[med-svn] [ariba] 01/02: remove unavailable tests, adjust binary names

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository ariba.

commit 66abfe45301b166c3e07f81c20b7380ad717719a
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sat Dec 5 12:49:10 2015 +0000

    remove unavailable tests, adjust binary names
---
 debian/patches/rename_cdhit_binary    | 40 +++++++++++++++++++++++++++++++++++
 debian/patches/series                 |  2 ++
 debian/patches/skip_unavailable_tests | 29 +++++++++++++++++++++++++
 3 files changed, 71 insertions(+)

diff --git a/debian/patches/rename_cdhit_binary b/debian/patches/rename_cdhit_binary
new file mode 100644
index 0000000..28078ab
--- /dev/null
+++ b/debian/patches/rename_cdhit_binary
@@ -0,0 +1,40 @@
+--- a/ariba/cdhit.py
++++ b/ariba/cdhit.py
+@@ -61,7 +61,7 @@
+         new_to_old_name = self._enumerate_fasta(self.infile, infile_renamed)
+ 
+         cmd = ' '.join([
+-            'cd-hit-est',
++            'cdhit-est',
+             '-i', infile_renamed,
+             '-o', cdhit_fasta,
+             '-c', str(self.seq_identity_threshold),
+--- a/ariba/external_progs.py
++++ b/ariba/external_progs.py
+@@ -16,7 +16,7 @@
+ prog_to_default = {
+     'bcftools': 'bcftools',
+     'bowtie2': 'bowtie2',
+-    'cdhit': 'cd-hit-est',
++    'cdhit': 'cdhit-est',
+     'gapfiller': 'GapFiller.pl',
+     'nucmer' : 'nucmer',
+     'samtools': 'samtools',
+@@ -31,7 +31,7 @@
+ prog_to_env_var = {
+     'bcftools': 'ARIBA_BCFTOOLS',
+     'samtools': 'ARIBA_SAMTOOLS',
+-    'spades': 'ARIBA_SPADES', 
++    'spades': 'ARIBA_SPADES',
+ }
+ 
+ 
+@@ -123,7 +123,7 @@
+         'sspace',
+         'gapfiller',
+     ]
+-    
++
+     if opts.assembler == 'spades':
+         to_check.append('spades')
+     elif opts.assembler == 'velvet':
diff --git a/debian/patches/series b/debian/patches/series
index e057d52..4fa99be 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
+rename_cdhit_binary
+skip_unavailable_tests
 spelling
diff --git a/debian/patches/skip_unavailable_tests b/debian/patches/skip_unavailable_tests
new file mode 100644
index 0000000..1831ac3
--- /dev/null
+++ b/debian/patches/skip_unavailable_tests
@@ -0,0 +1,29 @@
+--- a/ariba/tests/cluster_test.py
++++ b/ariba/tests/cluster_test.py
+@@ -134,7 +134,7 @@
+         clean_cluster_dir(cluster_dir)
+ 
+ 
+-    def test_assemble_with_spades(self):
++    def _test_assemble_with_spades(self):
+         '''test _assemble_with_spades'''
+         cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_spades')
+         clean_cluster_dir(cluster_dir)
+@@ -145,7 +145,7 @@
+         clean_cluster_dir(cluster_dir)
+ 
+ 
+-    def test_assemble_with_spades_fail(self):
++    def _test_assemble_with_spades_fail(self):
+         '''test _assemble_with_spades handles spades fail'''
+         cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_spades')
+         clean_cluster_dir(cluster_dir)
+@@ -630,7 +630,7 @@
+         clean_cluster_dir(cluster_dir)
+ 
+ 
+-    def test_make_assembly_vcf(self):
++    def _test_make_assembly_vcf(self):
+         '''test _make_assembly_vcf'''
+         cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
+         clean_cluster_dir(cluster_dir)

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