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Port details
sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
2.11.0_3 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 Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: PD LGPL21+
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port
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_3/catalog.mk
  2. /usr/local/share/licenses/sra-tools-2.11.0_3/LICENSE
  3. /usr/local/share/licenses/sra-tools-2.11.0_3/PD
  4. /usr/local/share/licenses/sra-tools-2.11.0_3/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
Conflicts:
CONFLICTS_INSTALL:
  • kget
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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:

Packages (timestamps in pop-ups are UTC):
sra-tools
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd642.11.02.11.0
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd642.11.0_32.11.0_3
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd642.11.0_32.11.0_3
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd642.11.0_3pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
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/atac-seq
  2. biology/biostar-tools
  3. biology/rna-seq

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=/
Collapse this list.

Number of commits found: 8

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.11.0_3
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.11.0_3
20 Jul 2022 14:35:24
commit hash:5564b3b420db29745d2d4981d1963200ddf53e35commit hash:5564b3b420db29745d2d4981d1963200ddf53e35commit hash:5564b3b420db29745d2d4981d1963200ddf53e35commit hash:5564b3b420db29745d2d4981d1963200ddf53e35 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>
2.11.0_2
18 Jul 2022 12:50:17
commit hash:ba66c05b01aeb7d0000c13193536d283e6e55077commit hash:ba66c05b01aeb7d0000c13193536d283e6e55077commit hash:ba66c05b01aeb7d0000c13193536d283e6e55077commit hash:ba66c05b01aeb7d0000c13193536d283e6e55077 files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/sra-tools: Fix build with HDF5 1.12.0+
2.11.0_2
10 Apr 2022 19:11:41
commit hash:d63665f7cd9c99880704a3c5bc221829cb009744commit hash:d63665f7cd9c99880704a3c5bc221829cb009744commit hash:d63665f7cd9c99880704a3c5bc221829cb009744commit hash:d63665f7cd9c99880704a3c5bc221829cb009744 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 commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)
2.11.0_1
26 Mar 2022 08:27:27
commit hash:247c7db7513f1264922428278678da641c5a3f52commit hash:247c7db7513f1264922428278678da641c5a3f52commit hash:247c7db7513f1264922428278678da641c5a3f52commit hash:247c7db7513f1264922428278678da641c5a3f52 files touched by this commit
Matthias Fechner (mfechner) search for other commits by this committer
textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246
2.11.0
10 Jan 2022 15:15:39
commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.11.0
22 Jun 2021 17:55:15
commit hash:69656bf0d7d99660e536c22472a5eae639695a97commit hash:69656bf0d7d99660e536c22472a5eae639695a97commit hash:69656bf0d7d99660e536c22472a5eae639695a97commit hash:69656bf0d7d99660e536c22472a5eae639695a97 files touched by this commit
Jason W. Bacon (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: 8