Michael R. Crusoe pushed to branch master at Debian Med / iva
Commits: e2bf816d by Michael R. Crusoe at 2019-12-25T11:36:28Z fix the samtools version logic - - - - - 076bf419 by Michael R. Crusoe at 2019-12-25T11:37:11Z routine-update: debhelper-compat 12 - - - - - 939480c4 by Michael R. Crusoe at 2019-12-25T11:41:31Z Standards-Version: 4.4.1 - - - - - 5 changed files: - debian/changelog - − debian/compat - debian/control - + debian/patches/samtools1.10 - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +iva (1.0.9+ds-7) unstable; urgency=medium + + * Team upload. + * debian/patches/samtools1.10: fix the samtools version logic + * debhelper-compat 12 + + -- Michael R. Crusoe <[email protected]> Wed, 25 Dec 2019 12:37:15 +0100 + iva (1.0.9+ds-6) unstable; urgency=medium * Use correct Vcs-Git URL. ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -5,7 +5,7 @@ Uploaders: Andreas Tille <[email protected]>, Sascha Steinbiss <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper-compat (= 12), dh-python, libssl-dev, bioperl, @@ -15,6 +15,7 @@ Build-Depends: debhelper (>= 11~), mummer, python3, python3-setuptools, + python3-packaging, python3-numpy, python3-nose, python3-networkx, @@ -22,7 +23,7 @@ Build-Depends: debhelper (>= 11~), samtools, smalt, default-jdk-headless -Standards-Version: 4.1.4 +Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/iva Vcs-Git: https://salsa.debian.org/med-team/iva.git Homepage: https://github.com/sanger-pathogens/iva @@ -31,6 +32,7 @@ Package: iva Architecture: any Depends: ${misc:Depends}, ${python3:Depends}, + ${perl:Depends}, fastaq (>= 1.6), kmc, mummer, ===================================== debian/patches/samtools1.10 ===================================== @@ -0,0 +1,22 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Fix samtools version parsing so that 1.10 > 1.2 +--- iva.orig/iva/mapping.py ++++ iva/iva/mapping.py +@@ -21,6 +21,8 @@ + from iva import common + from iva import external_progs + ++from packaging import version ++ + class Error (Exception): pass + + +@@ -93,7 +95,7 @@ + if sort: + threads = min(4, threads) + thread_mem = int(500 / threads) +- if str(external_progs.get_version('samtools')) >= '1.2': ++ if version.parse(external_progs.get_version('samtools')) >= version.parse("1.2"): + sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M -o ' + final_bam + ' ' + intermediate_bam + else: + sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ disable-multithreaded-test.patch perl-shebang.patch +samtools1.10 View it on GitLab: https://salsa.debian.org/med-team/iva/compare/7a61fefba06c49722109ae0dcaad2a4384b181b0...939480c456445d7a8ac871d9bb3c9ecdf48694ce -- View it on GitLab: https://salsa.debian.org/med-team/iva/compare/7a61fefba06c49722109ae0dcaad2a4384b181b0...939480c456445d7a8ac871d9bb3c9ecdf48694ce You're receiving this email because of your account on salsa.debian.org.
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