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can run tests if we let executeable find the exe
2002-11-13
jason
can run tests
i
f we
let executeable find
th
e
exe
commit
|
commitdiff
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tree
2002-11-13
jas
o
n
a
h
hah, test will run with
o
ut fugu
specific
s
tuf
f
commit
|
commitdiff
|
tree
2002-11-13
jason
N
a
me of program is pfscan
commit
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commitdiff
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tree
2002-11-13
jason
fail g
r
acef
u
l
l
y -- and secret m
e
ssa
g
e for Fugu guys
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
jason
f
ree res
o
u
r
ces
commit
|
commitdiff
|
tree
2002-11-13
j
ason
use new API
commit
|
commitdiff
|
tree
2002-11-13
ja
s
on
make sure
resources
are freed
commit
|
commitdiff
|
tree
2002-11-13
j
ason
codeml -
-
> tcoffee copy+paste silliness
commit
|
commitdiff
|
tree
2002-11-13
jason
C
o
n
vert StandAlo
n
eBlast to WrapperBase (finallyperl
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
ja
s
on
use proper Tools:
:
W
r
apperBase now
commit
|
commitdiff
|
tree
2002-11-13
jason
mis
s
i
n
g input files for StandAlon
e
Blast
commit
|
commitdiff
|
tree
2002-11-13
jason
insu
r
e fileha
n
dles are close
d
commit
|
commitdiff
|
tree
2002-11-13
j
a
son
17 te
s
ts now?
commit
|
commitdiff
|
tree
2002-11-13
jason
B
rough
t
up t
o
s
pec wi
t
h t
h
e new Object
s
and seq
n
am
e
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
ja
s
on
re
m
o
v
e Fugu system s
t
uff and in
s
ure
t
hat File tmp handles
.
.
.
commit
|
commitdiff
|
tree
2002-11-10
j
a
s
on
fixed
to work
w
ith ne
w
b
ase ob
j
e
ct and u
s
e bioperl
.
.
.
commit
|
commitdiff
|
tree
2002-11-10
jaso
n
skip if
r
et val is 0
commit
|
commitdiff
|
tree
2002-11-10
jason
consistency
commit
|
commitdiff
|
tree
2002-11-10
jason
c
ode beautification
commit
|
commitdiff
|
tree
2002-11-10
jason
platf
o
rm independe
n
t filename
commit
|
commitdiff
|
tree
2002-11-09
ja
s
on
respect the orig
i
nal cwd
commit
|
commitdiff
|
tree
2002-09-18
j
a
son
s
y
nopsis doc
commit
|
commitdiff
|
tree
2002-09-18
jaso
n
default should be F3X4
commit
|
commitdiff
|
tree
2002-09-18
ja
s
o
n
Matthew's Cha
n
ges commit
t
ed: Add suppo
r
t t
o
sav
e
_output
.
.
.
commit
|
commitdiff
|
tree
2002-09-18
jason
h
a
ndle exe apps
commit
|
commitdiff
|
tree
2002-09-05
jason
SAX
/
Sax -
>
Per
l
SAX
commit
|
commitdiff
|
tree
2002-08-14
jason
for
b
uilding manifest
commit
|
commitdiff
|
tree
2002-08-14
jas
o
n
c
o
smetic code
fix
commit
|
commitdiff
|
tree
2002-08-14
jason
descr
i
be the cu
r
re
n
t
state of affair
commit
|
commitdiff
|
tree
2002-07-30
ja
s
on
ski
p
t
e
sts
commit
|
commitdiff
|
tree
2002-07-29
jason
test file for TCoffe
e
commit
|
commitdiff
|
tree
2002-07-29
jaso
n
w
h
oops,one more time, cl
e
an
u
p tempfiles
a
nd dirs
commit
|
commitdiff
|
tree
2002-07-29
jason
cleanup of tempfiles wo
r
ks
commit
|
commitdiff
|
tree
2002-07-29
jason
handle bad
r
esult e
r
r by skipping tests
commit
|
commitdiff
|
tree
2002-07-29
jason
tests updated to han
d
l
e missing ex
e
be
t
ter
commit
|
commitdiff
|
tree
2002-07-29
jason
inherit from WrapperBas
e
commit
|
commitdiff
|
tree
2002-07-29
jason
code
formattin
g
commit
|
commitdiff
|
tree
2002-07-29
jason
API chang
e
d a little b
i
t
with
new
parser
commit
|
commitdiff
|
tree
2002-07-29
ja
s
on
handle windows exes
commit
|
commitdiff
|
tree
2002-07-29
jason
f
i
x test count
commit
|
commitdiff
|
tree
2002-07-29
jason
use ne
w
PAML par
s
er API
commit
|
commitdiff
|
tree
2002-07-27
j
ason
codem
l
->protml doc fixes
commit
|
commitdiff
|
tree
2002-07-27
j
a
son
added
a
dditions of
.
exe for on
w
indows
,
allo
w
a
lignm
e
nt
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jason
brou
g
ht
i
n
line with Wrappe
r
Bas
e
commit
|
commitdiff
|
tree
2002-07-27
jason
brou
g
ht module in-line
wi
t
h n
e
w Wrapp
e
rBase
commit
|
commitdiff
|
tree
2002-07-27
jason
b
u
mp test
c
o
unt
commit
|
commitdiff
|
tree
2002-07-27
jason
cop
y
+p
a
ste error
commit
|
commitdiff
|
tree
2002-07-27
jason
fix internal p
a
rameter name
commit
|
commitdiff
|
tree
2002-07-27
jason
add
e
d Pr
o
t
ML wrapper - part of Mo
l
ph
y
packager fo
r
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jason
t
est for prot
m
l running
commit
|
commitdiff
|
tree
2002-07-25
jason
migrate from
P
AMLB
a
se to
WrapperBase
commit
|
commitdiff
|
tree
2002-07-16
jas
o
n
print data
t
o file right away ra
t
h
e
r t
h
an
h
old
i
ng
array
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
j
a
s
o
n
don't re
d
irect to /
d
ev/null - make sure quiet r
e
ally
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
j
a
son
m
o
re robust
pr
o
gra
m
finding
commit
|
commitdiff
|
tree
2002-07-09
jason
c
hang
e
d
t
o
use
PAML t
e
mp
l
ate for find execu
t
ab
l
e i
n
sated
.
.
.
commit
|
commitdiff
|
tree
2002-07-06
jason
explicitly closin
g
some filehandles ap
p
ears to
d
o
a
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
tests fin
d
the
m
a
t and data
fil
e
now
,
and will skip
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
n
e
ed to
t
e
st when peo
p
le run Make
f
ile
.
PL, otherwise
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
prompt user
w
hen Makefile
.
P
L
i
s run
commit
|
commitdiff
|
tree
2002-07-05
jason
u
p
date test count
commit
|
commitdiff
|
tree
2002-07-03
jason
makefile
commit
|
commitdiff
|
tree
2002-07-02
jason
a
dded codeml data
commit
|
commitdiff
|
tree
2002-07-02
j
a
son
removed run w
r
a
p
pers tests fro
m
core - they have been
.
.
.
commit
|
commitdiff
|
tree
2002-06-26
ja
s
o
n
readme for run wrappers
commit
|
commitdiff
|
tree
2002-06-21
jason
testfile r
e
named
commit
|
commitdiff
|
tree
2002-06-21
jason
remove
debug copyfile
commit
|
commitdiff
|
tree
2002-06-21
jason
shorten f
i
lename to
a
void possible windo
w
s long filenames
.
.
.
commit
|
commitdiff
|
tree
2002-06-19
jason
doc
fix
commit
|
commitdiff
|
tree
2002-06-18
jaso
n
u
se the determined p
a
th to RP when attempting to fi
n
d
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jason
ret
u
rn the values as hash of hashes as
th
e
y are all
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jas
o
n
small doc tw
e
a
k
s and added runnable syno
p
s
i
s
commit
|
commitdiff
|
tree
2002-06-17
jason
yn00
w
rapper
for PAML
commit
|
commitdiff
|
tree
2002-06-15
j
a
son
quieter tests unless BIOPER
L
DEBUG env va
r
iable is set
commit
|
commitdiff
|
tree
2002-06-14
jason
set verbose to -1
commit
|
commitdiff
|
tree
2002-06-14
j
a
son
P
AML package
-
-
code
m
l
w
rapper and t
e
st committed
commit
|
commitdiff
|
tree
2002-05-31
jas
o
n
d
oc fix
commit
|
commitdiff
|
tree
2002-05-31
ja
s
on
handle case when PHYLIP is
installed but not clustalw
commit
|
commitdiff
|
tree
2002-05-30
jason
handle som
e
wei
r
d
boundary cas
e
s
commit
|
commitdiff
|
tree
2002-05-21
jason
update
s
o
m
e of the
d
ocs
commit
|
commitdiff
|
tree
2002-05-21
j
a
son
test value for protd
i
st
commit
|
commitdiff
|
tree
2002-04-22
jason
f
ixe
s
to remove warnin
g
s
commit
|
commitdiff
|
tree
2002-04-22
ja
s
on
fix warnings
commit
|
commitdiff
|
tree
2002-04-18
jason
POD
f
i
x
commit
|
commitdiff
|
tree
2002-03-22
jason
updated tests for v 1
.
22 problems on main trunk
commit
|
commitdiff
|
tree
2002-03-21
jason
simple
align has ov
e
rall percent id method
commit
|
commitdiff
|
tree
2002-03-19
jason
cleanup
before each
r
u
n of
a
n applic
a
tion
commit
|
commitdiff
|
tree
2002-03-15
jason
mer
g
e
from branch
commit
|
commitdiff
|
tree
2002-03-15
jason
merge ch
a
n
ge
s
from branch
commit
|
commitdiff
|
tree
2002-03-15
jason
upda
t
ed
t
o handl
e
tests with Sea
r
chIO
obje
c
t retu
r
ned
.
.
.
commit
|
commitdiff
|
tree
2002-03-15
jason
better synopsis and doc updat
e
commit
|
commitdiff
|
tree
2002-03-14
j
ason
io
c
l
ean
u
p
c
alled a
t
outset of
an analyses -- from
.
.
.
commit
|
commitdiff
|
tree
2002-03-14
jason
merged
exe chec
k
ing from bra
n
ch
commit
|
commitdiff
|
tree
2002-03-14
jason
skip
ni
c
ely, handle case where server is down
commit
|
commitdiff
|
tree
2002-03-11
jason
us
e
S
earchIO not To
o
ls::Blast
commit
|
commitdiff
|
tree
2002-03-09
jason
tu
r
n of
c
lustalw debugging
commit
|
commitdiff
|
tree
2002-03-05
j
ason
u
n
link test fi
l
e output
commit
|
commitdiff
|
tree
2002-03-04
jason
added ab
i
lity to dump alignm
e
nts as
w
ell as sequences
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
j
aso
n
a
d
ded exampl
e
d
o
c
um
e
ntation to th
e
POD
commit
|
commitdiff
|
tree
2002-02-18
ja
s
on
test for cmd line argument where value is a Bio::PrimarySeqI
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
jason
handle
c
m
d
l
i
ne argu
m
ent
s
pointing to a Bio::P
r
imaryS
e
qI
.
.
.
commit
|
commitdiff
|
tree
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