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 <[email protected]> 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. > > -- > http://fam-tille.de > > > -- > To UNSUBSCRIBE, email to [email protected] > with a subject of "unsubscribe". Trouble? Contact [email protected] > Archive: https://lists.debian.org/[email protected] > > -- http://fam-tille.de -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
