[med-svn] [ariba] 02/02: make velvet the default assembler

[Sascha Steinbiss]

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

commit df6a4815f84c2c84293841f55663f7d1c6722b4c
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sat Dec 5 12:56:37 2015 +0000

    make velvet the default assembler
    
    spades is not yet packaged...
---
 debian/patches/make_velvet_default | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/debian/patches/make_velvet_default b/debian/patches/make_velvet_default
new file mode 100644
index 0000000..e2d68ca
--- /dev/null
+++ b/debian/patches/make_velvet_default
@@ -0,0 +1,11 @@
+--- 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")

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