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dist.ini: make Win32 a dependency for Windows only (issue #291)
2018-09-30
C
a
r
n
ë
D
raug
dist
.
ini: ma
k
e Win32 a dep
e
nde
n
cy
for Windows only
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
B
i
o::SeqIO::a
g
av
e
: move to it
s
own distrib
u
t
ion
commit
|
commitdiff
|
tree
2018-09-29
Carn
ë
Draug
B
io:
:
S
e
qIO:
:
chad
o
xm
l
(and f
l
yba
s
e_
c
hadoxml): mov
e
t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
a
r
n
ë Dra
u
g
maint: li
s
t Data
:
:Stag
:
:XMLWrit
e
r as dropped dependency
commit
|
commitdiff
|
tree
2018-09-29
Carn
ë
Draug
Bi
o
::
S
eqIO::chaosxml (and chaos)
:
m
o
ve to
t
h
eir o
w
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
a
u
g
B
i
o
::Seq
I
O::strider: move
i
nto its
ow
n
distribution
commit
|
commitdiff
|
tree
2018-09-28
C
arnë Drau
g
Bio::Tools::Protpa
r
am:
m
ove to its
own distribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dra
u
g
main
t
: update and clean remo
v
ed modules and dependencies
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
n
ë
Draug
Bio:
:
DB::SeqVers
i
on: mo
v
e into its own
d
i
s
t
ribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::
T
ool
s
:
:
SiRNA and related
m
ov
e
d to sep
a
rate dis
t
ribution
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në
D
raug
Bio::Tools::Analysis::Prote
i
n: move modules into t
h
e
ir
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Drau
g
B
io::Tools::
A
nalysis::P
r
ot
e
in::
S
cansite: move to separa
t
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tools::Analysis::Prote
i
n:ELM:
move t
o
s
e
pa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::T
o
ols:
:
Ana
l
ysis
:
:DNA
:
:E
S
Ef
i
nder: move t
o
separa
t
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dra
u
g
Bio::DB
:
:RefSeq,
Bio::DB:
:
EMBL, and subclasses of
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bi
o
:
:
T
a
xo
n
omy: move depreca
t
ed namespace to its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
lib/BioPerl
.
pm: conv
e
rt line-ending dos2unix
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dr
a
ug
doc: upd
a
te HACKING
instr
u
c
t
ions with dzil i
n
str
u
ctions
commit
|
commitdiff
|
tree
2018-09-25
Carnë D
r
aug
t/*: r
e
move "use lib '
.
'" and t/lib/Error
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
B
io::DB::CUT
G
: mo
v
e into
i
t
s
o
w
n
distrib
u
tion
commit
|
commitdiff
|
tree
2018-09-25
Carn
ë
Drau
g
Bio
:
:DB::Taxonomy:
:
s
q
lite: move into
its o
w
n distribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::DB::GFF
mo
v
e into its
o
wn namesp
a
c
e (
e
xcept Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dr
a
ug
Bi
o
::D
B
::Se
q
Feature::* m
o
ve namespa
c
e into its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
main
t
:
update
changes from 1f7b54a281a
8
commit
|
commitdiff
|
tree
2018-09-25
Ca
r
në
Draug
Bio::V
a
riation:
:
* move namespac
e
i
n
t
o its own distrib
u
t
i
on
.
commit
|
commitdiff
|
tree
2018-09-24
C
arnë Draug
Remo
v
e Bio::SeqI
O
s
upport for a
b
i, alf,
ctf, e
x
p,
pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë Draug
Bio::Cluster
and Bio::Cluste
r
I
O
m
oved to
their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë
Draug
Bio::
P
henotype::* move what's left o
f
t
h
e nam
e
space
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
C
a
rn
ë
Draug
maint: remove
no lo
n
ger used
te
s
t
data files
.
commit
|
commitdiff
|
tree
2018-09-22
Ca
r
në
D
ra
u
g
Bio::Liv
e
Seq::
*
move whole
n
a
mespa
c
e to it
s
own distributio
n
.
commit
|
commitdiff
|
tree
2018-09-17
Carn
ë
Dr
a
ug
mai
n
t: update git
i
gnore rules
commit
|
commitdiff
|
tree
2018-09-17
Carnë Drau
g
m
a
int:
r
estructure to use Dist::Zi
l
la
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
t/AlignIO/Ali
g
nIO
.
t: fix number of tests in p
l
a
n
(fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë
D
r
a
ug
t/Ann
o
tation/Annotati
o
n
.
t: remove
test
f
o
r
Bio::Se
q
Feature
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/Tool
s
/R
u
n/Phylo/Phy
l
oBase
.
pm: br
i
ng base class
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/Tools/Phylo
/
Gumby
.
pm: move to its o
w
n
di
s
tributi
o
n
commit
|
commitdiff
|
tree
2018-09-17
Carn
ë
Dra
u
g
DB/S
e
qFeature/Stor
e
/berkeleydb3
.
pm:
f
i
x erro
r
s so it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Adjust tests in
d
irectly making use of Bio::Ali
g
nIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
bp
_
process_wormbase: m
o
ve progra
m
to
new Bio-DB
-
Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
b
p_netinstall: rem
o
ve out of date p
r
ogra
m
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë Drau
g
M
o
v
e modules depe
n
dent on Bio::Ext::Align
into d
e
func
t
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
në Draug
Bio::DB
:
:E
x
pression: move to defunct bioperl-m
i
croarray
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint:
64
4
permissi
o
ns
for a
l
mos
t
all files
commit
|
commitdiff
|
tree
2018-09-16
Carnë Drau
g
maint: s
e
t all
sou
r
ce code with utf-
8
enco
d
i
n
g
commit
|
commitdiff
|
tree
2018-09-16
Car
n
ë
D
r
aug
mai
n
t: remove maintainer out of date files
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
ide:
r
e
move modu
l
e
templates - n
o
longer nee
d
ed after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë D
r
aug
ide/bioperl-mode:
into its own repository to be
developed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
m
a
int: re
m
ove biop
e
rl-
m
o
de rel
e
a
s
e t
a
rballs
from version
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
arnë Draug
Bio::Index::Abstract->_type_and_version: check type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
arnë Draug
t
/
LocalDB/
I
ndex
/
BlastTable
.
t: use tempdir to
avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t/
L
ocalDB/Index/Bl
a
st
.
t: create
test
tempfiles wi
t
hin
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
a
rnë Draug
ma
i
nt: r
e
move unused test data files
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
Remov
e
AlignIO
a
nd Index stockholm mo
d
ules to new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
C
arnë Draug
Bio::DB::Univ
e
rsal: move into its own distribution
commit
|
commitdiff
|
tree
2018-09-14
C
arnë
D
ra
u
g
maint: simplify README
t
o cover
s
imple
ins
t
all i
n
structions
.
commit
|
commitdiff
|
tree
2018-09-13
C
a
r
në Dra
u
g
Bring
b
ase
c
lasses f
r
om BioPerl-run back to BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Remove use of Bio::Perl which has
b
een mov
e
d to Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
D
ra
u
g
Bio::DB::Me
S
H move to its own distribution
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
Dr
a
ug
Move HMMER
related modu
l
es, tests, and prog
r
ams to
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dra
u
g
Bio::DB::TFBS namespace has been
m
oved to its own
d
istr
i
buti
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
C
arnë Draug
Bi
o
::D
B
::HIV an
d
relat
e
d modules and
script
s
m
oved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
Dr
a
ug
Bio::Align::Graphi
c
s: move into its ow
n
d
istributio
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Dra
u
g
Bi
o
:
:
Tools::Run:
:
RemoteB
l
a
st: move
i
nto a new distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
arnë Draug
Bio::
P
erl: move its own distr
i
b
ution name
d
Bio-Procedura
l
commit
|
commitdiff
|
tree
2018-09-12
Carnë D
r
aug
B
io::Mol
E
vol::CodonMode
l
: mo
v
e
into it se
p
arate rep
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
D
raug
Bio::SeqIO::entrez
g
en
e
: move to
e
xist
i
ng B
i
o-ASN1-entrezgene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Dra
u
g
B
i
o/Restriction/*: move to an
o
ther repo with same
n
a
m
e
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Draug
Bio/Tools/Gel
.
pm: mov
e
t
o another repo
w
i
th same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bi
o
/Seq
E
volution/*: move
t
o another repo w
i
th sa
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
rnë Draug
Bio/Structure/*: m
o
ve
t
o
an
o
t
her
r
epo with same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
t/data: remove m
o
re test data fi
l
es
whic
h
m
oved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/Assembly*: mo
v
e to another re
p
o w
i
th same name
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në
D
raug
Bio/Phylo
N
etwork*: move to another repo w
i
th sa
m
e n
a
me
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/SeqIO/excel
.
pm:
m
ove t
o
a
n
other
r
epo
wit
h
same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
rnë
Draug
Bio/TreeIO/svg
g
raph
.
p
m
: move to another repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
C
arnë Draug
Bio/T
r
ee/Draw/
C
ladogram
.
pm: move to another r
e
po with
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë D
r
aug
Bio/Draw
/
Pict
o
gram
.
pm: move to
a
n
o
th
e
r repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Move all modules interf
a
cing to ACeDB serve
r
s
to
a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Move
a
l
l Ne
X
ML related
m
odules and tests to a new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Ca
r
në Draug
Remov
e
some unused test data file
s
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë
D
raug
Rem
o
ve enti
r
e
Bio::P
o
pGe
n
n
amespace
a
nd related modu
l
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
Carn
ë
Draug
scripts/tree/bp_blast2tr
e
e
.
p
l
: moved to bioperl-ru
n
commit
|
commitdiff
|
tree
2018-09-07
Carnë
D
raug
de
o
bfusca
t
or: remov
e
this wh
o
le project
commit
|
commitdiff
|
tree
2018-09-04
C
arnë Dr
a
ug
C
o
ns
i
s
ten
t
s
h
ebang
l
ine to '+#!/usr/bin/per
l
'
commit
|
commitdiff
|
tree
2018-08-23
Carnë Drau
g
deo
b
f
u
scator scripts:
u
se warnings
pragma inst
e
ad of
.
.
.
commit
|
commitdiff
|
tree
2018-07-25
Carnë Draug
Bio::
M
olEvo
l
::
C
o
donModel:
f
ix do
c
umentation (i
s
sue
.
.
.
commit
|
commitdiff
|
tree
2017-09-13
Carn
ë
Draug
e
xamples/align
/
clustalw
.
pl: r
e
mo
v
e file,
n
ow part of
.
.
.
commit
|
commitdiff
|
tree
2017-09-08
Carnë Draug
Rem
o
val
o
f
Bio::Tool
s
::Phylo::
P
A
ML
.
pm and related modules
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë Dra
u
g
Bio
:
:Phylo
N
etwork::muVecto
r
: revert n
o
n
-
typo from 54c99cf411
commit
|
commitdiff
|
tree
2017-08-30
Car
n
ë
D
r
aug
maint: fix multipl
e
typos id
e
ntified by li
n
tian
commit
|
commitdiff
|
tree
2015-11-29
Carnë Draug
bp
_
pairwise_kaks
.
pl:
do not mix spac
e
an
d
ta
b
s for
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
B
i
o::Align:
:
Uti
l
ities - re
m
ov
e
usage
o
f
/
r option to
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
C
arnë Draug
Fix n
o
nsense in code co
m
ments
.
commit
|
commitdiff
|
tree
2013-11-26
Car
n
ë Draug
Bio::
A
lign::Utilities - foll
o
w some perl best pra
c
tices
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
B
io::Align::Utiliti
e
s - new funct
i
on most_common_sequences
commit
|
commitdiff
|
tree
2013-11-26
Car
n
ë
Draug
B
io
:
:SimpleAlign - follow
s
ome perl best practice
s
commit
|
commitdiff
|
tree
2013-04-04
Carnë Draug
mai
n
t: remove files
t
hat hav
e
bee
n
moved t
o
a
s
ep
a
rat
e
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë
D
r
aug
maint: u
p
date Changes after remov
i
ng
f
iles fro
m
Bio
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë
Draug
mai
n
t: remove files that have
b
e
en mov
e
d to a sepa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
tests: move tests from Root to A
s
s
embly and SeqIO
.
.
.
commit
|
commitdiff
|
tree
next