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Holland Computing Center
chipathlon
Commits
2feb7312
Commit
2feb7312
authored
Feb 24, 2016
by
aknecht2
Browse files
Added individual job yaml files.
parent
c59ee118
Changes
6
Hide whitespace changes
Inline
Side-by-side
chipathlon/db.py
0 → 100644
View file @
2feb7312
from
pymongo
import
MongoClient
def
setup
chipathlon/jobs/bwa_align_paired.yaml
0 → 100644
View file @
2feb7312
bwa_align_paired
:
inputs
:
-
fna
-
fastq
-
fastq
outputs
:
-
sam
arguments
:
-
"
-M"
:
changeable
:
false
required
:
true
value
:
false
-
"
-t"
:
changeable
:
true
required
:
false
default
:
1
value
:
true
-
"
$inputs.0"
:
changeable
:
false
required
:
true
value
:
false
-
"
$inputs.1"
:
changeable
:
false
required
:
true
value
:
false
-
"
$inputs.2"
:
changeable
:
false
required
:
true
value
:
false
walltime
:
2000
memory
:
2000
chipathlon/jobs/bwa_align_single.yaml
0 → 100644
View file @
2feb7312
bwa_align_single
:
inputs
:
-
fna
-
fastq
outputs
:
-
sai
command
:
bwa
arguments
:
-
aln
:
changeable
:
false
required
:
true
value
:
false
-
"
-q"
:
changeable
:
true
required
:
false
default
:
5
value
:
true
-
"
-l"
:
changeable
:
true
required
:
false
default
:
32
value
:
true
-
"
-k"
:
changeable
:
true
required
:
false
default
:
2
value
:
true
-
"
-t"
:
changeable
:
true
required
:
false
default
:
1
value
:
true
-
"
$inputs.0"
:
changeable
:
false
required
:
true
value
:
false
-
"
$inputs.1"
:
changeable
:
false
required
:
true
value
:
false
walltime
:
2000
memory
:
2000
chipathlon/jobs/bwa_sai_to_sam.yaml
0 → 100644
View file @
2feb7312
bwa_sai_to_sam
:
inputs
:
-
fna
-
sai
-
fastq
outputs
:
-
sam
command
:
bwa
arguments
:
-
samse
:
changeable
:
false
required
:
true
value
:
false
-
"
$inputs.0"
:
changeable
:
false
required
:
true
value
:
false
-
"
$inputs.1"
:
changeable
:
false
required
:
true
value
:
false
-
"
$inputs.2"
:
changeable
:
false
required
:
true
value
:
false
walltime
:
2000
memory
:
2000
chipathlon/jobs/samtools_sam_to_bam.yaml
0 → 100644
View file @
2feb7312
samtools_sam_to_bam
:
inputs
:
-
sam
outputs
:
-
bam
arguments
:
-
view
:
changeable
:
false
required
:
true
value
:
false
-
"
-bS"
changeable
:
false
required
:
true
value
:
false
-
"
$inputs.0"
changeable
:
false
required
:
true
value
:
false
walltime
:
2000
memory
:
2000
chipathlon/utils.py
View file @
2feb7312
import
sys
def
progress
(
current
,
end
):
def
progress
(
current
,
end
,
length
=
20
):
percent
=
float
(
current
)
/
end
hashes
=
"#"
*
int
(
round
(
percent
*
20
))
spaces
=
" "
*
(
20
-
len
(
hashes
))
hashes
=
"#"
*
int
(
round
(
percent
*
length
))
spaces
=
" "
*
(
length
-
len
(
hashes
))
sys
.
stdout
.
write
(
"
\r
Processed %s / %s entries. [%s] %s%%"
%
(
current
,
end
,
hashes
+
spaces
,
int
(
round
(
percent
*
100
))))
sys
.
stdout
.
flush
()
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