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 <[email protected]> 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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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