{bio} [Celera Assembler aka Whole-Genome Shotgun Assembler ] (REVIEW) #960
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| # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild | ||
| # Author: Pablo Escobar Lopez | ||
| # Swiss Institute of Bioinformatics | ||
| # Biozentrum - University of Basel | ||
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| easyblock = 'MakeCp' | ||
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| name = 'Celera_Assembler' | ||
| version = '8.1' | ||
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| homepage = 'http://wgs-assembler.sourceforge.net/' | ||
| description = """ Celera Assembler is a de novo whole-genome shotgun (WGS) DNA | ||
| sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary | ||
| data produced by whole-genome shotgun sequencing. """ | ||
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| toolchain = {'name': 'goolf', 'version': '1.4.10'} | ||
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| source_urls = [('http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-%(version)s/', 'download')] | ||
| sources = ['wgs-%(version)s.tar.bz2'] | ||
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| dependencies = [('bzip2', '1.0.6')] | ||
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| parallel = 1 | ||
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| premakeopts = 'cd kmer && make install && cd .. && ' | ||
| premakeopts += 'cd samtools && make && cd .. && ' | ||
| premakeopts += 'cd src && ' | ||
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| files_to_copy = ["Linux-amd64/*"] | ||
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| sanity_check_paths = { | ||
| 'files': ["bin/%s" % x for x in ["bogus", "convert-fasta-to-v2.pl", "fastqAnalyze", "markUniqueUnique", | ||
| "pacBioToCA", "uidclient"]], | ||
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There was a problem hiding this comment. There are Perl scripts in there, why not add a Perl dependency here? There was a problem hiding this comment. I don't think adding perl as dependency makes any difference. Anyway I can add it if you prefer it... There was a problem hiding this comment. Hmm at least patch that to There was a problem hiding this comment. +1 on making sure |
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| 'dirs': ["lib"], | ||
| } | ||
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| moduleclass = 'bio' | ||
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There was a problem hiding this comment. @pescobar: remove empty line and address other comments |
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I know that CA uses some bioinformatics packages that are partially already in EB and they ship their own versions. I wonder what is more intuitive for the user?
The CA scripts have hard coded relative paths to use the internal versions of things like SAMtools, so this would be some additional work to make the external tools, that are already on the system as provided by EB, available. Would stick with how it is now. Just wanted to mention it.
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My first approach was to try to define kmer and samtools as depencies but the Makefiles for Celera Assembler looks for samtools libs in it's source folder. I tought that compiling it like the developers suggest is easier than patching the makefiles.
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I agree, disregard my previous comment!