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Port details
peak-classifier Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
0.1.1.21 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 0.1.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-06-14 16:45:08
Last Update: 2021-09-02 23:15:40
Commit Hash: 7e94c6d
License: BSD2CLAUSE
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (15 items)
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  1. /usr/local/share/licenses/peak-classifier-0.1.1.21/catalog.mk
  2. /usr/local/share/licenses/peak-classifier-0.1.1.21/LICENSE
  3. /usr/local/share/licenses/peak-classifier-0.1.1.21/BSD2CLAUSE
  4. bin/extract-genes
  5. bin/feature-view
  6. bin/filter-overlaps
  7. bin/peak-classifier
  8. libexec/extract-genes.awk
  9. man/man1/extract-genes.1.gz
  10. man/man1/feature-view.1.gz
  11. man/man1/filter-overlaps.1.gz
  12. man/man1/peak-classifier.1.gz
  13. @owner
  14. @group
  15. @mode
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Dependency lines:
  • peak-classifier>0:biology/peak-classifier
To install the port: cd /usr/ports/biology/peak-classifier/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/peak-classifier
  • pkg install peak-classifier
PKGNAME: peak-classifier
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
peak-classifier
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd640.1.1.210.1.1
FreeBSD:11:armv6--
FreeBSD:11:i3860.1.1.210.1.1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.1.1.21
FreeBSD:12:amd640.1.1.210.1.1.21
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.1.1.210.1.1.21
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-0.1.1.21
FreeBSD:13:amd640.1.1.210.1.1.21
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.1.1.210.1.1.21
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch640.1.1.21-
FreeBSD:14:amd640.1.1.21-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3860.1.1.21-
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. python3.8 : lang/python38
Runtime dependencies:
  1. bedtools : biology/bedtools
  2. py38-matplotlib>0 : math/py-matplotlib@py38
  3. python3.8 : lang/python38
Library dependencies:
  1. libxtend.so : devel/libxtend
  2. libbiolibc.so : biology/biolibc
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
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  1. https://codeload.github.com/auerlab/peak-classifier/tar.gz/0.1.1-21-gc1b21c2?dummy=/
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Number of commits found: 3

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
02 Sep 2021 23:15:40
 files touched by this commit commit hash:7e94c6d1f86cebaa77367f9a86ca452efaf70bae  0.1.1.21
jwb search for other commits by this committer
biology/peak-classifier: Update to 0.1.1.21

Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks
28 Aug 2021 01:34:46
 files touched by this commit commit hash:b16616b283a7564fbd6a001b47decd2d89fcc5c5  0.1.1.20
jwb search for other commits by this committer
biology/peak-classifier: Update to 0.1.1.20

Updates for libxtend and biolibc API changes
14 Jun 2021 16:40:33
 files touched by this commit commit hash:5a2a6eb32954aa49c79269b08fd7e26ca4436f3d  0.1.1
jwb search for other commits by this committer
biology/peak-classifier: Classify peaks based on GFF features

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF

Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons.  This is the default for
common data sources.

Number of commits found: 3