| Port details |
- py-crossmap Lift over genomics coordinates between assemblies
- 0.5.4_1 biology
 =2      0.5.4_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-04-12 23:39:05
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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.
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- 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>)
- 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):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-nose>0.10.4 : devel/py-nose@py39
- cython-3.9 : lang/cython@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-pysam>0 : biology/py-pysam@py39
- py39-bx-python>0 : biology/py-bx-python@py39
- py39-pyBigWig>0 : biology/py-pybigwig@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- 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:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.5.4_1
27 Jun 2023 19:34:34
 |
Rene Ladan (rene) |
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
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
0.5.4
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
0.5.4
25 Mar 2022 13:38:04
|
Po-Chuan Hsieh (sunpoet) |
biology/py-crossmap: Fix build with setuptools 58.0.0+
With hat: python |
0.5.4
14 Oct 2021 00:53:16
|
Jan Beich (jbeich) |
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
|
Jason W. Bacon (jwb) |
biology/py-crossmap: Update to 0.5.4
Add viewchain command
Reported by: portscout |
0.5.2_1
21 Apr 2021 07:44:44
|
Kai Knoblich (kai) |
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
|
Jason W. Bacon (jwb) |
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. |
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