Package Details: python-pysam 0.18.0-1

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
Licenses: MIT
Provides: python-pysam
Submitter: iosonofabio
Maintainer: PumpkinCheshire
Last Packager: PumpkinCheshire
Votes: 11
Popularity: 0.000104
First Submitted: 2013-10-14 17:12 (UTC)
Last Updated: 2021-11-24 08:01 (UTC)

Latest Comments

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) {

Stunts commented on 2014-04-16 15:57 (UTC)

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

iosonofabio commented on 2014-04-16 14:48 (UTC)

Maybe the package is precompiled for python2...

Stunts commented on 2014-04-16 13:42 (UTC)

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 (UTC)

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.

Stunts commented on 2014-04-13 15:33 (UTC)

All my packages are up-to-date... Could you please try to run namcap against the built package and see if something is missing please? Thanks!

iosonofabio commented on 2014-04-13 15:06 (UTC)

Hi Stunts, I built it today and it works for me, there might be some dependency inconsistency. Is your gcc up to date? Fabio

Stunts commented on 2014-04-13 14:38 (UTC)

Fails to build for me... Here's what I'm getting: pysam/csamtools.c:3832:18: note: expected ‘struct bam_pileup1_t **’ but argument is of type ‘const struct bam_pileup1_t **’ static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) { ^ pysam/csamtools.c: In function ‘__Pyx_TraceSetupAndCall’: pysam/csamtools.c:45773:17: error: ‘PyFrameObject’ has no member named ‘f_tstate’ (*frame)->f_tstate = PyThreadState_GET(); ^ error: command 'gcc' failed with exit status 1 python2-pysam builds and works just fine.