notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)

/commits.php is going away

I'm proposing to take /commits.php away - it mainly duplicates the home page. Details in this GitHub issue.
Port details
py-crossmap Lift over genomics coordinates between assemblies
0.5.4 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 0.5.4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-12 23:39:05
Last Update: 2021-10-14 00:53:16
Commit Hash: 818989d
Also Listed In: python
License: GPLv2
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}crossmap>0:biology/py-crossmap@${PY_FLAVOR}
To install the port: cd /usr/ports/biology/py-crossmap/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-crossmap
  • pkg install py38-crossmap
NOTE: This is a Python port. Instead of py38-crossmap listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py38-crossmap
Package flavors (<flavor>: <package>)
  • py38: py38-crossmap
distinfo:
Packages (timestamps in pop-ups are UTC):
py37-crossmap
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
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--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc640.5.2-
 
py38-crossmap
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd640.5.40.5.4
FreeBSD:11:armv6--
FreeBSD:11:i3860.5.40.5.4
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.5.4
FreeBSD:12:amd640.5.40.5.4
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.5.40.5.4
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-0.5.4
FreeBSD:13:amd640.5.40.5.4
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.5.40.5.4
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch640.5.4-
FreeBSD:14:amd640.5.4-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3860.5.4-
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. py38-nose>0.10.4 : devel/py-nose@py38
  2. cython-3.8 : lang/cython@py38
  3. py38-setuptools>0 : devel/py-setuptools@py38
  4. python3.8 : lang/python38
Runtime dependencies:
  1. py38-pysam>0 : biology/py-pysam@py38
  2. py38-bx-python>0 : biology/py-bx-python@py38
  3. py38-pyBigWig>0 : biology/py-pybigwig@py38
  4. py38-setuptools>0 : devel/py-setuptools@py38
  5. python3.8 : lang/python38
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 (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/C/CrossMap/
  2. https://pypi.org/packages/source/C/CrossMap/
Collapse this list.

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
14 Oct 2021 00:53:16
 files touched by this commit commit hash:818989d766eb792e9c362c6bfd0244e0c94d8b00  0.5.4
jbeich search for other commits by this committer
biology/py-crossmap: chase ad5a0604c41c

make_index: biology/py-crossmap: no entry for biology/py-bigwig

Reported by:	indexbuild
21 Apr 2021 13:31:13
 files touched by this commit commit hash:3c21e709e89943d84cc2ba5211f715467ab17cc7  0.5.4
jwb search for other commits by this committer
biology/py-crossmap: Update to 0.5.4

Add viewchain command
Reported by:  portscout
21 Apr 2021 07:44:44
 files touched by this commit commit hash:256e9bc3b5b97069231e16e2be057e313e9bb7bc  0.5.2_1
kai search for other commits by this committer
biology/py-crossmap: Fix build with Python 3.8+

* Add missing dependency devel/py-nose that is required to build.  With
  Python 3.6/3.7 there are no build issues because the sdist contains
  Python Eggs of "nose" for these versions.

While I'm here:

* Set NO_ARCH because the port has no architecture specific files.
* Make it concurrent safe, package installs a script and bump
  PORTREVISION due package change.

PR:		253815
Approved by:	portmgr (build fix)
MFH:		No (The port was added after the 2021Q1 branch)
12 Apr 2021 23:37:51
 files touched by this commit commit hash:9128727562651ebcc304714cccd03d9643165a74  0.5.2
jwb search for other commits by this committer
biology/py-crossmap: Lift over genomics coordinates between assemblies

CrossMap is a program for genome coordinates conversion between different
assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used
file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF,
and gVCF.

Number of commits found: 4