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commit 077607947b3d1c0220e69e9cb31f9d54c6ef0aee
Author: Sascha Steinbiss <sas...@steinbiss.name>
Date: Fri May 27 14:12:42 2016 +0000
get packaging up to date with new version
---
ariba/cdhit.py | 2 +-
ariba/external_progs.py | 6 +++---
ariba/reference_data.py | 2 +-
debian/control | 5 +++--
debian/patches/fix-spades-call.patch | 20 ++++++++++++++++++
debian/patches/relax-pysam-version.patch | 15 +++++++++++++
debian/patches/rename-cdhit.patch | 36 ++++++++++++++++++++++++++++++++
debian/patches/series | 3 +++
debian/rules | 5 +++--
setup.py | 2 +-
10 files changed, 86 insertions(+), 10 deletions(-)
diff --git a/ariba/cdhit.py b/ariba/cdhit.py
index c49750c..d5dac57 100644
--- a/ariba/cdhit.py
+++ b/ariba/cdhit.py
@@ -15,7 +15,7 @@ class Runner:
threads=1,
length_diff_cutoff=0.9,
verbose=False,
- cd_hit_est='cd-hit-est',
+ cd_hit_est='cdhit-est',
rename_suffix='x',
):
diff --git a/ariba/external_progs.py b/ariba/external_progs.py
index 35fca54..4c5fa12 100644
--- a/ariba/external_progs.py
+++ b/ariba/external_progs.py
@@ -12,7 +12,7 @@ class Error (Exception): pass
prog_to_default = {
'bcftools': 'bcftools',
'bowtie2': 'bowtie2',
- 'cdhit': 'cd-hit-est',
+ 'cdhit': 'cdhit-est',
'gapfiller': 'GapFiller.pl',
'nucmer' : 'nucmer',
'samtools': 'samtools',
@@ -69,8 +69,8 @@ class ExternalProgs:
# python3.4, not python2. SPAdes throws an error about not being
# compatible with python3.4.
# This means we need to explicitly run SPAdes with python2.
- if prog == 'spades' and self.progs[prog] is not None:
- self.progs[prog] = 'python2 ' + self.progs[prog]
+ #if prog == 'spades' and self.progs[prog] is not None:
+ # self.progs[prog] = 'python2 ' + self.progs[prog]
if self.progs[prog] is None:
if prog in optional_progs:
warnings.append(prog + ' not found in path. Looked for ' +
prog_exe + '. But it is optional so will be skipped during assembly')
diff --git a/ariba/reference_data.py b/ariba/reference_data.py
index 3251a05..9956398 100644
--- a/ariba/reference_data.py
+++ b/ariba/reference_data.py
@@ -459,7 +459,7 @@ class ReferenceData:
pyfastaq.utils.close(f_out)
- def cluster_with_cdhit(self, inprefix, outprefix,
seq_identity_threshold=0.9, threads=1, length_diff_cutoff=0.9, nocluster=False,
verbose=False, cd_hit_est='cd-hit-est', clusters_file=None):
+ def cluster_with_cdhit(self, inprefix, outprefix,
seq_identity_threshold=0.9, threads=1, length_diff_cutoff=0.9, nocluster=False,
verbose=False, cd_hit_est='cdhit-est', clusters_file=None):
files_to_cat = []
clusters = {}
diff --git a/debian/control b/debian/control
index 693bb9e..c474bf7 100644
--- a/debian/control
+++ b/debian/control
@@ -12,6 +12,7 @@ Build-Depends: debhelper (>= 9),
python3-nose,
python3-lxml,
bowtie2 (>= 2.1.0),
+ r-cran-ape,
cd-hit,
samtools (>= 1.2),
bcftools (>= 1.2),
@@ -19,8 +20,7 @@ Build-Depends: debhelper (>= 9),
spades,
fastaq (>= 3.10.0),
help2man
-Standards-Version: 3.9.7
-Testsuite: autopkgtest
+Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ariba.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/ariba.git
Homepage: https://github.com/sanger-pathogens/ariba
@@ -39,6 +39,7 @@ Depends: ${misc:Depends},
python3-pysam,
python3-openpyxl,
fastaq (>= 3.10.0),
+ r-cran-ape,
python3-lxml
Description: Antibiotic Resistance Identification By Assembly
ARIBA is a tool that identifies antibiotic resistance genes by running local
diff --git a/debian/patches/fix-spades-call.patch
b/debian/patches/fix-spades-call.patch
new file mode 100644
index 0000000..8190f5a
--- /dev/null
+++ b/debian/patches/fix-spades-call.patch
@@ -0,0 +1,20 @@
+Description: fix SPAdes call
+ In Debian, spades.py is an alternative name for spades, a wrapper
+ around a script located elsewhere. ARIBA assumes it's the original
+ Python script and tries to call it as an argument of 'python2'.
+ This is no longer necessary in Debian; it will determine its Python
+ version by itself.
+Author: Sascha Steinbiss <sas...@steinbiss.name>
+--- a/ariba/external_progs.py
++++ b/ariba/external_progs.py
+@@ -69,8 +69,8 @@
+ # python3.4, not python2. SPAdes throws an error about not being
+ # compatible with python3.4.
+ # This means we need to explicitly run SPAdes with python2.
+- if prog == 'spades' and self.progs[prog] is not None:
+- self.progs[prog] = 'python2 ' + self.progs[prog]
++ #if prog == 'spades' and self.progs[prog] is not None:
++ # self.progs[prog] = 'python2 ' + self.progs[prog]
+ if self.progs[prog] is None:
+ if prog in optional_progs:
+ warnings.append(prog + ' not found in path. Looked for '
+ prog_exe + '. But it is optional so will be skipped during assembly')
diff --git a/debian/patches/relax-pysam-version.patch
b/debian/patches/relax-pysam-version.patch
new file mode 100644
index 0000000..aa7114f
--- /dev/null
+++ b/debian/patches/relax-pysam-version.patch
@@ -0,0 +1,15 @@
+Description: relax pysam version
+ Pysam was restricted by upstream to <0.8.3 because newer versions fail
+ to build when installed via pip. This is no longer necessary in Debian.
+Author: Sascha Steinbiss <sas...@steinbiss.name>
+--- a/setup.py
++++ b/setup.py
+@@ -20,7 +20,7 @@
+ install_requires=[
+ 'openpyxl >= 1.6.2',
+ 'pyfastaq >= 3.12.0',
+- 'pysam >= 0.8.1, <= 0.8.3',
++ 'pysam >= 0.8.1',
+ 'pymummer>=0.6.1',
+ ],
+ license='GPLv3',
diff --git a/debian/patches/rename-cdhit.patch
b/debian/patches/rename-cdhit.patch
new file mode 100644
index 0000000..374cf78
--- /dev/null
+++ b/debian/patches/rename-cdhit.patch
@@ -0,0 +1,36 @@
+Description: use Debian name for CD-HIT
+ Debian's CD-HIT-EST executable is named cdhit-est, not cd-hit-est.
+Author: Sascha Steinbiss <sas...@steinbiss.name>
+--- a/ariba/external_progs.py
++++ b/ariba/external_progs.py
+@@ -12,7 +12,7 @@
+ prog_to_default = {
+ 'bcftools': 'bcftools',
+ 'bowtie2': 'bowtie2',
+- 'cdhit': 'cd-hit-est',
++ 'cdhit': 'cdhit-est',
+ 'gapfiller': 'GapFiller.pl',
+ 'nucmer' : 'nucmer',
+ 'samtools': 'samtools',
+--- a/ariba/cdhit.py
++++ b/ariba/cdhit.py
+@@ -15,7 +15,7 @@
+ threads=1,
+ length_diff_cutoff=0.9,
+ verbose=False,
+- cd_hit_est='cd-hit-est',
++ cd_hit_est='cdhit-est',
+ rename_suffix='x',
+ ):
+
+--- a/ariba/reference_data.py
++++ b/ariba/reference_data.py
+@@ -459,7 +459,7 @@
+ pyfastaq.utils.close(f_out)
+
+
+- def cluster_with_cdhit(self, inprefix, outprefix,
seq_identity_threshold=0.9, threads=1, length_diff_cutoff=0.9, nocluster=False,
verbose=False, cd_hit_est='cd-hit-est', clusters_file=None):
++ def cluster_with_cdhit(self, inprefix, outprefix,
seq_identity_threshold=0.9, threads=1, length_diff_cutoff=0.9, nocluster=False,
verbose=False, cd_hit_est='cdhit-est', clusters_file=None):
+ files_to_cat = []
+ clusters = {}
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..22823e7
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+rename-cdhit.patch
+fix-spades-call.patch
+relax-pysam-version.patch
diff --git a/debian/rules b/debian/rules
index 8992bd9..20880fd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,6 +4,7 @@ export PYBUILD_NAME=ariba
mandir := $(CURDIR)/debian/man
debfolder := $(CURDIR)/debian
+ARIBA_VERSION := $(shell grep -Po "(?<=version=')([0-9.]+)" setup.py)
%:
dh $@ --with python3 --buildsystem=pybuild
@@ -13,11 +14,11 @@ override_dh_installman:
PYTHONPATH=. help2man -N -o debian/man/ariba.1 \
-n 'Antibiotic Resistance Identification by Assembly' \
--no-discard-stderr \
- --version-string=`PYTHONPATH=. scripts/ariba version` scripts/ariba
+ --version-string="$(ARIBA_VERSION)" scripts/ariba
sed -i 's/.SH DESCRIPTION/.SH DESCRIPTION\\n.nf/' $(mandir)/ariba.1
scripts/ariba 2>&1 | tail -n +13 | debian/make_man
dh_installman --
override_dh_auto_test:
python3 setup.py nosetests
- dh_auto_test --
\ No newline at end of file
+ dh_auto_test --
diff --git a/setup.py b/setup.py
index ccc1607..df13f53 100644
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,7 @@ setup(
install_requires=[
'openpyxl >= 1.6.2',
'pyfastaq >= 3.12.0',
- 'pysam >= 0.8.1, <= 0.8.3',
+ 'pysam >= 0.8.1',
'pymummer>=0.6.1',
],
license='GPLv3',
--
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