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Port details
samtools Tools for manipulating next-generation sequencing data
1.6 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
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Dec 2014 21:59:37
License: MIT
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

WWW: http://www.htslib.org/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (26 items)
  1. /usr/local/share/licenses/samtools-1.6/catalog.mk
  2. /usr/local/share/licenses/samtools-1.6/LICENSE
  3. /usr/local/share/licenses/samtools-1.6/MIT
  4. bin/samtools
  5. bin/samtools_misc/ace2sam
  6. bin/samtools_misc/blast2sam.pl
  7. bin/samtools_misc/bowtie2sam.pl
  8. bin/samtools_misc/export2sam.pl
  9. bin/samtools_misc/interpolate_sam.pl
  10. bin/samtools_misc/maq2sam-long
  11. bin/samtools_misc/maq2sam-short
  12. bin/samtools_misc/md5fa
  13. bin/samtools_misc/md5sum-lite
  14. bin/samtools_misc/novo2sam.pl
  15. bin/samtools_misc/plot-bamstats
  16. bin/samtools_misc/psl2sam.pl
  17. bin/samtools_misc/sam2vcf.pl
  18. bin/samtools_misc/samtools.pl
  19. bin/samtools_misc/seq_cache_populate.pl
  20. bin/samtools_misc/soap2sam.pl
  21. bin/samtools_misc/varfilter.py
  22. bin/samtools_misc/wgsim
  23. bin/samtools_misc/wgsim_eval.pl
  24. bin/samtools_misc/zoom2sam.pl
  25. man/man1/samtools.1.gz
  26. man/man1/wgsim.1.gz
  27. Collapse this list.

To install the port: cd /usr/ports/biology/samtools/ && make install clean
To add the package: pkg install samtools

PKGNAME: samtools

distinfo:

TIMESTAMP = 1508304738
SHA256 (samtools-samtools-1.6_GH0.tar.gz) = c0d1ffefe441297ee0eec0e032ac3131519f82fd1a11d38fbcec19e2d5822b28
SIZE (samtools-samtools-1.6_GH0.tar.gz) = 4014195


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. htslib>=1.6 : biology/htslib
  2. autoconf-2.69 : devel/autoconf
  3. autoheader-2.69 : devel/autoconf
  4. autoreconf-2.69 : devel/autoconf
  5. aclocal-1.15 : devel/automake
  6. automake-1.15 : devel/automake
  7. gmake : devel/gmake
Library dependencies:
  1. libhts.so : biology/htslib
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
autoreconf gmake ncurses perl5 python shebangfix

Master Sites:
  1. https://codeload.github.com/samtools/samtools/tar.gz/1.6?dummy=/

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
04 Dec 2017 15:27:29
Refresh Original commit files touched by this commit
Revision:455518  Sanity Test Failure
mat search for other commits by this committer
Add a USES=python:env, that will not add a dependency on Python.

It has the same effect than setting PYTHON_NO_DEPENDS, but in a more
compact way.

Sponsored by:	Absolight
25 Oct 2017 10:19:50
Original commit files touched by this commit  1.6
Revision:452840
pizzamig search for other commits by this committer
biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768
26 May 2016 20:28:55
Original commit files touched by this commit  1.3.1
Revision:415914
pi search for other commits by this committer
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)
19 May 2016 11:09:14
Original commit files touched by this commit  1.3
Revision:415503
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.3
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
01 Feb 2016 21:59:15
Original commit files touched by this commit  1.3
Revision:407776
marino search for other commits by this committer
biology/samtools: document ncurses requirement (USES+=ncurses)

approved by:	infrastructure blanket
25 Dec 2015 01:31:09
Original commit files touched by this commit  1.3
Revision:404398
junovitch search for other commits by this committer
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)
06 May 2015 15:16:54
Original commit files touched by this commit  1.2
Revision:385521
mat search for other commits by this committer
Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
06 Mar 2015 12:53:59
Original commit files touched by this commit  1.2
Revision:380597
robak search for other commits by this committer
biology/samtools: update 1.1 -> 1.2

PR:		198292
Submitted by:	Reed Cartwright <cartwright@asu.edu>
15 Dec 2014 21:59:20
Original commit files touched by this commit  1.1
Revision:374767
pawel search for other commits by this committer
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

WWW: http://www.htslib.org/

PR:		195592
Submitted by:	Reed A. Cartwright <cartwright@asu.edu>

Number of commits found: 10

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