{bio}[intel/2017a] dammit 0.3.2 /w Python 2.7.13 (REVIEW)#5125
{bio}[intel/2017a] dammit 0.3.2 /w Python 2.7.13 (REVIEW)#5125boegel merged 15 commits intoeasybuilders:developfrom
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| homepage = 'http://matplotlib.org' | ||
| description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of | ||
| hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python | ||
| and ipython shell, web application servers, and six graphical user interface toolkits.""" |
| ('crb-blast', '0.6.9', '-Ruby-2.3.4'), | ||
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| is that LAST finds initial matches based on their multiplicity, | ||
| instead of using a fixed length (e.g. BLAST uses 11-mers).""" | ||
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| toolchain = {'name': 'GCCcore', 'version': '6.3.0'} |
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hmm, wouldn't intel make more sense here, for performance reasons?
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@boegel Good question, I am afraid of intel compiler in biostuff.
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| name = 'dammit' | ||
| version = '0.3.2' | ||
| versionsuffix = '-Python-%(pyver)s' |
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Either include Python, Perl & Ruby in the versionsuffix, or none of them...
Since the versionsuffix would become very long here, I consider it OK to just drop it here as an exception to our rule of including Python/Perl version in there...
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@boegel I included Python, because dammit is actually written in Python. It have deps needs Ruby and Perl. Anyway, I will drop all of them.
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Well, OK, in that case I guess it makes sense to keep it.
Python is definitely way more common than Perl or Ruby, so it kind of makes sense to make only that one explicit in the versionsuffix...
hajgato
changed the title
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Apparently BUSCO needs Python3 |
hajgato
changed the title
| 'checksums': ['6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705'], | ||
| }), | ||
| (name, version, { | ||
| 'patches': ['dammit-0.3.2_nodocs.patch', 'dammit-0.3.2_py2busco.diff'], |
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@hajgato Please rename dammit-0.3.2_py2busco.diff to dammit-0.3.2_py2busco.patch, and include one patch per line:
'patches': [
'dammit-0.3.2_nodocs.patch',
'dammit-0.3.2_py2busco.patch',
],| instead of using a fixed length (e.g. BLAST uses 11-mers).""" | ||
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| toolchain = {'name': 'intel', 'version': '2017a'} | ||
| toolchainopts = {'cstd': 'c++11', 'opt': True} |
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@hajgato Why the 'opt': True (which enables using -O3 rather than -O2), any particular reason for this?
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@boegel: taken form last-869/makefile, line 1:
CXXFLAGS = -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
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OK so you're trying to mimic this behaviour, I see.
In general, -O3 is less "safe" than -O2 though (in terms of precision, etc.).
And the benefit is usually fairly small.
| sources = ['%(namelower)s-%(version)s.zip'] | ||
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| patches = ['%(name)s-%(version)s_makefile.patch'] | ||
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please drop this empty line, and the one above as well
| 'b7b697b048e22c913eb196449eb895fc70b22fb72db5cca1f8dc948cde164309', # LAST-869_makefile.patch | ||
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| builddependencies = [('binutils', '2.27')] |
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this is not needed when using a full toolchain like intel, it's already included
| 'doc', | ||
| 'examples', | ||
| 'README.txt', | ||
| 'src', |
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@boegel: some executables in the src dir, dammit directly calls some of those (for example src/last-split and others, I do not remember specifically.)
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| easyblock = 'MakeCp' | |||
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We have an existing easyconfig for LAST (for a more recent version) which uses ConfigureMake and does make install prefix=%(installdir)s.
But maybe that's not supported yet with this older version of LAST?
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@boegel: this version has only a simple makefile, no configure provided.
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Which is exactly why we skip the configure step in the existing LAST easyconfig, see https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/l/LAST/LAST-914-intel-2017b.eb .
| source_urls = ['http://last.cbrc.jp/'] | ||
| sources = ['%(namelower)s-%(version)s.zip'] | ||
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| patches = ['%(name)s-%(version)s_makefile.patch'] |
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There should be no need for a patch, in the existing easyconfig for LAST we use:
buildopts = 'CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS -pthread -DHAS_CXX_THREADS"'There was a problem hiding this comment.
@boegel: CC, CXX, CFLAGS, and CXXFLAGS hard encoded in last-869/src/makefile, lines 1-9:
CXX = g++
CC = gcc
CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \
-Wcast-align -pedantic -g -std=c++11 -pthread -DHAS_CXX_THREADS
# -Wconversion
# -fomit-frame-pointer ?
CFLAGS = -Wall -O2
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Even with a makefile like this, you can override values by passing arguments to make, like we do in the existing LAST easyconfig...
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| source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/'] | ||
| sources = ['v%(version)s.tar.gz'] | ||
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style nitpicking: please drop empty line
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| sanity_check_paths = { | ||
| 'files': ['TransDecoder.%s' % x for x in ['Predict', 'LongOrfs']], |
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no need to use a list comprehension here:
'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'],
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Test report by @boegel |
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Test report by @boegel |
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Going in, thanks @hajgato! |
2 participants
Needs
#5119#5120#5121 #5122 #5123 #5124I would also like to discuss the naming conventions in the PR and the dep PRs, I want clearly avoid suffix
-Ruby-2.3.4-Perl-5.24.1-Python-2.7.13...