Package Details: python2-pysam 0.11.2-1

Git Clone URL: (read-only, click to copy)
Package Base: python2-pysam
Description: Python interface for the SAM/BAM sequence alignment and mapping format
Upstream URL:
Licenses: MIT
Provides: python2-pysam
Submitter: iosonofabio
Maintainer: iosonofabio
Last Packager: iosonofabio
Votes: 6
Popularity: 0.000000
First Submitted: 2012-11-06 16:59
Last Updated: 2017-05-14 23:47

Latest Comments

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iosonofabio commented on 2016-04-25 18:41

external htslib currently broken, please report upstream

wookietreiber commented on 2016-04-22 08:23

pysam can be built with an external htslib dependency (c.f., i.e. one that we provide via aur (c.f.

would you be open to add htslib as a dependency?

this would mean setting the following before running install

export HTSLIB_LIBRARY_DIR=/usr/lib
export HTSLIB_INCLUDE_DIR=/usr/include

this then correctly links to /usr/lib/

iosonofabio commented on 2013-10-18 14:19

Thanks for your quick reply. Please report this upstream, it is a general bug and not related to the archlinux package in particular.

vejnar commented on 2013-10-18 13:58

Because with 640 and files ownership as root.root, nobody else than root can read them. User might (my case...) want to read these files; not only root should be allowed to compile a module that uses the headers of pysam.

iosonofabio commented on 2013-10-17 20:04

Why is the default not fine? If that's how the developer set it...

vejnar commented on 2013-10-17 20:03

The files in /usr/lib/python2.7/site-packages/pysam/include/samtools/ are 640. They should be 644. Same for Python 3. Could you please fix it? Thanks

iosonofabio commented on 2013-10-14 17:13


vejnar commented on 2013-10-14 17:04

Yes, apparently you have to create 2 packages (see biopython for example). Could you please do it (or should I)?

iosonofabio commented on 2013-10-04 17:04

I tried your PKGBUILD and it works, but I cannot upload it, because AUR complains that the package name can have only "lowercase letters". Any suggestions, apart from splitting the package into two packages?

iosonofabio commented on 2013-10-04 17:00

Thanks for the changes, I'll rename the package python-pysam since it supports both architectures. This package is designed to be deleted now.