialize(version)
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106
116
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@version = version
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@@ -111,7 +121,7 @@ MSG
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111
121
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def to_s
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112
122
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<<MSG
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113
123
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Your BLAST+ version #{version} is outdated.
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114
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-
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124
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+
GV needs NCBI BLAST+ version #{MINIMUM_BLAST_VERSION} or higher.
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115
125
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MSG
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116
126
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end
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117
127
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end
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@@ -167,7 +177,7 @@ Tried: #{cmd}
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167
177
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Error:
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168
178
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#{out.strip}
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169
179
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170
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-
Please could you report this to 'https://groups.google.com/forum/#!forum/
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180
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+
Please could you report this to 'https://groups.google.com/forum/#!forum/GV'?
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171
181
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MSG
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172
182
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end
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173
183
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end
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