Date: Fri, 27 Oct 2017 09:37:54 +0000 From: bugzilla-noreply@freebsd.org To: freebsd-ports-bugs@FreeBSD.org Subject: [Bug 223273] [NEW PORT] biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives Message-ID: <bug-223273-13@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D223273 Bug ID: 223273 Summary: [NEW PORT] biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: freebsd-ports-bugs@FreeBSD.org Reporter: mzaki@niid.go.jp SRA tools is a toolkit for using data in the INSDC Sequence Read Archives. SRAs operated by International Nucleotide Sequence Database Collaboration houses sequence reads and alignments generated by "next-gen" sequencers. SRA tools allows conversion of SRA files, which INSDC SRAs maintain, from/to other formats that the sequenecers generate including fastq, sff, e= tc. The source codes are available in 3 components, ngs, ncbi-vdb, and sra-tool= s, to which the ports basically correspond. biology/ngs-sdk: C++ front-end API and others (a part of GitHub repo ncbi/ngs) biology/ncbi-vdb: virtualized back-end engine library (GitHub repo ncbi/ncbi-vdb) biology/sra-tools: executables (GitHub repo ncbi/sra-tools) However, separation and dependencies among them are somewhat strange: * ncbi-vdb depends on the source code of ngs-sdk * sra-tools depends on the build results of ncbi-vdb as well as ngs-sdk lib= rary Java- and Python-related libraries are excluded from the ports, since they are not necessary for building sra-tools executables and thus out of popular demand, I believe; somebody can make separate ports. Other changes * to modify the build system to adapt FreeBSD * to respect CC, CXX, CFLAGS, LDFLAGS, etc. * to use system or locally installed libraries rather than bundled one Note: Building of sra-tools is successful on i386; however, resultant binary prod= uces somewhat strange outputs. The upstream says "[...] we can look at providing support for an x32 build, although since we can't guarantee that it works." https://github.com/ncbi/ncbi-vdb/issues/8 So I dare to mark BROKEN_i386. On the other hand, amd64 binary seems OK. --=20 You are receiving this mail because: You are the assignee for the bug.=
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