I'm testing my LeMoNe viewer on vampire as well as on my own pc...
Weird observation:
Running the viewer on my own pc takes about 35".
Doing the very same thing on vampire keeps the bits flowing for over 2'20".
The data is located on my home share, so both vampire as my machine have
to fetch it there. Both are running a 64bit JVM.
So... is vampire that slow? Is my pc that fast? Or is the network
connection between vampire and the home share the bad?
T.
--
==================================================================
Thomas Van Parys
Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be
==================================================================
Op 18-08-10 11:33, Thomas Van Parys schreef:
> Op 18-08-10 11:22, Michiel Van Bel schreef:
>>
>> Stel ik heb in 1 directory 2 soorten files
>> ath.gff
>> ptr.gff
>> ....
>>
>> en
>> ath_cds.gff
>> ptr_cds.gff
>> ...
>>
>> Nu moet ik, afhankelijk van het feit of die "_cds" erin voorkomt iets
>> anders met die file doen
>>
>> #NIET MET _CDS
>> for i in `ls -a [a-z,0-9]+.gff`
>
> This works:
>
> for i in `find -maxdepth 1 -regex ".*\/[a-z,0-9]*\.DAT"`
Above was my test case... this is better:
for i in `find -maxdepth 1 -regex ".*\/[a-z,0-9]+\.gff"`
the first '.*\/' is because find returns a full path...
>
>
>> do
>> # GFF sorteren op reference (1) en start coordinate (4)
>> sort -k1,1 -k4,4n $i | ./bgzip -c> $i.gz
>> # Index stuff
>> ./tabix -p gff $i.gz
>> done
>> #WEL MET _CDS
>> for i in `ls -a *_cds.gff`
>> do
>> #CDS gffs dienen gewoon gezipt te worden gzip -f $i done
>>
>> ok, so far so good...
>> probleem is enkel dat die
>> for i in `ls -a [a-z,0-9]+.gff`
>> niet werkt....
>> Iemand enig idee?
>>
>
>
--
==================================================================
Thomas Van Parys
Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be
==================================================================
