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Bio::SeqIO::agave: move to its own distribution
2018-09-29
Carnë
Dr
a
ug
Bio:
:
SeqIO::aga
v
e: move
to i
t
s ow
n
distributio
n
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
Bio::
S
eq
I
O::
c
hadoxml (and flybase_chadoxml):
move to
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
a
r
në Drau
g
main
t
: list Data::Stag::XMLWrit
e
r as
droppe
d
depe
n
denc
y
commit
|
commitdiff
|
tree
2018-09-29
C
arnë Draug
Bi
o
::SeqIO:
:
chaosxml (and chaos
)
: mov
e
to
t
he
i
r own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dr
a
ug
B
io::S
e
qI
O
::strider: mov
e
i
n
to its
o
wn
d
i
strib
u
t
ion
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë Draug
Bio::Tool
s
:
:Protparam
:
move to its own
d
i
s
tr
i
but
i
on
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
m
aint:
update and
clean r
e
mov
e
d mod
u
les and dependencies
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::DB::SeqVersion
:
mov
e
into its own
d
ist
r
ibut
i
o
n
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë
D
raug
Bio
:
:To
o
l
s::SiRNA and related moved to
s
e
parate distr
i
bu
t
ion
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bi
o
::To
o
ls::Analysi
s
::
P
rotein:
move modules into their
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dra
u
g
B
i
o::Tools::Analysi
s
::Prote
i
n::Sca
n
si
t
e: move
t
o separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Draug
Bio::Tools::Anal
y
sis::Protein:ELM: m
o
ve to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio:
:
T
o
ols::Analysis:
:
D
NA
:
:
E
SE
f
inder: move to sep
a
rate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::DB:
:
R
e
fSeq, B
i
o::DB::E
M
BL, an
d
s
ub
c
l
asses of Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Draug
Bio::T
a
x
onomy
:
mov
e
de
p
reca
t
ed namespac
e
to its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Drau
g
lib/Bio
P
e
r
l
.
p
m: convert line-ending dos
2
uni
x
commit
|
commitdiff
|
tree
2018-09-28
Carnë Drau
g
doc: update HACKIN
G
inst
r
uct
i
ons wi
t
h dzil
i
nstructio
n
s
commit
|
commitdiff
|
tree
2018-09-25
C
arnë
D
raug
t/*
:
remov
e
"use li
b
'
.
'" an
d
t/
l
i
b/Error
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
raug
Bio::DB::CUTG: move into its own distribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::DB:
:
Taxonomy::sql
i
te: move int
o
its
o
wn distribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
rau
g
Bio::DB::GFF m
o
v
e
into its own namespac
e
(e
x
c
e
pt Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë
Dra
u
g
Bio::DB::SeqF
e
ature::* move namespace into its
own
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë D
r
aug
maint: update
c
h
anges
f
rom 1f7b5
4
a281a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dra
u
g
Bio
:
:
V
ariation::
*
mov
e
namespace in
t
o its own
d
istribution
.
commit
|
commitdiff
|
tree
2018-09-24
Car
n
ë Draug
Remove Bi
o
::Seq
I
O
s
upport for abi, alf, ct
f
, exp, pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
C
a
rn
ë
Draug
Bio::Cl
u
ster
and
Bio::Cluster
I
O move
d
to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
C
a
rnë
Draug
Bi
o
:
:Phenot
y
pe::* move what
'
s left of the namespace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Car
n
ë Draug
mai
n
t: remov
e
no lo
n
g
e
r
use
d
test da
t
a files
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
Bio:
:
LiveSeq::* move whol
e
n
amesp
a
ce to its own distr
i
b
u
tion
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
aug
maint: upd
a
te gitignore rules
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Dra
u
g
maint: restru
c
t
ure to use Dist::Zill
a
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Draug
t/
A
lignIO/AlignIO
.
t: fix num
b
er of tests in plan (fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë Draug
t/A
n
notat
i
on/Annotation
.
t: remove
t
e
st for
B
io::SeqFeat
u
re
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carn
ë
Draug
Bi
o
/Tools/Run/
P
hylo/P
h
y
loBase
.
pm: bring bas
e
class
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Drau
g
Bio/Tools
/
Phylo/G
u
mby
.
pm: mov
e
to its
own di
s
trib
u
ti
o
n
commit
|
commitdiff
|
tree
2018-09-17
Carn
ë
Dr
a
ug
DB/Se
q
Featu
r
e/Store/berkel
e
ydb3
.
pm: fix errors s
o
i
t
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
aug
Adjust tests
i
n
direct
l
y making use of Bio::AlignIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
u
g
bp
_
process_w
o
r
mbase: move progra
m
to
n
ew Bio-DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
a
r
në Draug
bp_netinstall: remove ou
t
of date prog
r
am
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
Move modules depe
n
d
e
n
t
on Bi
o
::Ex
t
:
:Align into d
e
funct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
në
D
raug
Bio::D
B
::Expressi
o
n: move to de
f
u
n
c
t bioperl-microarray
commit
|
commitdiff
|
tree
2018-09-16
Carnë D
r
aug
mai
n
t
:
644 permissions for almost
a
l
l
fil
e
s
commit
|
commitdiff
|
tree
2018-09-16
Carnë Dr
a
u
g
main
t
: set all so
u
rc
e
code wi
t
h utf-8 e
n
codi
n
g
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
ma
i
nt: re
m
o
v
e
maintainer out of dat
e
f
iles
commit
|
commitdiff
|
tree
2018-09-16
Carnë
D
raug
id
e
: remove module templ
a
t
e
s - no longer needed after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
ide/bioperl-
m
ode: into its ow
n
rep
o
sitory to be
d
eveloped
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
C
a
rnë Draug
main
t
: remove biop
e
rl-mode release tar
b
alls
from
version
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
a
rnë Drau
g
Bio::I
n
dex
:
:Abstract->_type_and_vers
i
on
:
chec
k
type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Ca
r
në
Draug
t/LocalDB/Index/Bla
s
tTabl
e
.
t: use
tempdir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Drau
g
t
/LocalDB
/
Index/Bla
s
t
.
t: creat
e
test
tempfiles within
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Dra
u
g
mai
n
t: remove
u
nused test data files
commit
|
commitdiff
|
tree
2018-09-14
C
a
r
n
ë D
r
aug
Remove A
l
ignIO and Index stockh
o
lm modules to
new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Carnë Dr
a
ug
B
i
o
::DB::Un
i
versal: m
o
v
e
i
n
to
its own distribution
commit
|
commitdiff
|
tree
2018-09-14
Ca
r
në Draug
maint:
sim
p
lify README
t
o
cover
s
impl
e
install instructions
.
commit
|
commitdiff
|
tree
2018-09-13
C
a
r
në D
r
aug
B
r
ing base classes
from Bio
P
er
l
-run b
a
ck to B
i
oPer
l
.
commit
|
commitdiff
|
tree
2018-09-13
C
arnë Dr
a
ug
Remove
use of
Bio::Perl which
has b
e
e
n
moved to Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
C
a
rnë
Draug
Bio::D
B
::MeSH move to its own di
s
t
ributio
n
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dr
a
ug
Move HMMER
r
ela
t
ed m
o
dules, tests, and programs to
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bio::DB::TFBS namespa
c
e has b
e
e
n
moved to
its own distri
b
uti
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bio::DB::HIV and rela
t
ed modu
l
es and scri
p
t
s moved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Alig
n
::Graphics: move into i
t
s o
w
n dis
t
ribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Car
n
ë Draug
Bio::Too
l
s::R
u
n::R
e
mote
B
last: move into
a ne
w
distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
Draug
B
io::Per
l
:
m
ove its own d
i
stri
b
u
t
ion named B
i
o
-
Procedural
commit
|
commitdiff
|
tree
2018-09-12
Carn
ë
Dr
a
ug
Bi
o
::MolEvol::CodonModel: move
i
n
t
o
i
t sepa
r
ate
r
epo
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio:
:
SeqIO::entrezgene: move to ex
i
sting
B
io-ASN1-entrezgene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Draug
Bio/
R
est
r
iction/
*
:
move to anot
h
er r
e
po wi
t
h same
n
ame
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/Tools/Gel
.
pm: mo
v
e to another r
e
p
o with
s
a
me name
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Draug
Bio/SeqEvolution/*: move to a
n
other repo with
s
a
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë
D
raug
Bio/Structure/*: move to another repo wi
t
h
same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë
D
ra
u
g
t/data:
rem
o
ve
m
ore t
e
s
t dat
a
files
which moved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
rnë
D
raug
Bio/Assemb
l
y*: m
o
ve to anothe
r
r
e
po
w
it
h
same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bi
o
/PhyloNetwork*: move to anoth
e
r r
e
po with sa
m
e
n
a
me
.
commit
|
commitdiff
|
tree
2018-09-11
Car
n
ë
Draug
Bio/SeqIO/excel
.
p
m
:
move
to another repo with sa
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Draug
Bio/T
r
eeIO
/
svgg
r
aph
.
p
m
:
m
o
v
e
t
o another repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
C
ar
n
ë Draug
Bio/Tre
e
/Draw/Cl
a
dogram
.
pm: move to another repo with
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Ca
r
në Draug
Bio/Draw/Pic
t
o
gram
.
pm: move to another re
p
o with
same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë
Dra
u
g
Move all modules interfaci
n
g to ACe
D
B servers to a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Move a
l
l
NeXML related m
o
dule
s
and tests to a
n
e
w Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Remove some
unused test da
t
a files
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Rem
o
ve
e
ntire
Bio:
:
Pop
G
en n
a
mespace and r
e
lated m
o
dules
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
Carnë Draug
script
s
/tree/bp
_
blast2tree
.
pl: m
o
v
e
d to bioper
l
-run
commit
|
commitdiff
|
tree
2018-09-07
Carnë D
r
aug
deobfuscator: remove this w
h
ole project
commit
|
commitdiff
|
tree
2018-09-04
C
a
r
në Draug
Consis
t
ent shebang line to '+#!/usr/bin/perl'
commit
|
commitdiff
|
tree
2018-08-23
Carnë
Draug
deobf
u
scator scri
p
ts: use w
a
rnings pragma instead of
.
.
.
commit
|
commitdiff
|
tree
2018-07-25
Carn
ë
Draug
B
i
o::MolEvol::CodonModel:
fix d
o
c
u
ment
a
t
i
o
n
(issue
.
.
.
commit
|
commitdiff
|
tree
2017-09-13
C
a
rnë Draug
examples/align/clu
s
talw
.
pl: remove f
i
l
e
,
n
ow
p
a
r
t of
.
.
.
commit
|
commitdiff
|
tree
2017-09-08
Carnë Draug
Removal of
B
io::Too
l
s::Phylo::PAML
.
pm and re
l
ated modules
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë Dr
a
ug
Bio::Phy
l
o
N
etwork
:
:muVector: revert non-t
y
p
o fr
o
m 54c99cf411
commit
|
commitdiff
|
tree
2017-08-30
Carnë
D
r
a
ug
m
a
int: fix multiple typo
s
i
d
entified by linti
a
n
commit
|
commitdiff
|
tree
2015-11-29
Ca
r
n
ë Dr
a
ug
bp_pairwise_kaks
.
pl: do
n
ot mix space an
d
t
a
bs
f
or
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Ca
r
në Draug
Bio::Align
:
:
U
ti
l
ities -
rem
o
ve
u
s
age
of /r option
to
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Car
n
ë Draug
Fix nonsense in code com
m
e
nts
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
B
i
o::A
l
i
g
n::Utilit
i
es - follow some
perl b
e
st
p
rac
t
ices
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::
A
lign::U
t
il
i
ties - new funct
i
on most_common_sequences
commit
|
commitdiff
|
tree
2013-11-26
Carnë D
r
a
u
g
Bio::S
i
mpleAlign
-
follow
s
ome perl be
s
t
pr
a
ctices
commit
|
commitdiff
|
tree
2013-04-04
Carnë D
r
aug
maint: remove files that have been moved to a sep
a
r
ate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë
D
r
a
u
g
m
a
i
nt: update
C
hanges after removing files fr
o
m B
i
o
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
ma
i
nt: re
m
ove files that
h
ave been
m
oved
to a separate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
tests
:
move tests fr
o
m
Root to A
s
s
e
mbly a
n
d SeqIO
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Dr
a
ug
m
aint: r
e
move hard tabs and trailing w
h
i
t
espace
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