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requires network connection to work
2009-02-09
cjfields
requires n
e
t
w
ork co
n
nection to work
commit
|
commitdiff
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tree
2009-02-05
c
jfields
TODO no
w
pa
s
ses (tha
n
ks to Mahmut Uludag
and
M
artin
.
.
.
commit
|
commitdiff
|
tree
2009-02-03
cjfields
Fix Bio::
D
B::EUtilities (API
changed c
o
nsiderably
from
.
.
.
commit
|
commitdiff
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tree
2009-02-02
cjfields
v
e
rsion to 1
.
6
.
9
(pre-1
.
7
)
commit
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commitdiff
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tree
2009-01-31
cjfields
swit
c
h to simple die
commit
|
commitdiff
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tree
2009-01-31
cjfields
use eval to check
fo
r
Bio::Root::Build, di
e
gracefu
l
ly
commit
|
commitdiff
|
tree
2009-01-31
c
j
fiel
d
s
TCoff
e
e
now passes
commit
|
commitdiff
|
tree
2009-01-30
cjfields
remove de
b
u
gging line
commit
|
commitdiff
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tree
2009-01-30
cjfields
partial fix for TCoffee ver
s
ion
a
bove v
5
(
stil
l
break
i
ng
.
.
.
commit
|
commitdiff
|
tree
2009-01-30
cjfiel
d
s
com
m
a cau
s
ing tests to fail on some systems if Jav
a
.
.
.
commit
|
commitdiff
|
tree
2009-01-29
cjfields
add some flexibility
f
o
r older m
o
del name
s
commit
|
commitdiff
|
tree
2009-01-28
c
jf
i
elds
sm
a
l
l
tweaks
to p
r
imer3 (should tr
y
getting this to
.
.
.
commit
|
commitdiff
|
tree
2009-01-27
cjfields
tweak error message
commit
|
commitdiff
|
tree
2009-01-27
cjf
i
elds
* newer
versions of
t
_coffee failing this test,
may
.
.
.
commit
|
commitdiff
|
tree
2009-01-27
cj
f
i
e
lds
*
TODO failing Ana
l
ysisFac
t
ory_soap
.
t test
(app
e
a
rs
.
.
.
commit
|
commitdiff
|
tree
2009-01-27
cjfields
c
atch version if
it con
t
a
ins alphanumer
i
c
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|
commitdiff
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tree
2009-01-13
c
j
fields
* small
u
pda
t
es
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|
commitdiff
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tree
2009-01-13
cjfields
Remove
P
i
se-
r
elated stuf
f
, update with other depen
d
e
n
cies
commit
|
commitdiff
|
tree
2009-01-13
cjfields
Add DEPE
N
DE
N
CIES f
i
le
.
commit
|
commitdiff
|
tree
2009-01-13
cjfields
Remo
v
e P
i
se-
r
e
l
ated
e
xamples
(
m
oved into b
i
operl-pi
s
e)
commit
|
commitdiff
|
tree
2009-01-13
c
j
fie
l
ds
Remove
Pise-related
module (m
o
ved into b
i
op
e
rl
-
pis
e
)
commit
|
commitdiff
|
tree
2009-01-13
cjfields
Remove
Pise mo
d
ules and tests
(
mov
e
d into bi
o
perl-p
i
s
e
)
commit
|
commitdiff
|
tree
2009-01-13
cjfields
Remove Pise modules
and
t
e
sts (moved into bio
p
erl
-
pis
e
)
commit
|
commitdiff
|
tree
2009-01-10
cjfiel
d
s
D
o
n
't TODO
the test, actual
l
y at
t
empt
t
o
run
i
t
a
n
d
.
.
.
commit
|
commitdiff
|
tree
2009-01-10
cjfields
A
c
tually make tests
c
omplete (not s
k
ipped i
f
there
.
.
.
commit
|
commitdiff
|
tree
2009-01-10
cjfields
T
ODO f
a
iling test (
p
r
oblem with SOAP protocol
)
commit
|
commitdiff
|
tree
2009-01-10
cjfi
e
lds
*
f
i
n
i
sh up bioperl-r
u
n c
o
nversion
commit
|
commitdiff
|
tree
2009-01-08
cjfield
s
req
u
ires
n
ot required
commit
|
commitdiff
|
tree
2009-01-08
cjfields
* convert
o
ver to
B
io::Root::T
e
st and
update s
o
me to
.
.
.
commit
|
commitdiff
|
tree
2009-01-08
cjfields
*
convert to Bio::Ro
o
t::Test
commit
|
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tree
2009-01-08
cjfields
* convert to Bio::Root::T
e
st
commit
|
commitdiff
|
tree
2009-01-07
cj
f
iel
d
s
Getting a
failed tes
t
u
s
ing lat
e
st E
n
sEMB
L
perl
A
PI
.
.
.
commit
|
commitdiff
|
tree
2009-01-07
cjfields
Catch version, skip tes
t
s
i
f versio
n
isn't
supported
.
.
.
commit
|
commitdiff
|
tree
2008-11-14
cj
f
ields
[bu
g
2644]
commit
|
commitdiff
|
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2008-08-22
cjfields
*
a
dd_sequences o
p
tion (adds sequences to
an align
m
en
t
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
patchin
g
the c
o
rrect Primer3
.
pm (not Bio::To
o
ls::Primer3
.
pm)
commit
|
commitdiff
|
tree
2008-06-19
cjfields
bug 2523
commit
|
commitdiff
|
tree
2008-04-15
c
jfields
Update to 0
.
81 par
a
ms
.
Need to set up tests for thi
s
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cj
f
iel
d
s
bu
g
2
460
commit
|
commitdiff
|
tree
2008-01-15
cjf
i
elds
t
e
st
commit
|
commitdiff
|
tree
2007-07-16
c
j
f
i
elds
bug 2202
commit
|
commitdiff
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tree
2007-07-16
cjfields
bug 2299
commit
|
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|
tree
2007-07-01
cjfields
bug
229
9
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|
commitdiff
|
tree
2007-04-02
cjfie
l
ds
wrapper f
o
r tRNAscanSE
commit
|
commitdiff
|
tree
2007-03-30
cjfields
small
f
ix
:
RNAMo
t
if ca
n
hav
e
empty files (will a
d
d
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
cjf
i
elds
f
i
x some funkiness with pipes
;
may switch to IP
C
::Run
.
.
.
commit
|
commitdiff
|
tree
2007-03-20
cjfields
All i
n
f
ernal pro
g
ra
m
s now work; ne
e
ds some mor
e
fi
n
e
.
.
.
commit
|
commitdiff
|
tree
2007-03-19
cjfields
bug 2241
commit
|
commitdiff
|
tree
2007-03-14
c
j
f
i
e
l
d
s
small fixes
commit
|
commitdiff
|
tree
2007-03-13
cjfi
e
lds
IPC:
:
Run (required
for Gli
m
mer, Genemark wrappe
r
s)
commit
|
commitdiff
|
tree
2007-03-13
cjfield
s
GeneMark, Gl
i
mmer
wrap
p
er modules, tests, an
d
test
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
cjfields
c
m
search nows w
o
rks; rest hopefull
y
by M
o
n
.
commit
|
commitdiff
|
tree
2007-02-16
cjf
i
e
lds
Inferna
l
wr
a
pper (not functional
y
e
t)
commit
|
commitdiff
|
tree
2007-02-07
cjfields
up
d
ates and small tweaks
commit
|
commitdiff
|
tree
2007-02-07
cjfields
erpin wrapper (need
s
more work
.
.
.
)
commit
|
commitdiff
|
tree
2007-02-05
cjfields
Allow
o
utfile or t
e
mpfile (for downstream work)
commit
|
commitdiff
|
tree
2007-02-04
cjfields
obscu
r
e
o
r
i
g
ins a bit more (heh
e
he
commit
|
commitdiff
|
tree
2007-02-04
cjfields
R
NAMotif t
o
ols
w
rap
p
e
r
commit
|
commitdiff
|
tree
2006-10-26
cjf
i
elds
Change t
o
Test::More
commit
|
commitdiff
|
tree
2006-10-26
cj
f
ields
Add Test::More (apparen
t
ly wasn't
added)
commit
|
commitdiff
|
tree
2006-10-26
c
j
fields
A
d
d some POD for CLOSE()
commit
|
commitdiff
|
tree
2006-10-26
c
jfields
Added C
L
OSE() t
i
ed filehandle method (bug
2126)
commit
|
commitdiff
|
tree
2006-10-13
c
jfields
Revert tes
t
s; rep
e
ated
c
alls no
w
work (expe
c
t
e
d
b
e
havior)
commit
|
commitdiff
|
tree
2006-10-10
cjfi
e
lds
Fix tes
t
s; need
to l
o
ok at Analysis::soa
p
::res
u
lts()
commit
|
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|
tree
2006-07-11
cjfields
Bug 20
4
0
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tree