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t/SeqFeature/Generic.t: fix typo on required module for testing
2019-02-05
Carnë
D
ra
u
g
t/SeqFeatur
e
/Generic
.
t: fix typo on required
m
o
dule
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë D
r
aug
Bio::Root::Test: fix test_network us
e
of Test::
R
equires
I
n
terne
t
commit
|
commitdiff
|
tree
2019-02-05
C
arnë Draug
mai
n
t: fix r
e
pository link
s
on metadat
a
(issue #306)
commit
|
commitdiff
|
tree
2019-01-30
Carn
ë
Drau
g
v1
.
7
.
3
commit
|
commitdiff
|
tree
2019-01-29
Ca
r
në Draug
bin/bp
_
genbank2gff3: fix sor
t
i
ng
b
y
feature type (issue
.
.
.
commit
|
commitdiff
|
tree
2019-01-29
Carnë Dra
u
g
Bio::Seq
I
O::lase
r
gene
:
move to
its own
d
i
st
r
ibution
commit
|
commitdiff
|
tree
2018-10-03
Carnë Draug
Changes: more
details and philosophy are on HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
Carnë Dra
u
g
Changes: mo
r
e det
a
i
l
e
d com
p
lete list of mo
d
u
le
s
/
d
epen
d
encies
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
C
arn
ë
Draug
lib/Bi
o
Perl
.
pm: star
t
c
onversi
o
n of POD to make
u
s
e
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë
D
r
a
u
g
bin
/
b
p
_biofetch_g
e
n
bank_proxy: move to Bio-DB-NC
B
IHelp
e
r
commit
|
commitdiff
|
tree
2018-10-01
Car
n
ë Draug
Bio:
:
DB::SwissProt: m
o
ve to its own
d
istributi
o
n
commit
|
commitdiff
|
tree
2018-10-01
Carnë Drau
g
B
i
o::DB::B
i
oFetch: move
to its own di
s
tribu
t
ion
commit
|
commitdiff
|
tree
2018-09-30
Carnë
D
raug
Automatic
h
andl
i
ng of VERSION
i
n
all modules (issue
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
t/SeqFea
t
ure/Gene
r
ic
.
t:
f
ix
f
ailing tests (
f
ixup fde
6
03f22aa)
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
b
i
n/bp_
f
etc
h
:
move requi
r
e of optional
m
od
u
les where
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë D
r
aug
Bio
:
:
Ma
p
::* and
B
i
o::MapIO::
*
:
move
i
nto their ow
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë
D
raug
Remove ma
n
ipul
a
ti
o
n of @INC a
n
d use of l
i
b
- require
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
ar
n
ë Draug
dis
t
.
ini:
make Win32 a de
p
e
n
dency
f
o
r
W
indows only
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
arnë Draug
Bio::
S
e
q
IO
:
:agave
:
mov
e
to its own distri
b
ution
commit
|
commitdiff
|
tree
2018-09-29
Carnë
D
raug
Bio:
:
SeqIO::chadoxml (and fl
y
b
a
se_chadoxml):
move to
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carnë Drau
g
maint:
list Data::Sta
g
:
:
X
MLWri
t
er as
dropped
d
e
penden
c
y
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
Bio::SeqIO:
:
ch
a
osxml
(and chaos
)
: m
o
ve to the
i
r ow
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::SeqIO::strider: move int
o
i
t
s own distribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
B
io::T
o
ols::P
r
otp
a
ram:
m
o
v
e to its o
w
n distribution
commit
|
commitdiff
|
tree
2018-09-28
C
a
r
në Draug
maint: update and clean re
m
ove
d
mo
d
ule
s
and
depend
e
n
cies
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dra
u
g
Bio::DB::SeqVersion: move into
i
t
s
own distribut
i
on
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dra
u
g
B
i
o
::Tools::SiRNA and rel
a
ted m
o
ved to separate distr
i
bution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tools::Analysis::Protein: mov
e
module
s
in
t
o th
e
ir
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
B
i
o::Tools::Analysis::Protein::Scansit
e
: move to separat
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
B
io::Tools::A
n
alys
i
s::Pro
t
ein:ELM: move to
s
e
para
t
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
a
ug
Bi
o
::T
o
ols::Analysis::DNA::
E
SEfi
n
der: move to sepa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në
Draug
B
i
o::DB::Ref
S
e
q
, Bio::
D
B::EMBL, and subcla
s
ses of Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Draug
Bio::Taxonomy: move deprecated namespace to its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
aug
lib/BioPerl
.
pm: convert
l
i
n
e-ending dos2un
i
x
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
doc: updat
e
HACKING
instr
u
ctions with dzil
i
nst
r
u
ctions
commit
|
commitdiff
|
tree
2018-09-25
Car
n
ë
D
rau
g
t/*: remo
v
e "use lib '
.
'" and
t/lib/Error
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::DB::C
U
TG: move int
o
its o
w
n distri
b
ution
commit
|
commitdiff
|
tree
2018-09-25
Carn
ë
Draug
Bi
o
::DB::Taxonomy::sqlite: move int
o
its own
d
i
s
t
ri
b
ution
commit
|
commitdiff
|
tree
2018-09-25
C
arnë
Dr
a
ug
B
i
o
::D
B
::GFF move in
t
o
i
ts
own
namespace (except Bi
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio
:
:DB::SeqFeatu
r
e::*
move n
a
mespac
e
into
i
ts own
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dr
a
ug
maint: update ch
a
n
ges fro
m
1f7b54
a
2
8
1a8
commit
|
commitdiff
|
tree
2018-09-25
C
arnë Draug
Bio::Variati
o
n::* move namespace into its own d
i
stribution
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë D
r
a
ug
Remove
B
i
o::SeqIO s
u
pport fo
r
a
bi,
a
lf, ctf
,
e
xp,
p
ln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
C
arn
ë
Draug
Bio::Cl
u
ster a
n
d Bio::ClusterIO m
o
v
e
d to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë D
r
aug
Bio::Ph
e
n
otype::*
move what's left of the
n
amespa
c
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Dra
u
g
maint: remo
v
e no longer used te
s
t
data files
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
Bio::LiveS
e
q:
:
* move whole namespace to it
s
own
distri
b
ution
.
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë Dra
u
g
maint:
u
p
d
a
t
e gitign
o
re r
u
les
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë
Draug
maint: restruct
u
r
e
to use
D
i
st
:
:Zil
l
a
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
t/Al
i
gnIO/AlignIO
.
t: fix number of tests in plan (fixu
p
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
t
/
Annotation/Ann
o
tation
.
t: remove test for Bio::SeqFea
t
u
re
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/T
o
ols/Run
/
Phy
l
o/PhyloBa
s
e
.
pm: bring base
c
l
ass
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/Tools
/
Phylo/Gu
m
b
y
.
pm: move to its
o
wn distribu
t
i
on
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
në Draug
DB/SeqFea
t
ure/Store/berkeleydb3
.
pm: fix errors so
it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Draug
Adjust tests indirectly
making use o
f
Bi
o
::AlignI
O
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
bp
_
process_w
o
r
m
ba
s
e: m
o
ve
pro
g
ram to new B
i
o-
D
B-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Drau
g
bp_netin
s
tall: remove
o
ut of dat
e
p
rogra
m
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
a
u
g
Move modul
e
s dependen
t
on Bio::Ext::Align into defunct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë Drau
g
Bio::DB
:
:Ex
p
ress
i
o
n
: move
to defunct
b
ioper
l
-micr
o
a
r
ray
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
m
a
int: 6
4
4 permissio
n
s for al
m
ost all file
s
commit
|
commitdiff
|
tree
2018-09-16
Carnë
D
raug
maint:
s
et
all source code
with
utf-8 encoding
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint: remove maintainer out of da
t
e fi
l
es
commit
|
commitdiff
|
tree
2018-09-16
Carnë Drau
g
i
de: re
m
ove module templates - no longer nee
d
ed after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Ca
r
n
ë
D
raug
ide/b
i
o
p
erl-mode:
i
nto its own rep
o
sito
r
y to be
d
e
velope
d
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë D
r
aug
ma
i
nt: remove
bioperl-mod
e
re
l
eas
e
tarb
a
lls
from version
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
Bio
:
:
I
nd
e
x::Abstract->_type_and_version: check type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t
/
LocalDB/In
d
ex
/
Bl
a
s
t
Tabl
e
.
t: use
t
empdir t
o
avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t
/Lo
c
alDB/Index/Blast
.
t
:
create test
t
empfiles
within
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
arn
ë
Draug
maint: rem
o
ve u
n
used test data files
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
Remove Alig
n
I
O
a
n
d Index stockhol
m
module
s
t
o new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
Bio::DB::Univ
e
r
s
al: move int
o
its own distribu
t
i
o
n
commit
|
commitdiff
|
tree
2018-09-14
Car
n
ë
Draug
m
a
int: simplify README
t
o c
o
ver simpl
e
install
instru
c
tions
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bring b
a
se classes from BioPerl-r
u
n back to BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Re
m
ove use of Bio:
:
Perl which has been mov
e
d t
o
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Ca
r
në Draug
Bio::DB::Me
S
H move to
i
t
s own
distribut
i
on
.
commit
|
commitdiff
|
tree
2018-09-13
Car
n
ë Drau
g
Move
H
MMER related
modul
e
s, t
e
s
ts, and pr
o
grams to
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carn
ë
D
raug
Bio::DB::TFB
S
namespace has been
moved to
i
ts own distributi
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bio::DB::HIV and
related
m
od
u
les and script
s
m
oved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carn
ë
Dr
a
u
g
Bi
o
::A
l
ign::Graphics: move
i
nt
o
its own dist
r
ibution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë D
r
aug
Bio::Tools::Run::RemoteB
l
ast: move in
t
o a new distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Perl: move its own distri
b
u
t
ion na
m
ed Bio-Procedu
r
al
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
B
i
o
::MolEvol::CodonModel: m
o
ve into
it se
p
arate repo
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
a
rnë Draug
Bio::
S
eqIO::entrezgene: move to existing Bio-AS
N
1-entrezgene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bi
o
/R
e
striction/*:
move to another re
p
o
w
i
t
h
s
ame
n
a
me
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/Tools/Gel
.
p
m
:
move to
ano
t
her repo with sam
e
name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Dr
a
ug
Bio/SeqEvolution/*: mov
e
t
o
another
r
epo with sam
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Draug
Bio/Stru
c
tur
e
/*: move to
a
nother repo with same
name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
t/data: remove more test
d
a
t
a files whic
h
moved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/Asse
m
b
l
y*: move to another repo
with sa
m
e name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Drau
g
B
i
o/Ph
y
lo
N
etwor
k
*:
m
ove to
anot
h
er repo wit
h
same n
a
me
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Drau
g
Bio/SeqIO/exce
l
.
pm: m
o
ve
t
o
ano
t
he
r
repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në
D
raug
Bio/Tree
I
O/svggrap
h
.
pm: move
t
o anothe
r
repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
C
arnë Dr
a
ug
B
i
o
/Tree/Draw/C
l
adogram
.
pm: move
t
o another r
e
po wit
h
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Bi
o
/Draw/Pictogram
.
pm: m
o
ve to anothe
r
repo with
same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
M
ove al
l
modules interfacing to ACeDB server
s
to a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Dr
a
ug
Mov
e
all NeXML re
l
at
e
d modul
e
s and tests to a
new
B
io
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë
D
ra
u
g
Re
m
ove some
unused test data
f
iles
.
commit
|
commitdiff
|
tree
2018-09-10
C
a
rnë D
r
aug
Remov
e
e
ntire Bio::PopGen
n
amespac
e
and relate
d
module
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
Carnë Draug
s
c
ripts/tree/
b
p_blast2tree
.
pl: moved t
o
bio
p
erl
-
run
commit
|
commitdiff
|
tree
2018-09-07
Carnë Draug
deobfuscator: rem
o
ve thi
s
whole project
commit
|
commitdiff
|
tree
next