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Port details
sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
2.11.0 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.11.0Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-06-22 18:00:14
Last Update: 2021-06-22 17:55:15
Commit Hash: 69656bf
License: PD LGPL21+
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (64 items)
Collapse this list.
  1. /usr/local/share/licenses/sra-tools-2.11.0/catalog.mk
  2. /usr/local/share/licenses/sra-tools-2.11.0/LICENSE
  3. /usr/local/share/licenses/sra-tools-2.11.0/PD
  4. /usr/local/share/licenses/sra-tools-2.11.0/LGPL21+
  5. bin/abi-dump
  6. bin/abi-load
  7. bin/align-cache
  8. bin/align-info
  9. bin/bam-load
  10. bin/cache-mgr
  11. bin/ccextract
  12. bin/cg-load
  13. bin/check-corrupt
  14. bin/copycat
  15. bin/fasterq-dump
  16. bin/fastq-dump
  17. bin/fastq-load
  18. bin/helicos-load
  19. bin/illumina-dump
  20. bin/illumina-load
  21. bin/kar
  22. bin/kar+
  23. bin/kar+meta
  24. bin/kdb-index
  25. bin/kdbmeta
  26. bin/kget
  27. bin/latf-load
  28. bin/make-read-filter
  29. bin/md5cp
  30. bin/ngs-pileup
  31. bin/pacbio-correct
  32. bin/pacbio-loadxml
  33. bin/prefetch
  34. bin/qual-recalib-stat
  35. bin/rcexplain
  36. bin/read-filter-redact
  37. bin/sam-dump
  38. bin/samview
  39. bin/schema-replace
  40. bin/sff-dump
  41. bin/sff-load
  42. bin/sra-pileup
  43. bin/sra-sort
  44. bin/sra-sort-cg
  45. bin/sra-stat
  46. bin/srapath
  47. bin/sratools
  48. bin/srf-load
  49. bin/test-read-write-cursor
  50. bin/test-sra
  51. bin/vdb-config
  52. bin/vdb-copy
  53. bin/vdb-decrypt
  54. bin/vdb-diff
  55. bin/vdb-dump
  56. bin/vdb-encrypt
  57. bin/vdb-lock
  58. bin/vdb-passwd
  59. bin/vdb-sql
  60. bin/vdb-unlock
  61. bin/vdb-validate
  62. @owner
  63. @group
  64. @mode
Collapse this list.
Dependency lines:
  • sra-tools>0:biology/sra-tools
To install the port: cd /usr/ports/biology/sra-tools/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/sra-tools
  • pkg install sra-tools
PKGNAME: sra-tools
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64
distinfo:
Packages (timestamps in pop-ups are UTC):
sra-tools
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.11.02.11.0
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd642.11.02.11.0
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd642.11.02.11.0
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd642.11.0-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. libngs-c++.a : biology/ngs-sdk
  3. gmake>=4.3 : devel/gmake
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Library dependencies:
  1. libxml2.so : textproc/libxml2
  2. libhdf5.so : science/hdf5
  3. libepoll-shim.so : devel/libepoll-shim
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ncbi/sra-tools/tar.gz/2.11.0?dummy=/
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Number of commits found: 1

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
22 Jun 2021 17:55:15
 files touched by this commit commit hash:69656bf0d7d99660e536c22472a5eae639695a97  2.11.0
jwb search for other commits by this committer
biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read
Archives

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.

This port is a bit convoluted due to the fact that the sra-tools build
requires access to the ncbi-vdb source tree.  Hence, ncbi-vdb is treated
as a submodule here rather than a separate library port.  We are working
with upstream with hope for long-term improvements.

Number of commits found: 1