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Port details
subread High-performance read alignment, quantification and mutation discovery
2.0.2 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 2.0.2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-06-05 01:55:58
Last Update: 2021-04-07 08:09:01
Commit Hash: cf118cc
License: GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (22 items)
Collapse this list.
  1. /usr/local/share/licenses/subread-2.0.2/catalog.mk
  2. /usr/local/share/licenses/subread-2.0.2/LICENSE
  3. /usr/local/share/licenses/subread-2.0.2/GPLv3
  4. bin/detectionCall
  5. bin/exactSNP
  6. bin/featureCounts
  7. bin/flattenGTF
  8. bin/genRandomReads
  9. bin/propmapped
  10. bin/qualityScores
  11. bin/removeDup
  12. bin/repair
  13. bin/subindel
  14. bin/subjunc
  15. bin/sublong
  16. bin/subread-align
  17. bin/subread-buildindex
  18. bin/subread-fullscan
  19. bin/txUnique
  20. @owner
  21. @group
  22. @mode
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Dependency lines:
  • subread>0:biology/subread
To install the port:
cd /usr/ports/biology/subread/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/subread
  • pkg install subread
PKGNAME: subread
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
subread
ABIlatestquarterly
FreeBSD:11:aarch64-2.0.1
FreeBSD:11:amd642.0.22.0.2
FreeBSD:11:armv6-2.0.1
FreeBSD:11:i3862.0.22.0.2
FreeBSD:11:mips--
FreeBSD:11:mips64-2.0.1
FreeBSD:12:aarch64-2.0.2
FreeBSD:12:amd642.0.22.0.2
FreeBSD:12:armv6-2.0.1
FreeBSD:12:armv7-2.0.1
FreeBSD:12:i3862.0.22.0.2
FreeBSD:12:mips--
FreeBSD:12:mips64-2.0.1
FreeBSD:12:powerpc64-2.0.2
FreeBSD:13:aarch642.0.22.0.2
FreeBSD:13:amd642.0.22.0.2
FreeBSD:13:armv62.0.12.0.2
FreeBSD:13:armv72.0.12.0.2
FreeBSD:13:i3862.0.22.0.2
FreeBSD:13:mips--
FreeBSD:13:mips642.0.12.0.1
FreeBSD:13:powerpc642.0.12.0.2
FreeBSD:14:aarch642.0.2-
FreeBSD:14:amd642.0.2-
FreeBSD:14:armv62.0.2-
FreeBSD:14:armv72.0.2-
FreeBSD:14:i3862.0.2-
FreeBSD:14:mips--
FreeBSD:14:mips642.0.2-
FreeBSD:14:powerpc642.0.2-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
Library dependencies:
  1. libsysinfo.so : devel/libsysinfo
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 (22 items)
Collapse this list.
  1. http://downloads.sourceforge.net/project/subread/subread-2.0.2/
  2. http://excellmedia.dl.sourceforge.net/project/subread/subread-2.0.2/
  3. http://freefr.dl.sourceforge.net/project/subread/subread-2.0.2/
  4. http://jaist.dl.sourceforge.net/project/subread/subread-2.0.2/
  5. http://nchc.dl.sourceforge.net/project/subread/subread-2.0.2/
  6. http://netcologne.dl.sourceforge.net/project/subread/subread-2.0.2/
  7. http://netix.dl.sourceforge.net/project/subread/subread-2.0.2/
  8. http://superb-dca2.dl.sourceforge.net/project/subread/subread-2.0.2/
  9. http://superb-sea2.dl.sourceforge.net/project/subread/subread-2.0.2/
  10. http://ufpr.dl.sourceforge.net/project/subread/subread-2.0.2/
  11. http://vorboss.dl.sourceforge.net/project/subread/subread-2.0.2/
  12. https://downloads.sourceforge.net/project/subread/subread-2.0.2/
  13. https://excellmedia.dl.sourceforge.net/project/subread/subread-2.0.2/
  14. https://freefr.dl.sourceforge.net/project/subread/subread-2.0.2/
  15. https://jaist.dl.sourceforge.net/project/subread/subread-2.0.2/
  16. https://nchc.dl.sourceforge.net/project/subread/subread-2.0.2/
  17. https://netcologne.dl.sourceforge.net/project/subread/subread-2.0.2/
  18. https://netix.dl.sourceforge.net/project/subread/subread-2.0.2/
  19. https://superb-dca2.dl.sourceforge.net/project/subread/subread-2.0.2/
  20. https://superb-sea2.dl.sourceforge.net/project/subread/subread-2.0.2/
  21. https://ufpr.dl.sourceforge.net/project/subread/subread-2.0.2/
  22. https://vorboss.dl.sourceforge.net/project/subread/subread-2.0.2/
Collapse this list.

Number of commits found: 5

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.0.2
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.0.2
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
30 Mar 2021 15:30:27
Original commit files touched by this commit Revision:569561  2.0.2
jwb search for other commits by this committer
biology/subread: Update to 2.0.2

Minor bug fixes and enhancements

Reported by:    portscout
18 Sep 2020 00:57:36
Original commit files touched by this commit Revision:548871  2.0.1
jwb search for other commits by this committer
biology/subread: Add -fcommon for clang 11

Reported by:    pkg-fallout
05 Jun 2020 01:55:49
Original commit files touched by this commit Revision:537982  2.0.1
jwb search for other commits by this committer
biology/subread: Read alignment, quantification and mutation discovery

The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.

Number of commits found: 5