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Remove manipulation of @INC and use of lib - require install for use.
2018-09-30
Carnë Draug
Remove manipula
t
ion of @INC and use of lib - require
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
arnë Draug
dist
.
ini
:
m
a
k
e Win32 a depen
d
e
n
cy
f
or Windo
w
s
only
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
Bio::SeqIO::ag
a
ve:
m
ove to its o
w
n distribution
commit
|
commitdiff
|
tree
2018-09-29
Car
n
ë Draug
Bio::S
e
qIO::c
h
adoxml (
a
n
d flybas
e
_chadoxml): move to
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Ca
r
n
ë
Draug
ma
i
nt: list
Dat
a
::Stag::XML
W
ri
t
er a
s
d
r
o
pped depende
n
cy
commit
|
commitdiff
|
tree
2018-09-29
Carnë D
r
a
u
g
Bio
:
:
SeqI
O
::chaosxml (and chaos): mo
v
e to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë D
r
aug
Bio::SeqIO::strider: mo
v
e
into its o
w
n distribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Drau
g
Bio::
T
o
o
ls::Protparam: move to its own distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-28
Carnë
D
raug
maint: upd
a
te a
n
d clean rem
o
ve
d
m
odules
and dependencies
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::D
B
::SeqVersion: move
i
nto its own d
i
s
t
r
i
b
u
tion
commit
|
commitdiff
|
tree
2018-09-28
Carnë Drau
g
Bio::Tools::
S
iRNA and related mov
e
d to se
p
ara
t
e distribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tool
s
::Analysis::Protein: move modul
e
s in
t
o their
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në
D
raug
Bio::Tools::Analysis::Protein::Scansite: mov
e
to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Drau
g
Bio::T
o
o
l
s::Analysis::P
r
o
t
ein:E
L
M
:
move
to sep
a
rate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio:
:
Tools:
:
Analysis::DNA::ESEfinder: mov
e
to sepa
r
a
te
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
B
io::DB::Ref
S
e
q, Bio::DB::EMBL
,
and s
u
bc
l
asses
of B
i
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::T
a
x
onomy: mo
v
e
deprecated name
s
pace to its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
lib/Bio
P
er
l
.
pm: convert line-ending dos2uni
x
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dr
a
ug
doc:
u
p
d
ate
HACKIN
G
inst
r
uc
t
ions with
dzil instr
u
ctions
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
t/*: remove "use
l
i
b
'
.
'"
a
n
d
t
/
lib/Error
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bi
o
::DB::CUTG
:
move into its own
d
istribution
commit
|
commitdiff
|
tree
2018-09-25
C
arnë
D
raug
Bio::DB::Taxonomy::s
q
lite:
m
ove
int
o
its own dist
r
i
b
ution
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::DB::GFF move into its
o
wn namespace (ex
c
ept Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
C
a
r
në D
r
aug
Bi
o
::DB::SeqFeature::* move namespace int
o
its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
maint:
updat
e
c
h
anges from 1f7b54a281a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio
:
:Variation::*
m
ove names
p
ace into
its
o
w
n dist
r
i
b
ution
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë Draug
Remove Bio::SeqIO s
u
ppo
r
t
for abi, alf
,
ctf, exp,
pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
C
a
rnë Drau
g
Bio::Clu
s
ter and Bio::
C
lusterI
O
m
o
ved to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë
Dr
a
ug
Bio::Phe
n
otype::* move what's left o
f
t
h
e na
m
espace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
C
arn
ë
Draug
main
t
: remo
v
e
no
l
onger used t
e
st dat
a
fil
e
s
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë D
r
a
u
g
Bio:
:
Li
v
eSeq:
:
*
mo
v
e
whol
e
namesp
a
c
e
t
o its own distribution
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë
Draug
ma
i
nt
:
update g
i
tignore rules
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë
Draug
mai
n
t: r
e
structure to
u
se Dist::
Z
illa
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
t/AlignI
O
/Alig
n
IO
.
t:
f
ix numb
e
r of
tests in pl
a
n
(
fixu
p
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Draug
t/
A
nnotation/Annotation
.
t: remove
t
est for Bio:
:
S
e
q
Featu
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
B
i
o/Tools/R
u
n
/Phy
l
o/PhyloBase
.
pm: bring bas
e
class
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
Bio/
T
oo
l
s/Phyl
o
/
G
um
b
y
.
pm: move t
o
its o
w
n d
i
stribution
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
DB/SeqFeature/S
t
o
r
e/berkeleydb
3
.
pm: fix errors so
i
t
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
Adjust tests i
n
direct
l
y makin
g
use o
f
B
io::AlignIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
u
g
b
p
_process_
w
ormbas
e
: move
p
rogram to
n
ew Bio-DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
a
u
g
bp_netinstall: remove ou
t
of date prog
r
am
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Draug
Move mod
u
les
dependent on Bio
:
:
Ext::
A
lign i
n
to defunct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
Bio::DB
:
:Ex
p
ression: m
o
v
e
to def
u
nct bio
p
e
r
l-microarray
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
m
aint: 644 permissions for almost a
l
l files
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint
:
set al
l
source c
o
de wit
h
utf-8 encoding
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint:
r
e
m
ov
e
maintainer out o
f
date f
i
les
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
ide: remove module templates - no longer needed after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
ide/b
i
operl-mod
e
: into its own repos
i
tory to be developed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Drau
g
ma
i
nt: remove bioperl-mode release tar
b
alls from
version
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Dra
u
g
Bio
:
:
I
ndex::Abstract->_type
_
and_
v
ersion: c
h
eck type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t/LocalDB/In
d
ex/BlastTable
.
t: use te
m
p
d
ir t
o
avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t/LocalDB/I
n
dex
/
Blas
t
.
t: cr
e
ate test tempfiles w
i
thin
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
arnë Draug
maint: remove u
n
us
e
d test data files
commit
|
commitdiff
|
tree
2018-09-14
Ca
r
n
ë
Draug
Re
m
ov
e
A
lignIO
a
nd In
d
ex stockh
o
lm
m
odu
l
es to ne
w
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Ca
r
në Draug
B
i
o::D
B
::Universal: move into its
o
wn distribution
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
maint:
s
implify READ
M
E to cover sim
p
le in
s
ta
l
l
instruction
s
.
commit
|
commitdiff
|
tree
2018-09-13
Ca
r
në Draug
B
ring bas
e
cla
s
s
es fro
m
BioP
e
rl-run back to BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Remove u
s
e
of
Bio::Pe
r
l which ha
s
b
e
e
n moved to Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Drau
g
B
i
o::DB::Me
S
H move to
its
o
wn distributi
o
n
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Mo
v
e HMMER rela
t
ed
m
odules, tests, and programs
t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë D
r
a
ug
Bio::DB::TFBS
n
amespace ha
s
bee
n
moved to its own d
i
s
t
ri
b
uti
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
C
a
rnë D
r
aug
Bi
o
:
:
DB::HIV and re
l
a
t
ed
m
odules
an
d
s
c
ript
s
moved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Dra
u
g
Bio::
A
li
g
n:
:
Gr
a
phics: mov
e
into
its own distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë D
r
aug
Bio
:
:
T
o
ols::Run::Remot
e
Blast: move into a
n
ew d
i
stribu
t
ion
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
a
rnë
D
raug
Bio:
:
P
e
r
l:
move its
own di
s
tr
i
bution named B
i
o-Procedural
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Mol
E
vol::
C
odonMo
d
el: move into it separa
t
e re
p
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
D
r
a
ug
Bio::SeqIO::ent
r
e
zg
e
ne: mov
e
t
o existin
g
B
i
o
-ASN1-entrezg
e
ne
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Dra
u
g
Bio/Restricti
o
n
/*
:
m
o
ve to another
r
ep
o
with
s
a
m
e
n
ame
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë D
r
aug
Bio/Tools/Gel
.
pm: m
o
ve to anoth
e
r repo with same name
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
r
në Dr
a
ug
Bio/SeqEvolution/*: move to
another repo
with s
a
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
B
i
o
/Structure
/
*: move to another rep
o
w
i
t
h same na
m
e
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Dra
u
g
t/data: rem
o
v
e
m
ore te
s
t dat
a
files
which moved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në Draug
Bio/Assembly*: move to anothe
r
repo
with same nam
e
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/P
h
y
loNetwork*: mo
v
e to another
r
e
p
o with same name
.
commit
|
commitdiff
|
tree
2018-09-11
Car
n
ë Draug
Bio/SeqIO
/
excel
.
pm:
m
ove to another repo with
same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në Draug
B
io/T
r
eeIO/svggr
a
p
h
.
pm: move to another
r
e
po with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Bio/T
r
ee/Draw/C
l
adogram
.
pm: mov
e
to another
r
epo with
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carn
ë
D
raug
Bio/Draw/Pic
t
ogram
.
pm: move to anothe
r
repo wit
h
sa
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Mo
v
e all modu
l
es int
e
rfacing to ACeDB
s
er
v
ers
t
o a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë
Draug
Move
a
ll NeXML
relat
e
d m
o
d
u
les and tests
t
o a ne
w
Bi
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
C
arnë Dra
u
g
Rem
o
ve some unused
t
est
d
a
ta files
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
R
emove entire Bio::PopGen nam
e
spac
e
and relate
d
modules
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
Carnë Draug
script
s
/
t
r
ee/bp_blast2
t
ree
.
pl: moved to bio
p
erl-run
commit
|
commitdiff
|
tree
2018-09-07
Carnë Drau
g
deobfuscat
o
r: rem
o
ve this whole project
commit
|
commitdiff
|
tree
2018-09-04
Carnë Dr
a
ug
Cons
i
s
t
ent s
h
ebang line to '+#!/usr/bin/perl'
commit
|
commitdiff
|
tree
2018-08-23
Carnë Drau
g
deob
f
usc
a
tor scripts: use warnings pragma i
n
s
t
ead of
.
.
.
commit
|
commitdiff
|
tree
2018-07-25
Carnë Draug
Bio::Mol
E
vol::
C
odonMo
d
el: fix document
a
tion (issue
.
.
.
commit
|
commitdiff
|
tree
2017-09-13
Car
n
ë
D
r
aug
ex
a
m
p
l
e
s/align/clustalw
.
pl
:
r
emo
v
e file, now pa
r
t
of
.
.
.
commit
|
commitdiff
|
tree
2017-09-08
Carnë
D
rau
g
R
e
moval of Bi
o
::Tools::Phylo::PAML
.
pm and related modules
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë Drau
g
B
io:
:
P
hyloNetwork:
:
muVecto
r
:
revert non-typ
o
from 54c99cf411
commit
|
commitdiff
|
tree
2017-08-30
C
a
rnë Draug
maint: fix multip
l
e t
y
pos
i
dentified by lin
t
i
an
commit
|
commitdiff
|
tree
2015-11-29
Carnë Draug
bp_
p
airwise
_
kaks
.
p
l: do not mix sp
a
ce
a
nd tabs f
o
r
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë
D
raug
Bio::Ali
g
n::Util
i
ties - remove usag
e
of /r option t
o
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carn
ë
Draug
Fix nonsense
i
n code
c
om
m
ents
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::
A
l
ig
n
:
:
Utilitie
s
- follow some perl
best practices
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
B
i
o::
A
lign::Utiliti
e
s - new fu
n
ct
i
on mos
t
_common_se
q
uences
commit
|
commitdiff
|
tree
2013-11-26
Carnë
D
r
aug
Bio::Simp
l
eAlig
n
- follow some
p
erl best practi
c
e
s
commit
|
commitdiff
|
tree
2013-04-04
Carnë
Draug
maint: remo
v
e files that have
be
e
n
moved to a
s
epa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
m
a
i
n
t: upda
t
e Changes
a
fter removing fi
l
e
s
from Bio
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë
Draug
maint: remove
f
iles that have been mov
e
d
to a separate
.
.
.
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