Commit 74d1bf9fbe9264a65461d52b236c986c8d8eff01 - ariba

Imported Upstream version 1.0.1 Sascha Steinbiss 7 years ago

4 changed file(s) with 51 addition(s) and 11 deletion(s). Raw diff Collapse all Expand all

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README.md less more

	0	Disclaimer
	1	==========
	2
	3	This is pre-publication software that is currently under active development.
	4	Use it at your own risk. Bug reports are welcome, but
	5	user support is not provided at this time.
	6
	7
0	8	ARIBA
1	9	=====
2	10
3	11	Antibiotic Resistance Identification By Assembly
	12
4	13
5	14	For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].
6	15

50	59	Otherwise ARIBA looks in your `$PATH` for the default name. This applies
51	60	to the following dependencies.
52	61
53		\| Dependency \| Default \| Environment variable name \|
	62	\| Dependency \| Default executable \| Environment variable name \|
54	63	\|----------------\|------------------------\|---------------------------\|
55	64	\| BCFtools \| `bcftools` \| `$ARIBA_BCFTOOLS` \|
56	65	\| Bowtie2 \| `bowtie2` \| `$ARIBA_BOWTIE2` \|

62	71	\| SSPACE \| `SSPACE_Basic_v2.0.pl` \| `$ARIBA_SSPACE` \|
63	72
64	73
65		For example, you could specify an exact version of Samtools using
66		(assuming BASH):
	74	For example, you could specify an exact version of a Samtools executable
	75	that you compiled and downloaded in your home directory (assuming BASH):
67	76
68		export ARIBA_SAMTOOLS=/path/to/samtools
	77	export ARIBA_SAMTOOLS=$HOME/samtools-1.2/samtools
69	78
70		The path need not be absolute. ARIBA looks for the value of the variable
71		in your $PATH. For example, suppose you have `samtools-0.1.19` and
72		`samtools-1.3` installed. You could use this:
	79	### Temporary files
73	80
74		export ARIBA_SAMTOOLS=samtools-1.3
	81	ARIBA can temporarily make a large number of files whilst running, which
	82	are put in a temporary directory made by ARIBA. The total size of these
	83	files is small, but there can be a many of them. This can be a
	84	problem when running large numbers (100s or 1000s) of jobs simultaneously
	85	on the same file system.
	86	By default, ARIBA creates a temporary directory for these files
	87	inside the output directory of each run.
75	88
	89	Each temporary directory
	90	is unique to one run of ARIBA, and is automatically deleted at the end
	91	of the run (even if ARIBA was killed by the user or crashed).
	92	The parent directory of the temporary
	93	directory can be changed using the environment variable
	94	`$ARIBA_TMPDIR`. The temporary directory for each run will be made
	95	inside `$ARIBA_TMPDIR`. For example,
	96
	97	export $ARIBA_TMPDIR=/tmp
	98
	99	will result in the creation of a new directory inside `/tmp`, which
	100	will have a name of the form
	101
	102	/tmp/ariba.tmp.abcdef
	103
	104	where the suffix `abcdef` is a random string of characters, chosen
	105	such that `/tmp/ariba.tmp.abcdef` does not already exist.
	106
	107	The temporary directory can also be changed using the option
	108	`--tmp_dir` when running `ariba run`. Using this option takes precedence
	109	over the environment variable `$ARIBA_TMPDIR`. If neither are
	110	set, then ARIBA creates the temporary directory inside
	111	the output directory given to `ariba run`.
	112
	113	The exception to the above is if the option `--noclean` is used.
	114	This forces the temporary directory to be placed in the output
	115	directory, and temporary files are kept. It is intended for
	116	debugging.
76	117
77	118
78	119

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ariba/assembly.py less more

114	114	'-o', self.assembler_dir,
115	115	'-k', str(self.assembly_kmer),
116	116	'--threads 1', # otherwise defaults to 16!
117		'--untrusted-contigs', self.ref_fasta,
118	117	])
119	118	if self.spades_other_options is not None:
120	119	cmd += ' ' + self.spades_other_options

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ariba/tasks/run.py less more

20	20	assembly_group = parser.add_argument_group('Assembly options')
21	21	assembly_group.add_argument('--assembly_cov', type=int, help='Target read coverage when sampling reads for assembly [%(default)s]', default=50, metavar='INT')
22	22	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)
23		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 (see --assembler_k), --untrusted-contigs (it is always used), or -t [%(default)s]', default="--only-assembler -m 4", metavar="OPTIONS")
	23	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 (see --assembler_k), or -t (use ariba option --threads) [%(default)s]', default="--only-assembler -m 4", metavar="OPTIONS")
24	24	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')
25	25
26	26	other_group = parser.add_argument_group('Other options')

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setup.py less more

6	6
7	7	setup(
8	8	name='ariba',
9		version='1.0.0',
	9	version='1.0.1',
10	10	description='ARIBA: Antibiotic Resistance Identification By Assembly',
11	11	packages = find_packages(),
12	12	package_data={'ariba': ['test_run_data/*']},