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Two two features were added on 2020-05-30:
  1. Repology links - each port now has a link to repology.org. See issue 148 for details.
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Port details
py-cutadapt Trim adapters from high-throughput sequencing reads
2.7 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. 2.7Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-11-29 22:17:53
Last Update: 2019-11-23 14:45:53
SVN Revision: 518242
Also Listed In: python
License: MIT
Description:
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • py36-cutadapt>0:biology/py-cutadapt
To install the port: cd /usr/ports/biology/py-cutadapt/ && make install clean
To add the package: pkg install py36-cutadapt
PKGNAME: py36-cutadapt
Package flavors (<flavor>: <package>)
  • py36: py36-cutadapt
distinfo:
Packages:
py27-cutadapt
ABIlatestquarterly
FreeBSD:11:aarch641.18-
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch641.18-
FreeBSD:12:amd64--
FreeBSD:12:armv61.18-
FreeBSD:12:armv71.18-
FreeBSD:12:i386--
FreeBSD:12:mips1.18-
FreeBSD:12:mips641.18-
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
 
py36-cutadapt
ABIlatestquarterly
FreeBSD:11:aarch641.18-
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch641.18-
FreeBSD:12:amd64--
FreeBSD:12:armv61.18-
FreeBSD:12:armv71.18-
FreeBSD:12:i386--
FreeBSD:12:mips1.18-
FreeBSD:12:mips641.18-
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
 
py37-cutadapt
ABIlatestquarterly
FreeBSD:11:aarch64-2.7
FreeBSD:11:amd642.72.7
FreeBSD:11:armv6-2.7
FreeBSD:11:i3862.72.7
FreeBSD:11:mips-2.7
FreeBSD:11:mips64-2.7
FreeBSD:12:aarch64-2.7
FreeBSD:12:amd642.72.7
FreeBSD:12:armv6-2.7
FreeBSD:12:armv7-2.7
FreeBSD:12:i3862.72.7
FreeBSD:12:mips-2.7
FreeBSD:12:mips64-2.7
FreeBSD:12:powerpc64-2.7
FreeBSD:13:aarch642.7-
FreeBSD:13:amd642.7-
FreeBSD:13:armv62.7-
FreeBSD:13:armv72.7-
FreeBSD:13:i3862.7-
FreeBSD:13:mips2.7-
FreeBSD:13:mips64--
FreeBSD:13:powerpc642.7-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py36-setuptools_scm>0 : devel/py-setuptools_scm@py36
  2. cython-3.6 : lang/cython@py36
  3. py36-setuptools>0 : devel/py-setuptools@py36
  4. python3.6 : lang/python36
Runtime dependencies:
  1. py36-xopen>=0.8.4 : archivers/py-xopen@py36
  2. py36-dnaio>=0.4.1 : biology/py-dnaio@py36
  3. py36-setuptools>0 : devel/py-setuptools@py36
  4. python3.6 : lang/python36
This port is required by:
for Run
  1. biology/p5-TrimGalore

Configuration Options

USES:

Master Sites:
  1. https://files.pythonhosted.org/packages/source/c/cutadapt/
  2. https://pypi.org/packages/source/c/cutadapt/
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2017-11-30
    Affects: */py*
    Author: mat@FreeBSD.org
    Reason: 
      Ports using Python via USES=python are now flavored.  All the py3-* ports
      have been removed and folded into their py-* master ports.
    
      People using Poudriere 3.2+ and binary packages do not have to do anything.
    
      For other people, to build the Python 3.6 version of, for example,
      databases/py-gdbm, you need to run:
    
        # make FLAVOR=py36 install
    
    

Number of commits found: 14

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Nov 2019 14:45:53
Original commit files touched by this commit  2.7
Revision:518242
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 2.7

Numerous minor fixes and enhancements.
Upstreamed setup.py patches for dependency versions.

Reported by:    portscout
13 Sep 2019 13:17:26
Original commit files touched by this commit  2.5
Revision:511957
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 2.5

Add pigz run depend for parallel gzip/gunzip
27 Apr 2019 01:26:17
Original commit files touched by this commit  2.3
Revision:500187
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 2.3

Numerous bugfixes and enhancements since 2.1
10 Apr 2019 06:18:32
Original commit files touched by this commit  2.1_1
Revision:498530
antoine search for other commits by this committer
Bump a few PORTREVISIONs after r498529

With hat:	portmgr
24 Mar 2019 21:20:24
Original commit files touched by this commit  2.1
Revision:496783
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 2.1

Add do-test target
24 Mar 2019 20:28:55
Original commit files touched by this commit  1.18
Revision:496776
antoine search for other commits by this committer
Unbreak
20 Sep 2018 14:10:52
Original commit files touched by this commit  1.18
Revision:480173
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 1.18

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D17099
20 Jun 2018 17:05:44
Original commit files touched by this commit  1.14
Revision:472884
mat search for other commits by this committer
Use PY_FLAVOR for dependencies.

FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight
25 Apr 2018 16:42:38
Original commit files touched by this commit  1.14
Revision:468282
amdmi3 search for other commits by this committer
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
they now redirect to anyway. All new urls checked to return 200,
I've fixed a couple of them in the process.

Approved by:	portmgr blanket, mat
08 Feb 2018 20:18:09
Original commit files touched by this commit  1.14
Revision:461265
amdmi3 search for other commits by this committer
Canonicalize PyPi WWWs:
- Switch to https://
- Remove trailing slashes

Approved by:	portmgr blanket
01 Dec 2017 06:18:17
Original commit files touched by this commit  1.14
Revision:455247  Sanity Test Failure
antoine search for other commits by this committer
Fix packaging with python3
30 Nov 2017 22:11:04
Original commit files touched by this commit  1.14
Revision:455235  Sanity Test Failure
jwb search for other commits by this committer
biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor comment

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13303
30 Nov 2017 15:50:34
Original commit files touched by this commit  1.14
Revision:455210  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
29 Nov 2017 22:17:44
Original commit files touched by this commit  1.14
Revision:455154
jwb search for other commits by this committer
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po
ly-A tails, etc
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13294

Number of commits found: 14

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