Subject: CVS commit: pkgsrc/biology/sra-tools
From: Jason Bacon
Date: 2023-08-29 02:00:25
Message id: 20230829000025.4E370FBDB@cvs.NetBSD.org

Log Message:
biology/sra-tools: NCBI's toolkit for SRA

SRA tools is a toolkit for using data in the INSDC Sequence Read
Archives.  SRAs operated by the International Nucleotide Sequence
Database Collaboration house 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
'next-gen' sequencers generate including:

* csfasta/csqual (ABI SOLiD)
* fastq (and fasta for writing)
* hdf5 (PacBio, reading only)
* qseq (older Illumina)
* sam (writing only) / bam (reading only)
* sff

The toolkit uses the NCBI-VDB back-end enabling seamless access to
remote SRA data and local SRA files.

Files:
RevisionActionfile
1.1addpkgsrc/biology/sra-tools/DESCR
1.1addpkgsrc/biology/sra-tools/Makefile
1.1addpkgsrc/biology/sra-tools/PLIST
1.1addpkgsrc/biology/sra-tools/distinfo
1.1addpkgsrc/biology/sra-tools/patches/patch-build_env.cmake
1.1addpkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
1.1addpkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
1.1addpkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp