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t/SeqFeature/Generic.t: fix typo on required module for testing
2019-02-05
Carnë Drau
g
t/
S
eqFeat
u
r
e/Ge
n
e
ri
c
.
t: fix typo on require
d
module
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë Draug
Bio::R
o
o
t::Test:
fix test_network
use of Te
s
t::Requi
r
esIntern
e
t
commit
|
commitdiff
|
tree
2019-02-05
Ca
r
në Draug
m
a
int: fi
x
repository
li
n
ks on
met
a
data (issue #30
6
)
commit
|
commitdiff
|
tree
2019-01-30
Carnë Draug
v1
.
7
.
3
commit
|
commitdiff
|
tree
2019-01-29
Carnë Draug
bi
n
/b
p
_genbank2gff3: fix
s
orting
b
y feature
type
(
i
s
sue
.
.
.
commit
|
commitdiff
|
tree
2019-01-29
Car
n
ë
D
raug
Bio::SeqIO::l
a
s
e
rgene
:
move to it
s
o
wn distribution
commit
|
commitdiff
|
tree
2018-10-03
Car
n
ë
D
raug
Changes: more d
e
t
a
ils
and philosophy are on HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
Carnë Draug
Changes
:
more detailed
comp
l
ete list o
f
mo
d
ules/dependen
c
ies
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
lib/Bio
P
erl
.
p
m
: start co
n
v
ersion of P
O
D to make
u
se
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë D
r
aug
bin/bp_b
i
ofetch_
g
e
n
bank_pro
x
y:
m
ov
e
to Bio-DB-NCB
I
He
l
pe
r
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
B
io:
:
DB:
:
SwissProt: mov
e
to its
own
distribution
commit
|
commitdiff
|
tree
2018-10-01
C
a
r
n
ë Draug
Bio::DB::Bi
o
Fetch:
move to
i
ts own di
s
tribu
t
ion
commit
|
commitdiff
|
tree
2018-09-30
Ca
r
n
ë Dr
a
ug
Automa
t
ic handling of VERSION in all modules (is
s
ue
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
t/Seq
F
eature/Generic
.
t
: fix failin
g
tests (fixup fde6
0
3f22aa)
commit
|
commitdiff
|
tree
2018-09-30
Carn
ë
D
r
au
g
bin/bp_fetch: move require of optional modules where
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Dra
u
g
B
io
:
:Map:
:
* an
d
Bio::MapIO::* : move into their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
Remove m
a
nipulati
o
n of @INC and use of lib - require
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
a
r
në Dra
u
g
dist
.
ini: make W
i
n32
a
d
epe
n
dency for
W
i
ndows onl
y
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
arnë Draug
B
i
o:
:
SeqI
O
::agav
e
: mo
v
e to its own
distribution
commit
|
commitdiff
|
tree
2018-09-29
Carnë Drau
g
Bio::SeqIO::chadoxml (and
f
l
y
base_c
h
adoxml): m
o
v
e
to
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Car
n
ë
Draug
m
ain
t
:
l
is
t
Da
t
a::Stag::X
M
LWriter a
s
dropped dependenc
y
commit
|
commitdiff
|
tree
2018-09-29
Carnë Dr
a
ug
Bio::SeqIO::chaos
x
m
l (and cha
o
s
)
:
m
ove to
their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë
D
r
aug
Bio::SeqIO::
s
tri
d
er: move into its own distr
i
bution
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
D
r
aug
B
io:
:
Tools
:
:P
r
otparam: move to its o
w
n distribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
maint: update
a
nd
c
le
a
n r
e
mov
e
d modules
an
d
depende
n
cies
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
au
g
Bio::DB::SeqVersion: mov
e
into its o
w
n d
i
stri
b
u
tion
commit
|
commitdiff
|
tree
2018-09-28
Carnë
D
raug
B
io::Tools::SiRN
A
and related mo
v
ed to se
p
arate
distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
D
raug
Bio::Tools::
A
naly
s
is::Protein: move modu
l
es into their
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio:
:
Tools::Analysi
s
::Protein::Scansite
:
m
ove t
o
separa
t
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë
D
raug
Bio::To
o
ls:
:
Analysis:
:
Protein:ELM: move to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
D
r
a
ug
Bi
o
::T
o
ols::Analysi
s
::DNA::ESEfinder: move
t
o se
p
arate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Draug
Bio
:
:DB::RefSe
q
, Bi
o
:
:
D
B::EMBL, and subclasses of Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
C
a
r
në
D
raug
Bio
:
:Taxo
n
omy: move deprecated namespace to its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
aug
lib/BioPerl
.
p
m
: conver
t
lin
e
-endi
n
g
d
o
s2uni
x
commit
|
commitdiff
|
tree
2018-09-28
C
ar
n
ë Draug
doc: up
d
ate HACKING instru
c
t
i
ons with dzil instru
c
tions
commit
|
commitdiff
|
tree
2018-09-25
Ca
r
në Draug
t/
*
: r
e
mo
v
e "use lib
'
.
'" and t/lib/Err
o
r
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dra
u
g
B
i
o::DB
:
:
CUT
G
: mo
v
e i
n
to its own d
i
str
i
bution
commit
|
commitdiff
|
tree
2018-09-25
C
arnë Dra
u
g
Bio::
D
B::Taxonomy::sqlite:
move i
n
to its own d
i
st
r
ibu
t
ion
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio:
:
DB:
:
G
FF move into it
s
ow
n
names
p
ac
e
(
e
xcept
B
io
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë
Draug
Bio::DB
:
:SeqFeature
:
:
*
move na
m
esp
a
ce into its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dr
a
u
g
maint
:
update changes
f
rom
1f7
b
54a281a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë D
r
aug
B
i
o::Varia
t
ion::* move
namespace into its own distribution
.
commit
|
commitdiff
|
tree
2018-09-24
Car
n
ë Draug
Remove Bio::SeqIO support for
ab
i
, alf, ctf, exp, pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë Draug
B
i
o
:
:Clust
e
r
an
d
Bio::ClusterIO moved to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Dr
a
ug
B
io::
P
h
eno
t
y
pe:
:
* move wh
a
t's left o
f
the namespace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carn
ë
Draug
maint: remove no
l
onger us
e
d te
s
t dat
a
f
il
e
s
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
Bio::LiveSeq::* move wh
o
le
n
ames
p
ace to its own di
s
tri
b
ution
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
aug
m
aint
:
update gitig
n
ore rules
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë
Draug
ma
i
nt: restru
c
tur
e
to
u
s
e
Dist::Zilla
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
në Draug
t/AlignIO/AlignIO
.
t: fix number of tests in
plan (fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carn
ë
Draug
t/A
n
nota
t
ion/Annotatio
n
.
t
: remove te
s
t for Bio::S
e
q
F
eature
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
Bio/Tools/Run/
P
hylo/PhyloBa
s
e
.
pm:
b
ring
b
ase class
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
n
ë
Draug
Bio/Tools/Phylo/Gumby
.
pm: move t
o
its own distributi
o
n
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
DB/
S
e
q
Feature/Store/berkele
y
db3
.
pm: fix errors so it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Draug
Adjus
t
t
e
sts i
n
directly mak
i
ng u
s
e of Bio::AlignIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
bp_proc
e
ss_wormbase: m
o
v
e
p
rogram to new
B
i
o-DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Draug
bp_net
i
nstall:
r
emove out
of date progr
a
m
commit
|
commitdiff
|
tree
2018-09-17
C
ar
n
ë Draug
Move modules dependen
t
on Bio
:
:Ext::Alig
n
into defunct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Draug
B
io::DB::Ex
p
ression: move to
def
u
nct bioperl-micro
a
rray
commit
|
commitdiff
|
tree
2018-09-16
Carnë
D
r
aug
mai
n
t:
6
44 permissions
f
or
a
l
most
all files
commit
|
commitdiff
|
tree
2018-09-16
Carnë
Drau
g
maint: set all source c
o
d
e
with utf-8 e
n
c
oding
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint: r
e
move mainta
i
ner out of
da
t
e f
i
les
commit
|
commitdiff
|
tree
2018-09-16
Carnë
Draug
i
d
e
:
re
m
ove module templates - no longer needed after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Dra
u
g
id
e
/b
i
operl-mode
:
i
nto its own repository
to be developed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Ca
r
n
ë Dr
a
ug
maint
:
remove bio
p
erl-
m
ode
r
elease tarballs
from ver
s
ion
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carn
ë
Draug
B
i
o::
I
ndex:
:
Abstr
a
ct
-
>_type_and_version: check type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Ca
r
në
D
raug
t/LocalDB/Ind
e
x/B
l
a
stTable
.
t:
u
se tem
p
dir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Car
n
ë Drau
g
t/
L
o
c
alDB/Index/
B
last
.
t
: create
tes
t
tempfi
l
es withi
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
a
rnë Draug
mai
n
t: remove unused test data files
commit
|
commitdiff
|
tree
2018-09-14
C
a
rnë Drau
g
R
e
m
ove
A
lig
n
IO
a
nd
Index sto
c
kholm modules to n
e
w Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
Bio::DB:
:
Universal: move
into its o
w
n
dist
r
ib
u
tion
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
maint
:
s
i
m
plify READM
E
to cover sim
p
le install instru
c
tions
.
commit
|
commitdiff
|
tree
2018-09-13
C
a
r
në
Draug
Bring bas
e
classes f
r
o
m
Bio
P
erl-run
b
ack to BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
D
raug
Remove
u
se of Bio::Perl which has been moved to Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dr
a
u
g
Bio::DB
:
:
M
eS
H
move
to its o
w
n dist
r
ibut
i
on
.
commit
|
commitdiff
|
tree
2018-09-13
Carn
ë
D
r
a
u
g
Move HMME
R
related
m
od
u
les,
t
ests, and programs to
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dr
a
ug
Bio:
:
DB::TFBS namespace has been moved to its own
d
istributi
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Car
n
ë
D
raug
Bio::D
B
::HIV
a
nd re
l
a
t
ed module
s
and sc
r
i
p
t
s
moved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Car
n
ë
Draug
Bio::Align::Graphics: move into its own distribu
t
ion
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Tools::R
u
n::Re
m
o
teBlast:
m
ov
e
into a n
e
w distri
b
ution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
a
rn
ë
Draug
Bio::Perl:
m
ove its own d
i
stribution named
B
io-Procedur
a
l
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Mo
l
E
v
ol::Codon
M
odel: move
into it separate repo
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::SeqIO::en
t
rezge
n
e: move to ex
i
stin
g
Bi
o
-ASN1-entrez
g
ene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/Restriction/*
:
m
o
ve to anot
h
er repo with same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
B
io/Tools/G
e
l
.
pm: move
to another
r
ep
o
w
i
th same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carn
ë
Draug
Bio/
S
eq
E
v
olution/*: mo
v
e to another repo w
i
th
s
am
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Draug
B
i
o/Structure/*: move to
a
nother re
p
o
w
i
t
h same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
t/data: r
e
move more
test d
a
t
a
f
iles which moved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carn
ë
Draug
Bio/
A
ssembly*: move to another repo with same n
a
me
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/PhyloNetwork*: move to
another repo
with same
name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/
S
eq
I
O/excel
.
pm:
m
ove to another repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio
/
TreeIO/svggraph
.
pm:
m
o
ve
to ano
t
he
r
repo
w
ith same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Bio/Tree/Dr
a
w/C
l
adogram
.
p
m
: move to
a
n
ot
h
e
r
r
e
po with
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Bio/Draw/Pictogram
.
pm:
move
t
o anot
h
er repo
w
ith s
a
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Mov
e
al
l
modules
i
nterfacing to ACeDB servers to a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë D
r
a
u
g
M
ove
a
ll N
e
XML re
l
ated modules and tests to a n
e
w Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
C
a
rnë
Draug
Remove some un
u
sed test dat
a
f
iles
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë
Draug
R
e
move
entire Bio::
P
opGen namespace
a
nd related modules
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
Carnë Draug
s
cripts/tree/
b
p
_
b
last
2
tree
.
pl: moved to bi
o
perl-run
commit
|
commitdiff
|
tree
2018-09-07
C
a
rnë Dr
a
ug
deobfuscator:
r
emo
v
e
t
h
is w
h
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