Mark Linimon 06e6677793 Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon, ... remove support for them from bsd.java.mk. As Jikes is not available in Java 1.5 or higher, remove it from bsd.java.mk too (suggested by hq@) and from the ports which used it (only occurences were USE_JIKES=no). Support for the Blackdown VM is also removed, as it is not available in Java 1.5 and higher. Also remove the mapping from Java 1.1-1.4 to Java 1.5+ in bsd.java.mk to detect old, broken ports; therefore bump the minimal value of JAVA_VERSION to 1.5. While here, replace static values of JAVA_VERSION in files/*.in by %%JAVA_VERSION%% . PR: ports/158969 Submitted by: rene Tested on: pointyhat-west -exp		2011-07-21 05:03:02 +00:00
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adun
ariadne
artemis	Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,	2011-07-21 05:03:02 +00:00
avida
babel
belvu
biococoa
biojava
blast
blat
boinc-simap
chemeq
clustalw
consed
crimap
crux
distribfold
dna-qc
dotter
embassy
emboss	- kick MD5	2011-07-02 11:33:17 +00:00
fasta
fasta3
fastdnaml
finchtv
fluctuate
garlic
genpak
gff2ps
gmap
gperiodic
grappa
hmmer
iolib
jalview	Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,	2011-07-21 05:03:02 +00:00
kinemage
L-Breeder
lagan
lamarc
libgenome
libsbml
linux-foldingathome
lsysexp
mafft
mapm3
migrate
molden
mopac
mrbayes
mummer
muscle
ncbi-toolkit
njplot
ortep3
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB	- Update to 1.20	2011-07-13 06:48:25 +00:00
p5-Bio-NEXUS
p5-Bio-Phylo	- Update to 0.38	2011-07-16 06:08:34 +00:00
p5-Bio-SCF
p5-bioperl
p5-bioperl-run
paml
phd2fasta
phrap
phred
phylip
phyml
platon
povchem
primer3
protomol
psi88
py-biopython
pycogent
pyfasta
pymol
python-nexus
rasmol
recombine
ruby-bio
seaview
seqio
sim4
ssaha
t_coffee
tinker
treepuzzle
treeviewx
tRNAscan-SE
velvet
wise
xdrawchem
xmolwt
Makefile