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Port details
py-crossmap Lift over genomics coordinates between assemblies
0.5.4_1 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 0.5.4_1Version 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: 2023-06-27 19:34:34
Commit Hash: 3d9a815
Also Listed In: python
License: GPLv2
WWW:
https://pypi.python.org/pypi/crossmap
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
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 py39-crossmap
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-crossmap listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-crossmap
Package flavors (<flavor>: <package>)
  • py39: py39-crossmap
distinfo:
TIMESTAMP = 1618936542 SHA256 (CrossMap-0.5.4.tar.gz) = 3419a5bf422754c3acb1e59ec9bba1a6c9a19d3673e962ae832e429ef0f768e5 SIZE (CrossMap-0.5.4.tar.gz) = 9511082

Packages (timestamps in pop-ups are UTC):
py39-crossmap
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.5.4_10.5.4_1-0.5.4_10.5.4_1---
FreeBSD:13:quarterly0.5.4_10.5.4_1--0.5.4_1-0.5.4_1-
FreeBSD:14:latest0.5.4_10.5.4_1-0.5.4_10.5.4_1---
FreeBSD:14:quarterly0.5.4_10.5.4_1--0.5.4_1-0.5.4_1-
FreeBSD:15:latest0.5.4_10.5.4_1n/a0.5.4_1n/a-0.5.4_10.5.4_1
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-nose>0.10.4 : devel/py-nose@py39
  2. cython-3.9 : lang/cython@py39
  3. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  4. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. py39-pysam>0 : biology/py-pysam@py39
  2. py39-bx-python>0 : biology/py-bx-python@py39
  3. py39-pyBigWig>0 : biology/py-pybigwig@py39
  4. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  5. python3.9 : lang/python39
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
No options to configure
Options name:
biology_py-crossmap
USES:
python
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: 10

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.5.4_1
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
0.5.4_1
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
0.5.4
11 Jan 2023 15:58:34
commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
0.5.4
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.4
25 Mar 2022 13:38:04
commit hash: 0ffe3e7936844995675cbddb450a11aa59aa8393commit hash: 0ffe3e7936844995675cbddb450a11aa59aa8393commit hash: 0ffe3e7936844995675cbddb450a11aa59aa8393commit hash: 0ffe3e7936844995675cbddb450a11aa59aa8393 files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/py-crossmap: Fix build with setuptools 58.0.0+

With hat:	python
0.5.4
14 Oct 2021 00:53:16
commit hash: 818989d766eb792e9c362c6bfd0244e0c94d8b00commit hash: 818989d766eb792e9c362c6bfd0244e0c94d8b00commit hash: 818989d766eb792e9c362c6bfd0244e0c94d8b00commit hash: 818989d766eb792e9c362c6bfd0244e0c94d8b00 files touched by this commit
Jan Beich (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
0.5.4
21 Apr 2021 13:31:13
commit hash: 3c21e709e89943d84cc2ba5211f715467ab17cc7commit hash: 3c21e709e89943d84cc2ba5211f715467ab17cc7commit hash: 3c21e709e89943d84cc2ba5211f715467ab17cc7commit hash: 3c21e709e89943d84cc2ba5211f715467ab17cc7 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/py-crossmap: Update to 0.5.4

Add viewchain command
Reported by:  portscout
0.5.2_1
21 Apr 2021 07:44:44
commit hash: 256e9bc3b5b97069231e16e2be057e313e9bb7bccommit hash: 256e9bc3b5b97069231e16e2be057e313e9bb7bccommit hash: 256e9bc3b5b97069231e16e2be057e313e9bb7bccommit hash: 256e9bc3b5b97069231e16e2be057e313e9bb7bc files touched by this commit
Kai Knoblich (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)
0.5.2
12 Apr 2021 23:37:51
commit hash: 9128727562651ebcc304714cccd03d9643165a74commit hash: 9128727562651ebcc304714cccd03d9643165a74commit hash: 9128727562651ebcc304714cccd03d9643165a74commit hash: 9128727562651ebcc304714cccd03d9643165a74 files touched by this commit
Jason W. Bacon (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: 10