repo.or.cz
/
bioperl-run.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
support more models
2002-11-13
jason
Br
o
ught u
p
t
o s
p
ec with the new O
b
jects and seqname
.
.
.
commit
|
commitdiff
|
tree
2002-11-13
jason
remove Fugu
system s
t
uff and insure that File tmp
handles
.
.
.
commit
|
commitdiff
|
tree
2002-11-10
jason
fi
x
ed
t
o work with new ba
s
e ob
j
e
ct a
n
d use b
i
o
perl
.
.
.
commit
|
commitdiff
|
tree
2002-11-10
jason
ski
p
if ret val is 0
commit
|
commitdiff
|
tree
2002-11-10
jason
consisten
c
y
commit
|
commitdiff
|
tree
2002-11-10
ja
s
on
c
ode be
a
u
t
ification
commit
|
commitdiff
|
tree
2002-11-10
jason
platform
i
nd
e
pe
n
dent filename
commit
|
commitdiff
|
tree
2002-11-09
jason
re
s
pect the original cwd
commit
|
commitdiff
|
tree
2002-09-18
j
aso
n
s
y
nop
s
is doc
commit
|
commitdiff
|
tree
2002-09-18
jason
defaul
t
shou
l
d be F3X4
commit
|
commitdiff
|
tree
2002-09-18
jason
Ma
t
t
hew'
s
C
h
a
nges committed: Add supp
o
rt to save_output
.
.
.
commit
|
commitdiff
|
tree
2002-09-18
jason
handle exe app
s
commit
|
commitdiff
|
tree
2002-09-05
jason
SAX/Sa
x
-
>
Per
l
S
A
X
commit
|
commitdiff
|
tree
2002-08-14
j
ason
for building ma
n
i
fest
commit
|
commitdiff
|
tree
2002-08-14
jason
c
o
smetic code fix
commit
|
commitdiff
|
tree
2002-08-14
jason
describe the cur
r
ent sta
t
e o
f
a
ffair
commit
|
commitdiff
|
tree
2002-07-30
jason
skip tests
commit
|
commitdiff
|
tree
2002-07-29
jason
t
est
f
ile for TCoffee
commit
|
commitdiff
|
tree
2002-07-29
jason
whoops,on
e
more time
,
cleanup
tempfiles
a
nd dirs
commit
|
commitdiff
|
tree
2002-07-29
jaso
n
clean
u
p of
tempfil
e
s works
commit
|
commitdiff
|
tree
2002-07-29
jason
handl
e
bad result err by skip
p
in
g
t
e
sts
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
tests updated to handle mi
s
sing exe better
commit
|
commitdiff
|
tree
2002-07-29
j
ason
inher
i
t fr
o
m W
r
apperBase
commit
|
commitdiff
|
tree
2002-07-29
jason
c
o
de formatting
commit
|
commitdiff
|
tree
2002-07-29
jason
API
c
h
anged a little
b
it
with new
parser
commit
|
commitdiff
|
tree
2002-07-29
j
a
son
h
andl
e
windows e
x
e
s
commit
|
commitdiff
|
tree
2002-07-29
jason
f
i
x test count
commit
|
commitdiff
|
tree
2002-07-29
jason
use
new PAM
L
p
arser API
commit
|
commitdiff
|
tree
2002-07-27
jason
code
m
l-
>
protml doc
fixes
commit
|
commitdiff
|
tree
2002-07-27
jason
add
e
d additions of
.
exe
for on windows, allow alignmen
t
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
j
a
s
on
brought i
n
line with WrapperBase
commit
|
commitdiff
|
tree
2002-07-27
ja
s
on
brought mo
d
ule in-line with new Wrap
p
erBase
commit
|
commitdiff
|
tree
2002-07-27
j
ason
bump
t
est count
commit
|
commitdiff
|
tree
2002-07-27
jason
c
opy+paste error
commit
|
commitdiff
|
tree
2002-07-27
jaso
n
fix in
t
ern
a
l parameter name
commit
|
commitdiff
|
tree
2002-07-27
jason
adde
d
P
r
otML wrapper - par
t
of Molph
y
p
a
ckager for
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jason
test for protml running
commit
|
commitdiff
|
tree
2002-07-25
j
a
son
migrate from
PAMLBase to WrapperBase
commit
|
commitdiff
|
tree
2002-07-16
jason
print
d
ata to file r
i
ght away r
a
ther
than
h
old
i
ng arr
a
y
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jason
don't redire
c
t
t
o
/
dev/null
- make sure
q
uiet really
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jason
mo
r
e robust
pro
g
ram f
i
nding
commit
|
commitdiff
|
tree
2002-07-09
jaso
n
changed to use
PAML temp
l
ate for find
executable insated
.
.
.
commit
|
commitdiff
|
tree
2002-07-06
jason
e
x
plicitly c
l
osing some fi
l
ehandle
s
a
ppears t
o
do
a
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jas
o
n
test
s
find
t
he mat and
d
at
a
file now, and will skip
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jas
o
n
need to
tes
t
when people run Makef
i
l
e
.
P
L, othe
r
wise
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jaso
n
p
r
o
mpt use
r
w
h
e
n
Makefile
.
PL is run
commit
|
commitdiff
|
tree
2002-07-05
jason
upda
t
e test count
commit
|
commitdiff
|
tree
2002-07-03
jas
o
n
make
f
i
l
e
commit
|
commitdiff
|
tree
2002-07-02
jason
added co
d
eml
data
commit
|
commitdiff
|
tree
2002-07-02
jason
removed run wrappers tests from core -
they have
been
.
.
.
commit
|
commitdiff
|
tree
2002-06-26
ja
s
o
n
readme for run wrappers
commit
|
commitdiff
|
tree
2002-06-21
jas
o
n
testfile renamed
commit
|
commitdiff
|
tree
2002-06-21
jaso
n
remove debug
cop
y
fil
e
commit
|
commitdiff
|
tree
2002-06-21
j
a
son
shor
t
e
n
filename t
o
avoid
poss
i
b
l
e windows long
f
ilen
a
mes
.
.
.
commit
|
commitdiff
|
tree
2002-06-19
jason
doc fix
commit
|
commitdiff
|
tree
2002-06-18
jason
use the determ
i
ned
path to RP when
a
ttempting to
find
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
j
a
son
return
t
he
v
alues as h
a
sh of hashes as they
are all
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jas
o
n
s
m
all doc tweaks
a
nd added runnable sy
n
opsis
commit
|
commitdiff
|
tree
2002-06-17
jason
yn0
0
wrapp
e
r
for P
A
M
L
commit
|
commitdiff
|
tree
2002-06-15
jason
quieter tes
t
s
u
nless BIOPE
R
LDEBUG e
n
v vari
a
ble
i
s set
commit
|
commitdiff
|
tree
2002-06-14
jason
set verbose to -1
commit
|
commitdiff
|
tree
2002-06-14
jason
PA
M
L pac
k
age
-
-
c
ode
m
l w
r
apper an
d
test committed
commit
|
commitdiff
|
tree
2002-05-31
jason
d
o
c fi
x
commit
|
commitdiff
|
tree
2002-05-31
j
a
son
ha
n
dle case w
h
en PHYLIP is installed but not clustalw
commit
|
commitdiff
|
tree
2002-05-30
jason
h
andle some
weird bounda
r
y
cases
commit
|
commitdiff
|
tree
2002-05-21
j
ason
update some of the docs
commit
|
commitdiff
|
tree
2002-05-21
ja
s
on
test va
l
ue f
o
r protd
i
st
commit
|
commitdiff
|
tree
2002-04-22
j
ason
fix
e
s to remove
w
a
r
n
ings
commit
|
commitdiff
|
tree
2002-04-22
jason
fix warnings
commit
|
commitdiff
|
tree
2002-04-18
jason
P
OD
f
ix
commit
|
commitdiff
|
tree
2002-03-22
jason
updated tests
f
or v 1
.
22 problems
on main t
r
unk
commit
|
commitdiff
|
tree
2002-03-21
jason
s
i
mple align ha
s
o
ver
a
ll percent id
metho
d
commit
|
commitdiff
|
tree
2002-03-19
jason
cl
e
anup before eac
h
run
o
f
an applicatio
n
commit
|
commitdiff
|
tree
2002-03-15
jason
me
r
ge fro
m
b
r
anch
commit
|
commitdiff
|
tree
2002-03-15
j
a
s
o
n
merge
c
hanges from branch
commit
|
commitdiff
|
tree
2002-03-15
jaso
n
updated t
o
handl
e
tests with SearchIO objec
t
retur
n
e
d
.
.
.
commit
|
commitdiff
|
tree
2002-03-15
jason
better synopsis and doc update
commit
|
commitdiff
|
tree
2002-03-14
jaso
n
io cleanup
called at outset
of an
a
n
alyse
s
-- from
.
.
.
commit
|
commitdiff
|
tree
2002-03-14
jason
m
e
rged
exe chec
k
i
n
g
from bra
n
ch
commit
|
commitdiff
|
tree
2002-03-14
jaso
n
skip nic
e
l
y
, handle case where server is do
w
n
commit
|
commitdiff
|
tree
2002-03-11
jas
o
n
u
s
e S
e
arc
h
IO not Tool
s
::Blast
commit
|
commitdiff
|
tree
2002-03-09
jason
turn of cl
u
stalw deb
u
gging
commit
|
commitdiff
|
tree
2002-03-05
ja
s
on
un
l
ink t
e
st file output
commit
|
commitdiff
|
tree
2002-03-04
jason
added abil
i
ty to d
u
mp alignments as well
as sequences
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
jason
added example document
a
tion to th
e
PO
D
commit
|
commitdiff
|
tree
2002-02-18
jason
test
f
or cmd l
i
n
e
ar
g
ument whe
r
e
value
i
s a Bio::Prima
r
y
SeqI
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
jason
handle c
m
d line arguments pointing to
a Bio::Pri
m
a
r
y
Seq
I
.
.
.
commit
|
commitdiff
|
tree
2002-02-06
jaso
n
params
s
hould be appen
d
ed not overwriting
commit
|
commitdiff
|
tree
2002-01-30
ja
s
on
v
erb
o
sity=-1 is same as quiet
(
)
commit
|
commitdiff
|
tree
2002-01-11
j
a
son
debug me
s
sage
now uses th
e
debu
g
method
commit
|
commitdiff
|
tree
2002-01-09
jaso
n
warn
a
bout not
using old clusta
l
w
commit
|
commitdiff
|
tree
2002-01-09
jason
use the
u
pd
a
ted PROGR
A
M ex
e
l
oc
a
tion information to
.
.
.
commit
|
commitdiff
|
tree
2002-01-09
ja
s
on
check to
i
n
s
ure define
d
object bef
o
re callin
g
ISA
commit
|
commitdiff
|
tree
2001-12-14
jason
ski
p
msg updat
e
d
due to clustal 1
.
81 bug
commit
|
commitdiff
|
tree
2001-12-14
jaso
n
ni
c
e
message print
i
ng whe
n
b
l
ast
is not
r
unnable
commit
|
commitdiff
|
tree
2001-12-14
ja
s
on
more quie
t
warning so tests
are les
s
ch
a
tty
commit
|
commitdiff
|
tree
2001-12-14
jason
issue ni
c
e message
w
hen skipping EMBOS
S
t
e
sts
commit
|
commitdiff
|
tree
2001-12-14
jas
o
n
skip can print
a nice
m
e
ssage about why it skipped
commit
|
commitdiff
|
tree
2001-12-14
jason
emboss
factory be
h
ave
s
more quietly when EMBO
S
S
is
.
.
.
commit
|
commitdiff
|
tree
2001-11-19
ja
s
on
EM
B
OSS mo
r
e runn
a
b
l
e
and w/ test
s
commit
|
commitdiff
|
tree
next