repo.or.cz
/
bioperl-live.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Bio::Tools::CodonTable and Bio::Tools::IUPAC: use our and drop BEGIN blocks.
2024-04-26
David
Miguel Susano
.
.
.
B
i
o:
:
Tools:
:
CodonTable and B
i
o::Tools::IUPAC:
use our
.
.
.
commit
|
commitdiff
|
tree
2024-04-26
Da
v
id Miguel Su
s
ano
.
.
.
Bio::Tool
s
::CodonTab
l
e:
i
nclude
and par
s
e the gc
.
prt
.
.
.
commit
|
commitdiff
|
tree
2024-04-25
David Miguel S
u
sano
.
.
.
Bi
o
::Tool
s
::
C
odon
T
able: update
dat
a
from ver
s
in
o
4
.
.
.
commit
|
commitdiff
|
tree
2024-04-23
Dav
i
d Miguel Sus
a
no
.
.
.
CodonTa
b
l
e
.
t: incre
a
se
number of expected codon tables
.
.
.
commit
|
commitdiff
|
tree
2024-04-22
igort
r
u
Bio::Too
l
s::
C
o
d
onTable
:
a
d
d codo
n
table 15 (#389)
commit
|
commitdiff
|
tree
2024-01-21
David Miguel
S
usano
.
.
.
t/Ro
o
t/RootIO
.
t: mark
LWP::Protocol::https as prer
e
quesite
.
.
.
commit
|
commitdiff
|
tree
2024-01-20
David Miguel Susano
.
.
.
t/Root/Root
I
O
.
t: use bioperl
.
org instead of
g
oo
g
le
.
.
.
commit
|
commitdiff
|
tree
2020-05-18
Da
n
K
o
r
t
s
chak
examples/longorf
.
pl: remove note ab
o
ut cont
a
c
ting th
e
.
.
.
commit
|
commitdiff
|
tree
2019-09-14
Carnë Draug
HACKIN
G
.
md: document that som
e
docume
n
ted
n
amespaces
.
.
.
commit
|
commitdiff
|
tree
2019-08-29
Ca
r
në Draug
b
p
_c
h
a
o
s
_pl
o
t:
r
e
m
ove
scri
p
t (is
s
ue #
3
23)
commit
|
commitdiff
|
tree
2019-08-28
Carnë Draug
v1
.
7
.
6
commit
|
commitdiff
|
tree
2019-08-28
Carnë Draug
maint update Change
s
fil
e
commit
|
commitdiff
|
tree
2019-06-07
Carnë Drau
g
dist
.
i
n
i: list GD pr
e
req as suggestion
i
nstead of
r
equiremen
.
.
.
commit
|
commitdiff
|
tree
2019-05-12
Carnë Draug
bp_classify_hit
s
_kin
g
d
om:
m
ove from bin into examples
.
.
.
commit
|
commitdiff
|
tree
2019-02-15
Matt O
a
tes
maint:
u
p
d
ate aut
h
o
r
emai
l
address i
n
b
i
n
/bp_seqpar
t
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
v1
.
7
.
5
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
Add empty
l
ine after pack
a
ge s
t
atement for
$VERSIO
N
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
Seq
U
t
i
ls
.
t:
avoid
d
e
p
recated usage of add_SeqFeatur
e
commit
|
commitdiff
|
tree
2019-02-11
C
arnë Draug
maint: mention remove
d
methods
i
n 2
c
be4591d572
on Changes
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë Drau
g
Bi
o
::Seq::
S
e
qWithQua
l
i
ty: remove depreca
t
ed c
l
ass
commit
|
commitdiff
|
tree
2019-02-11
C
a
rn
ë
Dra
u
g
Use
/
usr/bin/perl instead
o
f env even on example
s
commit
|
commitdiff
|
tree
2019-02-11
Carnë Drau
g
doc
:
fix POD
in Bio:
:
SeqIO::bs
m
l
s
o that man
c
an handle it
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë
D
raug
l
ib/Bio/To
o
ls/
R
un/
R
E
AD
M
E:
remove
fil
e
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
doc:
a
dd
NAME
sect
i
o
n
wi
t
h abstract to all modules P
O
D
commit
|
commitdiff
|
tree
2019-02-08
Carnë Drau
g
Bio::Symbol: mov
e
t
o
its o
w
n distr
i
bution
commit
|
commitdiff
|
tree
2019-02-08
Carnë Dr
a
ug
doc: fix
t
ypos on doc found by Debian's
l
int
i
a
n
commit
|
commitdiff
|
tree
2019-02-07
Carnë Draug
Bio::Ro
o
t::RootI->
d
eprecated: fix whe
n
no ver
s
i
o
n
a
r
gument
.
.
.
commit
|
commitdiff
|
tree
2019-02-07
Carnë Draug
Bio::Root::R
o
otI: de
p
recate
d
eprecated() met
h
od (issue
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
C
a
rnë Draug
v1
.
7
.
4
commit
|
commitdiff
|
tree
2019-02-05
Carnë Draug
maint: d
o
not include
t
r
a
vis configuration on release
commit
|
commitdiff
|
tree
2019-02-05
C
a
r
në Draug
maint: u
p
da
t
e Changes for upcoming
release
commit
|
commitdiff
|
tree
2019-02-05
Carnë
D
r
aug
t/SeqFeature/Gener
i
c
.
t: fi
x
typo on req
u
ired modu
l
e
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë Draug
B
io::Root::Test:
f
ix test_network use of Test::
R
equiresInte
r
n
e
t
commit
|
commitdiff
|
tree
2019-02-05
Carnë
D
raug
maint
:
fix r
e
po
s
i
t
ory l
i
nks
on metadata (i
s
s
ue #3
0
6
)
commit
|
commitdiff
|
tree
2019-01-30
Carnë Draug
v1
.
7
.
3
commit
|
commitdiff
|
tree
2019-01-29
Carnë Dra
u
g
bin/bp_genba
n
k2gff3: fix sorting by feature type
(
issue
.
.
.
commit
|
commitdiff
|
tree
2019-01-29
Carnë Draug
B
i
o::SeqIO::laser
g
ene: m
o
ve to its
own distribution
commit
|
commitdiff
|
tree
2018-10-03
Carnë Draug
C
hanges: more details
and ph
i
losophy are on HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
Ca
r
n
ë Dr
a
u
g
Changes: more detail
e
d compl
e
te li
s
t
o
f modules/depe
n
d
en
c
ies
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Ca
r
në Draug
li
b
/BioPerl
.
pm: sta
r
t conversion o
f
POD to make use
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
C
a
rnë
D
rau
g
bi
n
/bp_b
i
ofetch_genbank_proxy: move to Bio
-
D
B
-NCBIHe
l
per
commit
|
commitdiff
|
tree
2018-10-01
Carnë D
r
aug
Bio::DB
:
:SwissProt: mov
e
t
o its own distribution
commit
|
commitdiff
|
tree
2018-10-01
C
arnë Draug
B
io:
:
DB::
B
io
F
etch: mo
v
e to its own distrib
u
t
ion
commit
|
commitdiff
|
tree
2018-09-30
Car
n
ë Draug
Automa
t
ic handling of VERSION in
a
l
l
modul
e
s
(
issue
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
t
/
SeqFeature/G
e
n
e
ric
.
t:
f
ix
failing tests
(
fixup fde60
3
f22aa)
commit
|
commitdiff
|
tree
2018-09-30
Ca
r
në Draug
bin/b
p
_f
e
tch: move require of option
a
l modules where
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
a
rnë
D
r
au
g
Bio:
:
Map:
:
* and Bio
:
:
M
apIO
:
:* : move into their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
Remove
man
i
pulation o
f
@INC and use
o
f lib
-
requir
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Car
n
ë
D
r
aug
dist
.
i
n
i: make W
i
n
3
2 a de
p
endency for
W
indows on
l
y
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carn
ë
Draug
Bio::SeqIO::agave: move to
its own d
i
stribut
i
on
commit
|
commitdiff
|
tree
2018-09-29
C
arnë
Draug
Bio::SeqIO::chadoxm
l
(and flybase_chadoxml): move to
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
a
rnë
D
raug
maint: list Data::S
t
ag:
:
XMLWriter
a
s d
r
opped depen
d
ency
commit
|
commitdiff
|
tree
2018-09-29
Carnë Dr
a
u
g
Bio::Seq
I
O::chaosxml (and chaos): move to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::SeqIO::strider:
move
i
nto its own distribut
i
on
commit
|
commitdiff
|
tree
2018-09-28
C
arnë Draug
Bio::Tools
:
:Protpa
r
am: move to its
own distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-28
Carnë
D
r
aug
ma
i
nt
:
u
pdate and clean
removed
m
o
dules and
d
ependenc
i
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
C
a
r
në Draug
Bio::DB::
S
eqVersio
n
: move into
i
ts own distrib
u
ti
o
n
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dr
a
ug
Bio::Tool
s
::SiRNA a
n
d re
l
ated moved to se
p
arate
d
istribution
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Draug
Bio::Tools::Anal
y
sis::P
r
otein:
m
ove modu
l
es into
t
heir
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
aug
B
io::Tools::A
n
a
l
ysis::P
r
ote
i
n::Scansite
:
mov
e
to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
aug
Bi
o
::Tools::
A
nalysis::Protein:E
L
M: mov
e
to separat
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::
T
oo
l
s::A
n
alysis::DN
A
:
:ESEfin
d
e
r: move t
o
separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
B
io::DB::RefSeq, Bio::DB::EMBL, and subclasses
o
f
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Taxonomy: m
o
ve dep
r
ecated
namespace to its
o
w
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Draug
lib/BioPerl
.
pm: con
v
e
r
t l
i
ne-ending dos2unix
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë
Draug
doc: update HACKIN
G
instructio
n
s
with dz
i
l instructions
commit
|
commitdiff
|
tree
2018-09-25
C
a
rnë Draug
t/*: r
e
move "use lib '
.
'" and t/l
i
b/Error
.
pm
commit
|
commitdiff
|
tree
2018-09-25
C
arnë Draug
B
io::DB::C
U
TG:
m
ove into
i
ts own distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-25
C
a
rn
ë
Draug
Bio:
:
DB::Taxonomy::sqlite:
m
o
ve into its ow
n
distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::
D
B::GFF move into its
own namespace (ex
c
ept Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
C
a
rnë
D
raug
B
i
o::DB::Se
q
Fea
t
ure:
:
* move
namesp
a
c
e into
i
t
s ow
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
C
a
rnë Draug
mai
n
t: upd
a
te changes from 1f7b54a281a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë Drau
g
Bio::Vari
a
tion:
:
*
mov
e
namespa
c
e into its own
distribution
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë Dr
a
u
g
R
emove Bio:
:
SeqIO support
for abi, alf, ctf, exp, pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë
D
raug
Bio
:
:
C
luster
and Bio::ClusterIO moved to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
B
i
o::Phenotype
:
:*
m
ove what's left of the na
m
espace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Ca
r
në Dr
a
ug
maint: remove no longer used test d
a
ta
fil
e
s
.
commit
|
commitdiff
|
tree
2018-09-22
C
arnë D
r
aug
Bio::LiveSe
q
::* mo
v
e
whole
n
amespa
c
e
to its own distrib
u
tion
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
maint
:
update gitignor
e
rules
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
maint: rest
r
u
cture to
u
se Dist::Zilla
commit
|
commitdiff
|
tree
2018-09-17
C
arnë D
r
aug
t/AlignIO/AlignIO
.
t: fix number of te
s
ts in plan (fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Draug
t/Ann
o
tat
i
on
/
A
nn
o
tation
.
t: remov
e
test for
B
io::SeqF
e
at
u
re
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
B
io/Tools/R
u
n/Phyl
o
/PhyloBas
e
.
p
m
:
bring base class
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/Tools/Ph
y
lo/Gumby
.
pm: move to its o
w
n distribution
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
D
B
/
SeqF
e
a
t
ure/Store/berke
l
eydb3
.
pm
:
fix e
r
ro
r
s
so i
t
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Adjust t
e
st
s
ind
i
rectly makin
g
u
se of Bio::Al
i
gnIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
bp_process
_
worm
b
ase:
m
ove program to new Bi
o
-DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
bp_net
i
nstall: remove ou
t
of
date progra
m
commit
|
commitdiff
|
tree
2018-09-17
C
ar
n
ë Drau
g
Mov
e
modules dependent o
n
Bio
:
:
Ex
t
:
:
Align int
o
defu
n
c
t
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio::DB::Expressi
o
n: mov
e
to defunct biope
r
l-micro
a
rray
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
m
a
int: 644 permissions fo
r
almo
s
t all f
i
les
commit
|
commitdiff
|
tree
2018-09-16
Carnë Drau
g
mai
n
t
: set
a
ll so
u
rce code with ut
f
-8 encoding
commit
|
commitdiff
|
tree
2018-09-16
Carnë Dr
a
ug
m
a
i
n
t: r
e
move maintainer o
u
t
o
f dat
e
files
commit
|
commitdiff
|
tree
2018-09-16
C
arnë Drau
g
ide: remove module te
m
plat
e
s - no longer
needed af
t
e
r
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
ide/bioperl-mod
e
: in
t
o its own reposito
r
y to be
developed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint: re
m
ove bioperl
-
mode release tarballs
from version
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë
D
raug
Bio::
I
nde
x
::A
b
stract->_typ
e
_and_v
e
rsio
n
: che
c
k ty
p
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carn
ë
D
raug
t/Loca
l
DB/Index/BlastTable
.
t: us
e
tempdir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë D
r
au
g
t/Local
D
B
/Index/Blast
.
t
: cre
a
te test t
e
mpf
i
les wi
t
hin
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Drau
g
maint
:
remove unused test da
t
a files
commit
|
commitdiff
|
tree
next