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.
2019-09-14
Carnë Draug
HACKI
N
G
.
md: do
c
ument that s
o
me docume
n
ted na
m
e
spaces
.
.
.
commit
|
commitdiff
|
tree
2019-08-29
Carn
ë
Draug
bp_c
h
a
o
s_plot: remov
e
script (is
s
u
e #323)
commit
|
commitdiff
|
tree
2019-08-28
Carn
ë
D
r
a
ug
v1
.
7
.
6
commit
|
commitdiff
|
tree
2019-08-28
Carnë Draug
maint up
d
a
te Cha
n
ge
s
file
commit
|
commitdiff
|
tree
2019-06-07
C
arnë Drau
g
di
s
t
.
ini: list G
D
prereq as
s
ug
g
estion instead of re
q
uir
e
men
.
.
.
commit
|
commitdiff
|
tree
2019-05-12
Ca
r
në Draug
bp_classify_h
i
t
s_kingdom: move
from bin in
t
o examples
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
C
arnë D
r
aug
v1
.
7
.
5
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
Add e
m
p
t
y
l
i
ne after
p
a
c
kage statement f
o
r
$
VERSION
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë
Draug
SeqUtils
.
t: av
o
id
depr
e
cated usage of a
d
d
_
SeqFeature
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
main
t
: mention re
m
oved
method
s
i
n
2cbe
4
591d572
o
n
Chan
g
es
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
C
arnë Dr
a
ug
Bio::Seq::SeqW
i
thQuality: remove
d
epr
e
cated class
commit
|
commitdiff
|
tree
2019-02-11
C
arnë Dra
u
g
Use /usr/bin/perl
i
nstead
o
f env e
v
en o
n
exam
p
le
s
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
doc:
f
ix POD in Bi
o
::S
e
qIO::bs
m
l so t
h
at m
a
n can handl
e
i
t
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë Drau
g
l
ib
/
Bio/T
o
ols/Run/README: remove file
commit
|
commitdiff
|
tree
2019-02-11
Carnë
D
raug
doc
:
add N
A
ME
s
ection wi
t
h abstra
c
t to
all module
s
POD
commit
|
commitdiff
|
tree
2019-02-08
Carnë Draug
Bio::Symbol: move to
its
o
wn d
i
str
i
bution
commit
|
commitdiff
|
tree
2019-02-08
C
a
rnë Draug
doc
:
fi
x
t
y
pos on doc found
b
y
Debian'
s
lintian
commit
|
commitdiff
|
tree
2019-02-07
C
arn
ë
Draug
Bio
:
:R
o
o
t
::RootI-
>
deprecat
e
d:
fix w
h
en no versio
n
argument
.
.
.
commit
|
commitdiff
|
tree
2019-02-07
Carnë
Draug
B
i
o
:
:Root::RootI: deprecate deprecat
e
d() method
(i
s
sue
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
C
arnë Dra
u
g
v1
.
7
.
4
commit
|
commitdiff
|
tree
2019-02-05
C
a
rnë
Dra
u
g
maint: d
o
n
o
t
inclu
d
e travis
configuration on
r
e
lease
commit
|
commitdiff
|
tree
2019-02-05
Carnë
D
rau
g
maint: update Ch
a
nges
f
or
u
pcoming release
commit
|
commitdiff
|
tree
2019-02-05
C
arnë
D
r
a
u
g
t
/SeqFeat
u
re/Ge
n
eric
.
t: fix typo on re
q
uired
module
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Car
n
ë
Draug
B
i
o::R
o
o
t::Test: fi
x
test_ne
t
work use of Test:
:
Requi
r
e
sInte
r
ne
t
commit
|
commitdiff
|
tree
2019-02-05
Carnë
D
raug
mai
n
t: fix repository links on metadat
a
(issue #306)
commit
|
commitdiff
|
tree
2019-01-30
Carn
ë
Draug
v
1
.
7
.
3
commit
|
commitdiff
|
tree
2019-01-29
C
a
rnë Drau
g
bin/bp_genban
k
2gff3: fix sorting b
y
feature typ
e
(is
s
ue
.
.
.
commit
|
commitdiff
|
tree
2019-01-29
Carnë
Draug
Bio::SeqIO::
l
aserge
n
e: move to its own distribution
commit
|
commitdiff
|
tree
2018-10-03
Carnë D
r
aug
Change
s
:
more detail
s
and philosophy a
r
e
o
n HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
Carnë D
r
aug
C
hanges: more detai
l
e
d com
p
lete list of modules/dependencies
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
C
a
r
n
ë Drau
g
lib/B
i
oPerl
.
pm: start c
o
nvers
i
on
of POD t
o
ma
k
e use
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Ca
r
n
ë Draug
bin/bp
_
bio
f
etch_genb
a
nk_proxy: move to Bio-DB-NCBIH
e
l
p
e
r
commit
|
commitdiff
|
tree
2018-10-01
C
arnë Draug
B
io::DB::Swis
s
Pr
o
t: move to its own distribut
i
on
commit
|
commitdiff
|
tree
2018-10-01
C
a
r
në Draug
Bio::D
B
::BioFe
t
ch: mov
e
to
its o
w
n distribut
i
on
commit
|
commitdiff
|
tree
2018-09-30
Carnë
D
r
a
ug
Automati
c
h
a
n
d
ling of VERSION in
al
l
m
o
d
u
les (i
s
sue
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë
D
r
a
ug
t/SeqF
e
ature/Generic
.
t: fix
failing tests (f
i
xup fde603f22aa)
commit
|
commitdiff
|
tree
2018-09-30
C
arnë Draug
bin/bp_f
e
tch
:
mov
e
req
u
ire of optional mo
d
ules wh
e
re
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
Bio::Ma
p
::
*
and Bio::MapIO::*
:
m
o
ve into t
h
eir o
w
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
ar
n
ë Draug
Remov
e
ma
n
ipulation
of
@
I
NC and
use of lib
-
r
equire
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
dist
.
ini: make
Win32 a depen
d
e
ncy for
W
indow
s
only
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Ca
r
në Dra
u
g
Bi
o
:
:SeqIO
:
:a
g
ave: move t
o
i
t
s own distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-29
Car
n
ë Draug
Bio::Se
q
IO:
:
chadoxml (an
d
f
l
y
b
ase_chadoxml): move
t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carnë
Draug
m
aint: l
i
st
Data::Stag::XML
W
riter as droppe
d
d
e
pen
d
ency
commit
|
commitdiff
|
tree
2018-09-29
Carnë Dra
u
g
Bio::S
e
qI
O
::chaosxml (and
c
h
aos): move to t
h
e
i
r
o
w
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë D
r
aug
Bio::SeqIO::stride
r
:
m
ove into its
own distri
b
ution
commit
|
commitdiff
|
tree
2018-09-28
C
a
rnë Draug
Bio::Tools::Protparam:
m
ove to i
t
s own distri
b
ution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Drau
g
maint: up
d
ate an
d
cl
e
an
re
m
ove
d
m
o
dules a
n
d dep
e
ndencies
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bi
o
::DB::SeqVer
s
ion: move into its own
distr
i
buti
o
n
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Too
l
s
:
:S
i
RN
A
and rela
t
ed moved
t
o
separate
d
istribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio
:
:Tools::Analysis::Protein: move mo
d
u
l
e
s
i
nto the
i
r
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
D
r
aug
Bio::Tool
s
::Analysis::Protein::Scansite: move to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tools::Analysis::Protein:ELM: move to sep
a
ra
t
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në
D
raug
Bio::Tools::Analy
s
is::DNA::ES
E
f
i
nder: move to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Drau
g
B
i
o::DB::RefSeq,
Bio::D
B
::
E
M
B
L, and subclasses
o
f Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
B
i
o:
:
Taxonomy: m
o
ve
depr
e
cated namespace to
i
ts own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Draug
lib/
B
ioPerl
.
pm:
c
onvert
l
ine-e
n
ding dos2unix
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në Draug
doc: upd
a
te HACKI
N
G
i
ns
t
r
u
c
t
io
n
s wi
t
h d
z
il instructions
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dra
u
g
t
/
*: remove
"u
s
e li
b
'
.
'" and t/lib/Error
.
p
m
commit
|
commitdiff
|
tree
2018-09-25
Carnë
Dr
a
ug
Bio::DB::CU
T
G: move into
its own distribution
commit
|
commitdiff
|
tree
2018-09-25
C
a
rnë Dr
a
ug
Bi
o
::
D
B::Taxonomy::sqlite: move i
n
to i
t
s o
w
n distribut
i
on
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
ra
u
g
B
i
o:
:
DB::GFF move into
its own
namesp
a
ce (except
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
C
arnë Draug
Bio::
D
B::S
e
q
F
eat
u
re:
:
* move
namespace i
n
to i
t
s
ow
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dra
u
g
ma
i
nt:
update cha
n
ges fro
m
1f7b
5
4a281a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::Variat
i
on::* move
n
ame
s
pace
i
nto its own distrib
u
tion
.
commit
|
commitdiff
|
tree
2018-09-24
C
a
rnë D
r
aug
Remove Bi
o
:
:
S
e
qIO support for
a
bi, alf, ctf, e
x
p
, pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
Ca
r
në Draug
Bio::Cluster and Bio::ClusterIO moved
to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
Bio::Ph
e
n
ot
y
pe::
*
mo
v
e what's left of the namespace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
C
ar
n
ë Dr
a
ug
maint: remove no longer used test data files
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
B
io::LiveSeq::*
mov
e
whole n
a
m
espace to its
o
w
n dis
t
ribution
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
m
a
int:
u
pdate gitigno
r
e
r
ules
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
m
aint:
r
e
structure to u
s
e Dist::Zilla
commit
|
commitdiff
|
tree
2018-09-17
C
arnë
D
raug
t/AlignIO/A
l
ignIO
.
t
:
fix numb
e
r of
tests in pla
n
(fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Dr
a
ug
t/Annotation/Annotation
.
t:
r
emo
v
e test for B
i
o::S
e
q
F
eature
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë Draug
Bio/Tools/
R
u
n/
P
hylo/PhyloB
a
se
.
pm:
b
ring base cla
s
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Dr
a
ug
Bio/Tools/Phylo
/
Gumby
.
pm: move to its own distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-17
Carn
ë
Draug
DB/SeqFeature/Store/berkel
e
ydb3
.
pm: fix
e
r
rors s
o
it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
Adjust tests ind
i
rectly m
a
king use of Bio::AlignIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë Drau
g
b
p_proce
s
s_wormbase: mov
e
progra
m
to
n
ew Bio-DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Dra
u
g
b
p
_ne
t
ins
t
a
ll: remove
o
ut
o
f date pro
g
ram
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
aug
Mov
e
mod
u
les dep
e
nden
t
on
Bio::Ext:
:
Align into defunct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio::DB::Expres
s
i
on: move
t
o de
f
unct
bioperl-microarray
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint
:
644 permission
s
f
or almost all files
commit
|
commitdiff
|
tree
2018-09-16
Carnë
Draug
maint: set all source code with u
t
f
-
8 enco
d
ing
commit
|
commitdiff
|
tree
2018-09-16
Ca
r
n
ë Dr
a
ug
maint: r
e
move maintainer out of d
a
te files
commit
|
commitdiff
|
tree
2018-09-16
Carnë
D
raug
ide: rem
o
v
e
module templates
-
no longer n
e
eded after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Dra
u
g
ide/bioperl-mode: into it
s
own repository to
b
e develo
p
ed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
main
t
: remove bio
p
e
r
l-mod
e
relea
s
e tarballs fro
m
version
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
Bio::Inde
x
::Abstr
a
c
t
-
>
_type_and
_
versi
o
n: check type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë
Dr
a
u
g
t/
L
ocalD
B
/Index/
B
l
a
s
tTable
.
t
:
u
se temp
d
ir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Car
n
ë D
r
aug
t
/
LocalD
B
/
Index/Blast
.
t: crea
t
e
test
tempfi
l
es within
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
maint:
remove unused test data files
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
Remo
v
e AlignI
O
and Index stoc
k
ho
l
m
m
o
d
ules
t
o new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Carnë
D
raug
B
io::DB::Universal: move
i
nto
its own
d
istributi
o
n
commit
|
commitdiff
|
tree
2018-09-14
Carnë D
r
aug
maint:
simplify README to cover s
i
mple
i
nstall instructions
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë D
r
aug
Bring base cl
a
sses
from BioPerl-run b
a
ck to BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Ca
r
n
ë
Draug
Rem
o
ve use of Bio::Perl wh
i
ch ha
s
b
ee
n
m
oved
t
o Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dra
u
g
Bio::D
B
:
:
M
eSH mo
v
e
t
o
i
ts own distribu
t
ion
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Mov
e
HMMER related modul
e
s, tests
,
an
d
programs to
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
B
i
o::DB::TFBS
n
a
m
espac
e
has been move
d
to
i
ts ow
n
d
istrib
u
ti
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bio::DB::HIV and related mo
d
ules and scripts moved
.
.
.
commit
|
commitdiff
|
tree
next