[med-svn] [Git][med-team/iva][master] 3 commits: fix the samtools version logic

[Michael R. Crusoe]

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 <michael.crusoe at gmail.com>  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 <tille at debian.org>,
            Sascha Steinbiss <satta at debian.org>
 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 <michael.crusoe at gmail.com>
+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
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