[med-svn] [ariba] 01/04: Imported Upstream version 1.0.1
Sascha Steinbiss
satta at debian.org
Tue Jun 28 14:30:22 UTC 2016
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satta pushed a commit to branch master
in repository ariba.
commit 74d1bf9fbe9264a65461d52b236c986c8d8eff01
Author: Sascha Steinbiss <satta at debian.org>
Date: Tue Jun 28 14:12:07 2016 +0000
Imported Upstream version 1.0.1
---
README.md | 57 ++++++++++++++++++++++++++++++++++++++++++++++--------
ariba/assembly.py | 1 -
ariba/tasks/run.py | 2 +-
setup.py | 2 +-
4 files changed, 51 insertions(+), 11 deletions(-)
diff --git a/README.md b/README.md
index 697c2ac..cfbfb14 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,17 @@
+Disclaimer
+==========
+
+This is pre-publication software that is currently under active development.
+Use it at your own risk. Bug reports are welcome, but
+user support is not provided at this time.
+
+
ARIBA
=====
Antibiotic Resistance Identification By Assembly
+
For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].
@@ -51,7 +60,7 @@ The environment variable is checked first and is used if it is set.
Otherwise ARIBA looks in your `$PATH` for the default name. This applies
to the following dependencies.
-| Dependency | Default | Environment variable name |
+| Dependency | Default executable | Environment variable name |
|----------------|------------------------|---------------------------|
| BCFtools | `bcftools` | `$ARIBA_BCFTOOLS` |
| Bowtie2 | `bowtie2` | `$ARIBA_BOWTIE2` |
@@ -63,17 +72,49 @@ to the following dependencies.
| SSPACE | `SSPACE_Basic_v2.0.pl` | `$ARIBA_SSPACE` |
-For example, you could specify an exact version of Samtools using
-(assuming BASH):
+For example, you could specify an exact version of a Samtools executable
+that you compiled and downloaded in your home directory (assuming BASH):
+
+ export ARIBA_SAMTOOLS=$HOME/samtools-1.2/samtools
+
+### Temporary files
+
+ARIBA can temporarily make a large number of files whilst running, which
+are put in a temporary directory made by ARIBA. The total size of these
+files is small, but there can be a many of them. This can be a
+problem when running large numbers (100s or 1000s) of jobs simultaneously
+on the same file system.
+By default, ARIBA creates a temporary directory for these files
+inside the output directory of each run.
+
+Each temporary directory
+is unique to one run of ARIBA, and is automatically deleted at the end
+of the run (even if ARIBA was killed by the user or crashed).
+The parent directory of the temporary
+directory can be changed using the environment variable
+`$ARIBA_TMPDIR`. The temporary directory for each run will be made
+inside `$ARIBA_TMPDIR`. For example,
+
+ export $ARIBA_TMPDIR=/tmp
+
+will result in the creation of a new directory inside `/tmp`, which
+will have a name of the form
- export ARIBA_SAMTOOLS=/path/to/samtools
+ /tmp/ariba.tmp.abcdef
-The path need not be absolute. ARIBA looks for the value of the variable
-in your $PATH. For example, suppose you have `samtools-0.1.19` and
-`samtools-1.3` installed. You could use this:
+where the suffix `abcdef` is a random string of characters, chosen
+such that `/tmp/ariba.tmp.abcdef` does not already exist.
- export ARIBA_SAMTOOLS=samtools-1.3
+The temporary directory can also be changed using the option
+`--tmp_dir` when running `ariba run`. Using this option takes precedence
+over the environment variable `$ARIBA_TMPDIR`. If neither are
+set, then ARIBA creates the temporary directory inside
+the output directory given to `ariba run`.
+The exception to the above is if the option `--noclean` is used.
+This forces the temporary directory to be placed in the output
+directory, and temporary files are kept. It is intended for
+debugging.
diff --git a/ariba/assembly.py b/ariba/assembly.py
index 40aa2ed..4344ac2 100644
--- a/ariba/assembly.py
+++ b/ariba/assembly.py
@@ -115,7 +115,6 @@ class Assembly:
'-o', self.assembler_dir,
'-k', str(self.assembly_kmer),
'--threads 1', # otherwise defaults to 16!
- '--untrusted-contigs', self.ref_fasta,
])
if self.spades_other_options is not None:
cmd += ' ' + self.spades_other_options
diff --git a/ariba/tasks/run.py b/ariba/tasks/run.py
index f7392b8..a4abb29 100644
--- a/ariba/tasks/run.py
+++ b/ariba/tasks/run.py
@@ -21,7 +21,7 @@ def run():
assembly_group = parser.add_argument_group('Assembly options')
assembly_group.add_argument('--assembly_cov', type=int, help='Target read coverage when sampling reads for assembly [%(default)s]', default=50, 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 (see --assembler_k), --untrusted-contigs (it is always used), or -t [%(default)s]', default="--only-assembler -m 4", metavar="OPTIONS")
+ 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")
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')
other_group = parser.add_argument_group('Other options')
diff --git a/setup.py b/setup.py
index ccc1607..8c97908 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@ from setuptools import setup, find_packages
setup(
name='ariba',
- version='1.0.0',
+ version='1.0.1',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*']},
--
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