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sync with trunk
2009-02-11
cjfields
sync with
tru
n
k
commit
|
commitdiff
|
tree
2009-02-01
cjf
i
e
lds
b
r
anch-spe
c
ific versioning
commit
|
commitdiff
|
tree
2009-02-01
cjfields
syc with tr
u
nk
commit
|
commitdiff
|
tree
2009-01-28
cjfields
forgot to change versioning, will
retag
commit
|
commitdiff
|
tree
2009-01-28
cj
f
iel
d
s
sync
w
ith
r
u
n
trunk
commit
|
commitdiff
|
tree
2009-01-13
c
j
fields
* small updates
commit
|
commitdiff
|
tree
2009-01-13
c
j
fields
Remove Pise-related stu
f
f, updat
e
with other dependencies
commit
|
commitdiff
|
tree
2009-01-13
cjfields
Add DEPENDENCIE
S
fil
e
.
commit
|
commitdiff
|
tree
2009-01-13
cjfields
Remo
v
e Pise-related
e
x
a
mples (moved into
bioperl-pise)
commit
|
commitdiff
|
tree
2009-01-13
cjfie
l
ds
R
e
mov
e
Pise-
r
el
a
ted module
(
moved into bioperl-pise)
commit
|
commitdiff
|
tree
2009-01-13
cjfi
e
lds
Remove Pise modules
a
nd tests
(
m
oved into
b
ioperl-pise)
commit
|
commitdiff
|
tree
2009-01-13
cjfi
e
l
d
s
Remove Pise modules and tests (moved
into
biope
r
l-pise)
commit
|
commitdiff
|
tree
2009-01-10
cj
f
ields
Don'
t
T
O
DO th
e
test, actually att
e
mpt to
r
u
n it
a
nd
.
.
.
commit
|
commitdiff
|
tree
2009-01-10
cj
f
ields
Actually make
tests comp
l
ete (no
t
skipped if there
.
.
.
commit
|
commitdiff
|
tree
2009-01-10
cj
f
iel
d
s
TODO failing test (problem with
SOAP
p
rotocol)
commit
|
commitdiff
|
tree
2009-01-10
cjfields
* finish up biope
r
l-run
c
onversion
commit
|
commitdiff
|
tree
2009-01-08
cjfields
req
u
ires
n
ot required
commit
|
commitdiff
|
tree
2009-01-08
cjfields
* convert over to Bio::Root::Test a
n
d
u
pd
a
t
e
some
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-01-08
cjfie
l
ds
* convert t
o
Bio::
R
oot::Test
commit
|
commitdiff
|
tree
2009-01-08
cjfields
* conv
e
rt to Bio::Root::Test
commit
|
commitdiff
|
tree
2009-01-07
cj
f
ield
s
G
etting a
f
ail
e
d te
s
t using latest EnsEM
B
L perl API
.
.
.
commit
|
commitdiff
|
tree
2009-01-07
c
jfields
Catc
h
versi
o
n, skip tests if version isn
'
t supported
.
.
.
commit
|
commitdiff
|
tree
2008-11-14
c
j
fields
[bug
2
644]
commit
|
commitdiff
|
tree
2008-08-22
cj
f
ield
s
* add_sequenc
e
s op
t
ion (adds
s
e
q
uences to an al
i
gnment
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfields
patching the corr
e
ct Pri
m
er3
.
pm
(not
Bio::
T
ools::Primer3
.
p
m)
commit
|
commitdiff
|
tree
2008-06-19
cjfields
b
u
g 2523
commit
|
commitdiff
|
tree
2008-04-15
cjfields
Update to 0
.
81 params
.
Need to
set up tes
t
s for
this
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cjfields
b
u
g
2
460
commit
|
commitdiff
|
tree
2008-01-15
cjfields
t
e
st
commit
|
commitdiff
|
tree
2007-07-16
c
jfields
bug 2202
commit
|
commitdiff
|
tree
2007-07-16
c
j
fields
bug 2299
commit
|
commitdiff
|
tree
2007-07-01
cjfields
bug 2299
commit
|
commitdiff
|
tree
2007-04-02
cjfields
wrapper for tRNAscanSE
commit
|
commitdiff
|
tree
2007-03-30
cjfields
small fix:
RNAMotif can have e
m
pty f
i
les
(w
i
ll add
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
c
j
fields
f
i
x some funkin
e
ss with pipes; may sw
i
tch to IPC::Run
.
.
.
commit
|
commitdiff
|
tree
2007-03-20
cjf
i
elds
A
ll inf
e
rnal programs
no
w
work; needs some mo
r
e fine
.
.
.
commit
|
commitdiff
|
tree
2007-03-19
cjfi
e
l
d
s
bug
2
241
commit
|
commitdiff
|
tree
2007-03-14
cjfields
s
m
a
ll fixe
s
commit
|
commitdiff
|
tree
2007-03-13
cjfields
IPC::
R
u
n
(required for Glimme
r
, Genemark wrappers)
commit
|
commitdiff
|
tree
2007-03-13
cjfields
GeneMar
k
, Glimmer w
r
apper modules, tests, and test
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
cjfi
e
l
ds
cmsearc
h
nows work
s
;
r
est hopefully by M
o
n
.
commit
|
commitdiff
|
tree
2007-02-16
cjfields
Infernal wrapp
e
r
(not functional yet)
commit
|
commitdiff
|
tree
2007-02-07
cjfields
updates and small twea
k
s
commit
|
commitdiff
|
tree
2007-02-07
cjf
i
elds
er
p
in wrapper (
n
e
eds mor
e
work
.
.
.
)
commit
|
commitdiff
|
tree
2007-02-05
cjf
i
el
d
s
Allow out
f
ile or
tempfile (for down
s
tream work)
commit
|
commitdiff
|
tree
2007-02-04
cjf
i
e
l
ds
obscure origins a bit more (hehehe
commit
|
commitdiff
|
tree
2007-02-04
cjfield
s
RNA
M
otif to
o
l
s
w
rapper
commit
|
commitdiff
|
tree
2006-10-26
c
jfields
C
ha
n
ge to
T
est::More
commit
|
commitdiff
|
tree
2006-10-26
cj
f
ield
s
Add
T
est::More (apparently wasn't added)
commit
|
commitdiff
|
tree
2006-10-26
cjfields
Add some POD for CLOSE()
commit
|
commitdiff
|
tree
2006-10-26
cjf
i
elds
Added CLOSE()
tied filehandle
m
eth
o
d
(
bug 2126)
commit
|
commitdiff
|
tree
2006-10-13
cjfields
Revert tests; r
e
pea
t
ed call
s
n
ow work (expected
b
e
h
av
i
or)
commit
|
commitdiff
|
tree
2006-10-10
cjfields
Fi
x
tests; need to look
a
t Analy
s
is::soap::results
(
)
commit
|
commitdiff
|
tree
2006-07-11
cjf
i
elds
Bug 204
0
commit
|
commitdiff
|
tree