Skip to content
GitLab
Explore
Sign in
Register
Commits on Source (3)
fix the samtools version logic
· e2bf816d
Michael R. Crusoe
authored
Dec 25, 2019
e2bf816d
routine-update: debhelper-compat 12
· 076bf419
Michael R. Crusoe
authored
Dec 25, 2019
076bf419
Standards-Version: 4.4.1
· 939480c4
Michael R. Crusoe
authored
Dec 25, 2019
939480c4
Show whitespace changes
Inline
Side-by-side
debian/changelog
View file @
939480c4
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@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
100644 → 0
View file @
7a61fefb
11
debian/control
View file @
939480c4
...
...
@@ -5,7 +5,7 @@ Uploaders: Andreas Tille <tille@debian.org>,
Sascha Steinbiss <satta@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (
>
= 1
1~
),
Build-Depends: debhelper
-compat
(= 1
2
),
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 → 100644
View file @
939480c4
From: Michael R. Crusoe <michael.crusoe@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
View file @
939480c4
disable-multithreaded-test.patch
perl-shebang.patch
samtools1.10