Re: HTSlib code copy in python-pysam.
Hi,
just a quick note: I just found something in setup.py some interesting
switch and I'm experimenting with the following patch (not yet
commited):
Author: Andreas Tille <tille@debian.org>
Date: Tue, 19 Aug 2014 21:26:37 +0200
Description: setup.py allows to use external htslib which we do hereby
--- a/setup.py
+++ b/setup.py
@@ -32,7 +32,7 @@ IS_PYTHON3 = sys.version_info[0] >= 3
# pysam.
# external: use shared libhts.so compiled outside of
# pysam
-HTSLIB = "separate"
+HTSLIB = "external"
HTSLIB_DIR = []
# collect pysam version
Kind regards
Andreas.
On Wed, Aug 20, 2014 at 09:55:54AM +0200, Andreas Tille wrote:
> Hi Charles,
>
> On Wed, Aug 20, 2014 at 06:53:49AM +0900, Charles Plessy wrote:
> >
> > I guess you spotted the code copy of the HTSlib in python-pysam ?
>
> Well, the code copy existed from the beginning of maintaining
> python-pysam (at this time compared to the predecessor of htslib). At
> this time we decided that it is to hard to link dynamically.
>
> > In theory, it should be easier to build python-pysam on the system's
> > copy, compared to the previsous situation with libbam, because
> > the HTSlib allows for dynamic linking.
> >
> > In practice, I do not know how to do it with python modules…
>
> Thanks for the hint - we might rethink the current packaging. However,
> my actual approach is targeting at an upgrade and recheck whether we
> could fix #753490 (I somehow missed this bug with patch and it does not
> apply to the new version ... :-()
>
> > I opened the following issue on GitHub's upstream tracker.
> >
> > https://github.com/pysam-developers/pysam/issues/34
>
> Cool. May be we get some help from upstream.
>
> Any help / enhancement is more than welcome. BTW, my push was more an
> accident since I wanted to write `quilt push` and instead issued `git
> push`. The current status in Git is not functional and I have some
> local changes here which also do not yet lead to a working package since
> the test suite fails. If anybody is interested - I'd be more than happy
> to hand over this task to somebody else (as always ;-)).
>
> Thanks again for the hint
>
> Andreas.
>
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