{bio} [intel/2017a] Trinity 2.5.1 #5451
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| description = """Trinity represents a novel method for the efficient and robust de novo reconstruction | ||
| of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, | ||
| Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" | ||
| toolchain = {'name': 'intel', 'version': '2017a'} |
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please include an empty line above
| Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" | ||
| toolchain = {'name': 'intel', 'version': '2017a'} | ||
| toolchainopts = {'optarch': True} | ||
| preinstallopts = "JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF8 " |
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This should be moved down, below the dependencies block (with an empty line above).
Maybe also include a comment why this is needed?
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This option did not work, I forgot to remove it. I had to set it in the easyblock file, see
easybuilders/easybuild-easyblocks#1302
| patches = [ | ||
| 'chrysalis_commandline_noconsts_2012-10-05.patch', | ||
| 'Trinity-2.5.1_plugins-Makefile.patch', | ||
| 'Trinity-2.5.1_icpc.patch', |
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please avoid hardcoding 2.5.1 here, use %(version)s instead
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| builddependencies = [ | ||
| ('Autotools', '20150215', '', ('GCCcore', '6.3.0')), |
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there should be no need to hardcode the toolchain, just use ('Autotools', '20150215')?
| ] | ||
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| dependencies = [ | ||
| ('Java', '1.8.0_121', '', True), |
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The latest ant-compatible version of Java is 1.8.0_144
| Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" | ||
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| toolchain = {'name': 'intel', 'version': '2017a'} | ||
| toolchainopts = {'optarch': True} |
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@smoors Please remove this line, optarch is already enabled by default.
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| dependencies = [ | ||
| ('Java', '1.8.0_144', '', True), |
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Use latest 1.8.0_152?
You will need to include an ant easyconfig that uses it (make that latest ant version too).
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Test report by @boegel |
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Test report by @boegel |
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Going in, thanks @smoors! |
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