Package Details: python-pysam 0.11.2-1

Git Clone URL: https://aur.archlinux.org/python-pysam.git (read-only)
Package Base: python-pysam
Description: Python interface for the SAM/BAM sequence alignment and mapping format
Upstream URL: https://github.com/pysam-developers/pysam
Licenses: MIT
Provides: python-pysam
Submitter: iosonofabio
Maintainer: iosonofabio
Last Packager: iosonofabio
Votes: 8
Popularity: 0.000451
First Submitted: 2013-10-14 17:12
Last Updated: 2017-05-14 23:47

Latest Comments

iosonofabio commented on 2016-05-04 22:42

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

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

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

iosonofabio commented on 2015-09-02 15:24

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

iosonofabio commented on 2015-09-02 15:23

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

I'll fix the dep to cython==0.22 for now.

balwierz commented on 2015-09-01 16:25

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) {

Stunts commented on 2014-04-16 15:57

Could be... regardless, it's working now...

iosonofabio commented on 2014-04-16 14:48

Maybe the package is precompiled for python2...

Stunts commented on 2014-04-16 13:42

Got it working.
Please add "cython" to the dependencies.
It's wierd that the python2 does not require this...

iosonofabio commented on 2014-04-13 16:33

For what it costs:

[python-pysam]$ namcap python-pysam-0.7.7-1-x86_64.pkg.tar.xz
python-pysam E: Missing custom license directory (usr/share/licenses/python-pysam)
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/samtools/win32/zlib.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/samtools/win32/zconf.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/samtools/win32/xcurses.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/samtools/bcftools/kmin.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/samtools/bcftools/bcf.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/samtools/bcftools/prob1.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/bgzf.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/khash.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/knetfile.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/kseq.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/tabix.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/kstring.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/bam_endian.h) does not have the world readable bit set.
python-pysam W: File (usr/lib/python3.4/site-packages/pysam/include/tabix/ksort.h) does not have the world readable bit set.

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