Date: Sat, 12 Mar 2016 18:19:43 +0000 From: bugzilla-noreply@freebsd.org To: freebsd-ports-bugs@FreeBSD.org Subject: [Bug 207929] [NEW PORT] biology/jellyfish: Fast, memory-efficient counting of k-mers in DNA Message-ID: <bug-207929-13@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D207929 Bug ID: 207929 Summary: [NEW PORT] biology/jellyfish: Fast, memory-efficient counting of k-mers in DNA Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Some People Priority: --- Component: Individual Port(s) Assignee: freebsd-ports-bugs@FreeBSD.org Reporter: bacon4000@gmail.com Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html portlint: OK (WARN: Makefile: [43]: use ${VARIABLE}, instead of $(VARIABLE). 0 fatal errors and 1 warning found.) testport: OK (poudriere: 10.1-{amd64,i386}, 9.3-amd64) Attempted to build on 9.3-i386, but it looks like too much work. Nobody is likely to run genomics tools on i386 anyway, so I considered ONLY_FOR_ARCHS=3Damd64, but the 10.1-i386 fix was simple. --=20 You are receiving this mail because: You are the assignee for the bug.=
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