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Port details on branch 2022Q2
sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
2.11.0_2 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 2.11.0_2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-04-24 04:16:20
Last Update: 2022-04-10 19:47:23
Commit Hash: 035e778
License: PD LGPL21+
WWW:
https://github.com/ncbi/sra-tools/wiki
Description:
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 'next-gen' sequenecers 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 NCBI-VDB back-end enabling seamless access to remote SRA data and local SRA files. WWW: https://github.com/ncbi/sra-tools/wiki
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (64 items)
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  1. /usr/local/share/licenses/sra-tools-2.11.0_2/catalog.mk
  2. /usr/local/share/licenses/sra-tools-2.11.0_2/LICENSE
  3. /usr/local/share/licenses/sra-tools-2.11.0_2/PD
  4. /usr/local/share/licenses/sra-tools-2.11.0_2/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
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Dependency lines:
  • sra-tools>0:biology/sra-tools
Conflicts:
CONFLICTS_INSTALL:
  • kget
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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: sra-tools
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64
distinfo:
TIMESTAMP = 1624382289 SHA256 (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 10ac0a4d1fafc274bc107de811891d3e803d0713a247581dece4448231883810 SIZE (ncbi-sra-tools-2.11.0_GH0.tar.gz) = 8966605

Expand this list (4 items)

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SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365 SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539

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Packages (timestamps in pop-ups are UTC):
sra-tools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest3.2.13.2.1------
FreeBSD:13:quarterly3.2.13.2.1------
FreeBSD:14:latest3.2.13.2.1------
FreeBSD:14:quarterly3.1.13.2.1------
FreeBSD:15:latest3.2.13.2.1n/a-n/a---
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
There are no ports dependent upon this port
Configuration Options:
===> The following configuration options are available for sra-tools-2.11.0_2: DEBUG=off: Build with debugging support OPTIMIZED_CFLAGS=off: Use extra compiler optimizations TEST=off: Build and/or run tests ===> Use 'make config' to modify these settings
Options name:
biology_sra-tools
USES:
compiler:c11 gmake localbase:ldflags perl5 shebangfix
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=/
Collapse this list.

Number of commits found: 1

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.11.0_2
10 Apr 2022 19:47:23
commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6 files touched by this commit		 Charlie Li (vishwin) search for other commits by this committer 
textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate and direct commit to quarterly as PORTREVISIONs
may not match from main.

PR: 262853, 262940, 262877
Approved by: fluffy (mentor)

Number of commits found: 1
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