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add Java 1.8 easyconfig that can be updated in-place to more recent JDK 1.8.x #6712

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Merged
bartoldeman merged 13 commits into from
Sep 21, 2018
Merged

add Java 1.8 easyconfig that can be updated in-place to more recent JDK 1.8.x #6712

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ae25239
add Java 1.8 easyconfig that can be updated in-place to more recent J…
boegel Aug 16, 2018
d9dc60a
use Java 1.8 wrapper as dependency for Bazel 0.16.0
boegel Aug 16, 2018
1ed65a5
switch to using Java/1.8 wrapper as dependency for R 3.5.1
boegel Aug 18, 2018
daca40e
rename Java/1.8 to Java/8
boegel Aug 18, 2018
34a8db1
Merge branch 'develop' into java18
boegel Aug 23, 2018
34da312
change Java easyconfig meant to be updated in-place to non-wrapper ap…
boegel Aug 23, 2018
cfdc6f3
use ModulesRC easyblock to make Java/1.8 a wrapper for Java/1.8.0_181
boegel Sep 14, 2018
a61233b
make exception for Java wrapper in dep variant check in easyconfig tests
boegel Sep 14, 2018
362a1fe
Merge branch 'develop' into java18
boegel Sep 18, 2018
a71fc4c
also use Java/1.8 wrapper in GATK easyconfig using foss/2018b
boegel Sep 14, 2018
7f31f88
Merge branch 'develop' into java18
boegel Sep 18, 2018
350acf7
also use Java/1.8 wrapper in other GATK easyconfig using foss/2018b
boegel Sep 18, 2018
82cc18f
fix exception for Java wrapper in dep variants test
boegel Sep 19, 2018
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb
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Expand Up @@ -16,6 +16,6 @@ checksums = [
]

builddependencies = [('binutils', '2.30')]
dependencies = [('Java', '1.8.0_172', '', True)]
dependencies = [('Java', '1.8', '', True)]

moduleclass = 'devel'
2 changes: 1 addition & 1 deletion easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb
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Expand Up @@ -35,7 +35,7 @@ checksums = ['e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9']

dependencies = [
('Python', '2.7.15'),
('Java', '1.8.0_181', '', True),
('Java', '1.8', '', True),
]

modextrapaths = {'PATH': ''}
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb
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Expand Up @@ -35,7 +35,7 @@ checksums = ['e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9']

dependencies = [
('Python', '3.6.6'),
('Java', '1.8.0_181', '', True),
('Java', '1.8', '', True),
]

modextrapaths = {'PATH': ''}
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14 changes: 14 additions & 0 deletions easybuild/easyconfigs/j/Java/Java-1.8.eb
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@@ -0,0 +1,14 @@
easyblock = 'ModuleRC'

name = 'Java'
version = '1.8'

homepage = 'http://java.com/'
description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
Java applications on desktops and servers."""

toolchain = {'name': 'dummy', 'version': 'dummy'}

dependencies = [('Java', '%(version)s.0_181')]

moduleclass = 'lang'
2 changes: 1 addition & 1 deletion easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb
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Expand Up @@ -28,7 +28,7 @@ dependencies = [
('libpng', '1.6.34'), # for plotting in R
('libjpeg-turbo', '2.0.0'), # for plottting in R
('LibTIFF', '4.0.9'),
('Java', '1.8.0_181', '', True),
('Java', '1.8', '', True),
('Tk', '8.6.8'), # for tcltk
('cURL', '7.60.0'), # for RCurl
('libxml2', '2.9.8'), # for XML
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10 changes: 10 additions & 0 deletions test/easyconfigs/easyconfigs.py
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Expand Up @@ -207,6 +207,16 @@ def check_dep_vars(dep, dep_vars):
if len(dep_vars) == 1:
break

# filter out Java 'wrapper'
# i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181)
elif dep == 'Java' and len(dep_vars) == 2:
key1, key2 = sorted(dep_vars.keys())
ver1, ver2 = [k.split(';')[0] for k in [key1, key2]]
if ver1.startswith(ver2):
dep_vars.pop(key2)
elif ver2.startswith(ver1):
dep_vars.pop(key1)

# filter out variants that are specific to a particular version of CUDA
cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v]
if len(dep_vars) > len(cuda_dep_vars):
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