[med-svn] [Git][med-team/minimap2][master] 2 commits: Provide Python3 interface

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / minimap2


Commits:
1cc6340d by Andreas Tille at 2020-05-13T12:58:10+02:00
Provide Python3 interface

- - - - -
bc4e160c by Andreas Tille at 2020-05-13T13:16:29+02:00
TODO: Fix simde linking

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/python3-mappy.install
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+minimap2 (2.17+dfsg-10) UNRELEASED; urgency=medium
+
+  * Provide Python3 interface
+  TODO: Fix simde linking:
+   >>> import mappy
+   Traceback (most recent call last):
+     File "<stdin>", line 1, in <module>
+   ImportError: /usr/lib/python3/dist-packages/mappy.cpython-38-x86_64-linux-gnu.so: undefined symbol: ksw_extz2_sse
+
+ -- Andreas Tille <tille at debian.org>  Wed, 13 May 2020 11:44:53 +0200
+
 minimap2 (2.17+dfsg-9) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -4,6 +4,9 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
+               dh-python,
+               cython3,
+               python3-all-dev,
                d-shlibs,
                zlib1g-dev,
                texlive-latex-extra,
@@ -61,3 +64,22 @@ Description: development headers for libminimap
  .
  This package contains the C library headers for using minimap in custom tools,
  along with a static library.
+
+Package: python3-mappy
+Architecture: any
+Section: python
+Depends: ${shlibs:Depends},
+         ${python3:Depends},
+         ${misc:Depends}
+Description: Python3 interface minimap2
+ Minimap2 is a versatile sequence alignment program that aligns DNA or
+ mRNA sequences against a large reference database. Typical use cases
+ include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
+ human genome; (2) finding overlaps between long reads with error rate up
+ to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
+ or Direct RNA reads against a reference genome; (4) aligning Illumina
+ single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-
+ genome alignment between two closely related species with divergence
+ below ~15%.
+ .
+ This package contains the Python3 interface for using minimap2.


=====================================
debian/python3-mappy.install
=====================================
@@ -0,0 +1 @@
+/usr/lib/python3*


=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
 RANLIB ?= ranlib
 
 %:
-	dh $@
+	dh $@ --with python3
 
 override_dh_auto_clean:
 	dh_auto_clean
@@ -26,6 +26,7 @@ endif
 override_dh_auto_build:
 	dh_auto_build -- $(build_vars)
 	cd tex && make
+	dh_auto_build --buildsystem=pybuild
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -33,6 +34,10 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	rm test.sam
 endif
 
+override_dh_auto_install:
+	dh_auto_install
+	dh_auto_install --buildsystem=pybuild
+
 override_dh_compress:
 	dh_compress --exclude=.pdf
 



View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/compare/8976720d09bd3f17167d5433594a9f10e17d4f45...bc4e160c7e75cd43a0c2e9b6e149006e76df22a8

-- 
View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/compare/8976720d09bd3f17167d5433594a9f10e17d4f45...bc4e160c7e75cd43a0c2e9b6e149006e76df22a8
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