Package Details: python-pysam 0.22.0-1

Git Clone URL: https://aur.archlinux.org/python-pysam.git (read-only, click to copy)
Package Base: python-pysam
Description: Python interface for the SAM/BAM sequence alignment and mapping format
Upstream URL: https://github.com/pysam-developers/pysam
Keywords: bioinformatics
Licenses: MIT
Provides: python-pysam
Submitter: iosonofabio
Maintainer: oldherl (lilac)
Last Packager: oldherl
Votes: 12
Popularity: 0.006960
First Submitted: 2013-10-14 17:12 (UTC)
Last Updated: 2024-04-16 07:41 (UTC)

Latest Comments

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iosonofabio commented on 2020-12-25 09:02 (UTC)

Sorry guys, my ssh is somehow broken and I can't seem to be able to push to AUR anymore... so I'll disown this package and someone else can pick it up. sorry about that!

luscinius commented on 2020-12-12 07:27 (UTC)

I think a release bump needs to be done to cause the rebuild now that python 3.9 is in extra.

iosonofabio commented on 2018-09-20 16:18 (UTC)

thanks, the .SRCINFO was inconsistent and slipped through the cracks

dburkhardt commented on 2018-09-20 14:19 (UTC)

Fyi, the package version in the AUR package name is different from the version in the PKGBUILD. Can that be updated?

iosonofabio commented on 2016-05-04 22:42 (UTC)

external htslib fails, I think the setup.py is buggy. For now using internal htslib still, but see PKGBUILD if you want to give it a go or report upstream.

wookietreiber commented on 2016-04-22 08:23 (UTC)

pysam can be built with an external htslib dependency (c.f. http://pysam.readthedocs.org/en/latest/installation.html#external), i.e. one that we provide via aur (c.f. https://aur.archlinux.org/packages/htslib/) would you be open to add htslib as a dependency? this would mean setting the following before running setup.py install export HTSLIB_LIBRARY_DIR=/usr/lib export HTSLIB_INCLUDE_DIR=/usr/include this then correctly links to /usr/lib/libhts.so.1

Stunts commented on 2015-10-23 12:53 (UTC)

PAtch available here: https://github.com/pysam-developers/pysam/commit/6efb22b1a3ee4bc57a691f163b456b417da56db3

iosonofabio commented on 2015-09-02 15:24 (UTC)

upstream: https://github.com/pysam-developers/pysam/issues/164

balwierz commented on 2015-09-01 16:25 (UTC)

Problems building: pysam/cbcf.c: At top level: pysam/cbcf.c:47530:67: error: unknown type name ‘htsFormatCategory’ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_htsFormatCategory(htsFormatCategory value) { ^ pysam/cbcf.c:47556:64: error: unknown type name ‘htsExactFormat’ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_htsExactFormat(htsExactFormat value) { ^ pysam/cbcf.c:47608:64: error: unknown type name ‘htsCompression’ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_htsCompression(htsCompression value) {

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