[med-svn] [ariba] 04/05: drop patches for old version
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 14:13:05 UTC 2016
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sascha-guest pushed a commit to branch master
in repository ariba.
commit ddaa4b41003e32223939be7f01a2973c240e02a1
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Fri May 27 11:02:16 2016 +0000
drop patches for old version
---
debian/patches/make_velvet_default | 12 ----------
debian/patches/rename_cdhit_binary | 41 -----------------------------------
debian/patches/series | 4 ----
debian/patches/skip_unavailable_tests | 30 -------------------------
debian/patches/spelling | 12 ----------
5 files changed, 99 deletions(-)
diff --git a/debian/patches/make_velvet_default b/debian/patches/make_velvet_default
deleted file mode 100644
index 5419cb5..0000000
--- a/debian/patches/make_velvet_default
+++ /dev/null
@@ -1,12 +0,0 @@
-Description: Make_velvet_default
---- a/ariba/tasks/run.py
-+++ b/ariba/tasks/run.py
-@@ -24,7 +24,7 @@
-
- assembly_group = parser.add_argument_group('Assembly options')
- allowed_assemblers = ['velvet', 'spades']
-- assembly_group.add_argument('--assembler', help='Assembler to use. Available options: ' + ','.join(allowed_assemblers) + ' [%(default)s]', choices=allowed_assemblers, default='spades', metavar='Assembler')
-+ assembly_group.add_argument('--assembler', help='Assembler to use. Available options: ' + ','.join(allowed_assemblers) + ' [%(default)s]', choices=allowed_assemblers, default='velvet', metavar='Assembler')
- assembly_group.add_argument('--min_scaff_depth', type=int, help='Minimum number of read pairs needed as evidence for scaffold link between two contigs. This is also the value used for sspace -k when scaffolding [%(default)s]', default=10, metavar='INT')
- assembly_group.add_argument('--assembler_k', type=int, help='kmer size to use with assembler. You can use 0 to set kmer to 2/3 of the read length. Warning - lower kmers are usually better. [%(default)s]', metavar='INT', default=21)
- assembly_group.add_argument('--spades_other', help='Put options string to be used with spades in quotes. This will NOT be sanity checked. Do not use -k or -t: for these options you should use the ariba run options --assembler_k and --threads [%(default)s]', default="--only-assembler", metavar="OPTIONS")
diff --git a/debian/patches/rename_cdhit_binary b/debian/patches/rename_cdhit_binary
deleted file mode 100644
index a89223d..0000000
--- a/debian/patches/rename_cdhit_binary
+++ /dev/null
@@ -1,41 +0,0 @@
-Description: Rename_cdhit_binary
---- 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
deleted file mode 100644
index d240e23..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,4 +0,0 @@
-rename_cdhit_binary
-skip_unavailable_tests
-spelling
-make_velvet_default
diff --git a/debian/patches/skip_unavailable_tests b/debian/patches/skip_unavailable_tests
deleted file mode 100644
index e07652f..0000000
--- a/debian/patches/skip_unavailable_tests
+++ /dev/null
@@ -1,30 +0,0 @@
-Description: Skip_unavailable_tests
---- 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)
diff --git a/debian/patches/spelling b/debian/patches/spelling
deleted file mode 100644
index 3ed170a..0000000
--- a/debian/patches/spelling
+++ /dev/null
@@ -1,12 +0,0 @@
-Description: Spelling
---- a/ariba/tasks/summary.py
-+++ b/ariba/tasks/summary.py
-@@ -8,7 +8,7 @@
- epilog = 'Files must be listed after the output file and/or the option --fofn must be used. If both used, all files in the filename specified by --fofn AND the files listed after the output file will be used as input. The input report files must be in tsv format, not xls.')
- parser.add_argument('-f', '--fofn', help='File of filenames of ariba reports in tsv format (not xls) to be summarised. Must be used if no input files listed after the outfile.', metavar='FILENAME')
- parser.add_argument('--min_id', type=float, help='Minimum percent identity cutoff to count as assembled [%(default)s]', default=90, metavar='FLOAT')
-- parser.add_argument('--no_filter', action='store_true', help='Do not filter rows or columns of output that are all 0 (by deafult, they are removed from the output)')
-+ parser.add_argument('--no_filter', action='store_true', help='Do not filter rows or columns of output that are all 0 (by default, they are removed from the output)')
- parser.add_argument('outfile', help='Name of output file. If file ends with ".xls", then an excel spreadsheet is written. Otherwise a tsv file is written')
- parser.add_argument('infiles', nargs='*', help='Files to be summarised')
- options = parser.parse_args()
--
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