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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-12 23:30:30 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-12 23:37:51 +0000 |
| commit | 9128727562651ebcc304714cccd03d9643165a74 (patch) | |
| tree | fb7fe38778d6f9963073b61044fe666e609dca41 /biology/py-crossmap | |
| parent | ffe8bdaf4de4c9b7a99cd4222001d98d7069998e (diff) | |
| download | ports-9128727562651ebcc304714cccd03d9643165a74.tar.gz ports-9128727562651ebcc304714cccd03d9643165a74.zip | |
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.
Diffstat (limited to 'biology/py-crossmap')
| -rw-r--r-- | biology/py-crossmap/Makefile | 21 | ||||
| -rw-r--r-- | biology/py-crossmap/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-crossmap/files/patch-lib_cmmodule_twoList.py | 18 | ||||
| -rw-r--r-- | biology/py-crossmap/files/patch-setup.py | 10 | ||||
| -rw-r--r-- | biology/py-crossmap/pkg-descr | 6 |
5 files changed, 58 insertions, 0 deletions
diff --git a/biology/py-crossmap/Makefile b/biology/py-crossmap/Makefile new file mode 100644 index 000000000000..7946de949b5e --- /dev/null +++ b/biology/py-crossmap/Makefile @@ -0,0 +1,21 @@ +PORTNAME= crossmap +DISTVERSION= 0.5.2 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= CrossMap-${DISTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Lift over genomics coordinates between assemblies + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}bx-python>0:biology/py-bx-python@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pyBigWig>0:biology/py-bigwig@${PY_FLAVOR} + +USES= python:3.5+ +USE_PYTHON= autoplist cython distutils + +.include <bsd.port.mk> diff --git a/biology/py-crossmap/distinfo b/biology/py-crossmap/distinfo new file mode 100644 index 000000000000..e78c67b1ddcf --- /dev/null +++ b/biology/py-crossmap/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1617575391 +SHA256 (CrossMap-0.5.2.tar.gz) = d996c7a17ca2665903d7bfa4ca67d35c37c800e1ce3129ed1274e65504b93d69 +SIZE (CrossMap-0.5.2.tar.gz) = 10866811 diff --git a/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py b/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py new file mode 100644 index 000000000000..efbb0c474374 --- /dev/null +++ b/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py @@ -0,0 +1,18 @@ +--- lib/cmmodule/twoList.py.orig 2021-04-04 22:42:53 UTC ++++ lib/cmmodule/twoList.py +@@ -5,7 +5,7 @@ from operator import mul,add,sub + def check_list(v1,v2): + '''check if the length of two list is same''' + if v1.size != v2.size: +- raise ValueError,"the lenght of both arrays must be the same" ++ raise ValueError("the length of both arrays must be the same") + pass + + def Add(v1,v2): +@@ -50,4 +50,4 @@ def Min(v1,v2): + def euclidean_distance(v1,v2): + '''return euclidean distance''' + check_list(v1,v2) +- return (sum((v1.__sub__(v2))**2) / v1.size)**0.5 +\ No newline at end of file ++ return (sum((v1.__sub__(v2))**2) / v1.size)**0.5 diff --git a/biology/py-crossmap/files/patch-setup.py b/biology/py-crossmap/files/patch-setup.py new file mode 100644 index 000000000000..4fa46ca7cc20 --- /dev/null +++ b/biology/py-crossmap/files/patch-setup.py @@ -0,0 +1,10 @@ +--- setup.py.orig 2021-04-05 15:27:07 UTC ++++ setup.py +@@ -11,7 +11,6 @@ def main(): + setup( name = "CrossMap", + version = "0.5.2", + python_requires='>=3.5', +- py_modules = [ 'psyco_full' ], + packages = find_packages( 'lib' ), + package_dir = { '': 'lib' }, + package_data = { '': ['*.ps'] }, diff --git a/biology/py-crossmap/pkg-descr b/biology/py-crossmap/pkg-descr new file mode 100644 index 000000000000..dfb768a40775 --- /dev/null +++ b/biology/py-crossmap/pkg-descr @@ -0,0 +1,6 @@ +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. + +WWW: https://pypi.python.org/pypi/crossmap |