October 2008 - binari@psb.ugent.be - maillist.psb.ugent.be

[Binari] fffffff
by Kenny Billiau 17 Oct '08

17 Oct '08

So .. to summarize .. 1 small with mayo 1 small with stoofvlees 1 middle with mayo 1 big with stoofvlees 1 grieslie 2 sate 1 kipcorn (individual orders where: - een kleintse mee majoneis en ne grieslie! - klein, stoofvleessaus, sate - groot, stoofvleessaus, kipcorn/viandel - middle, mayonnaise, sate ) -Kenny -- ================================================================== Kenny Billiau Web Developer 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 kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] human genbanks
by Sofie Van Landeghem 16 Oct '08

16 Oct '08

Ok, this is completely non-binari, but I'm getting a little tired of d/l and extracting wrong files I just want a list of all human genbank identifiers. It shouldn't be too big so I don't want to d/l the whole of Genbank, just the identifiers... please? Sofie

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[Binari] Dany called...
by Sebastian Proost 16 Oct '08

16 Oct '08

... to inform us we have a new entry in our list. https://bioinformatics.psb.ugent.be/knowledge/wiki-bioinformatics/Hall_of_s… Sorry Sara :) --Seb PS. Sara it's up to you to add the details, I for one am very curious how this is even possible :p -- ================================================================== Sebastian Proost PhD Student Tel:+32 (0)9 331 36 92 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM sepro(a)psb.ugent.be http://www.psb.ugent.be ================================================================== "If I knew what I was doing, it wouldn't be called research." --Albert Einstein

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[Binari] Re: mounting SMB (fwd)
by Kenny Billiau 16 Oct '08

16 Oct '08

Wel ja .. op deze manier is alles natuurlijk onder je eigen naam gemount, maar staan de permissies op je files nog steeds niet goed. Stukje bij beetje komen we er. -- ---------- Forwarded message ---------- Date: Thu, 16 Oct 2008 13:03:41 +0200 From: HelpDesk <help(a)psb.ugent.be> To: Kenny Billiau <kebil(a)psb.ugent.be> Subject: Re: mounting SMB ik mount m'n shares zo (fstab entry): //psbnas04/psb /mnt/public cifs user=frlae,password=******,uid=frlae,gid=ict,auto,rw,nouser 0 0 en die komen als frlae:ict terecht in /mnt/public denk dat het uid en het gid deeltje in die mount lijn daarvoor zorgen Kenny Billiau wrote: > Hoi, > > dit is wat ik doe: > > [kebil@psbpc057 ~]$ sudo mount -t cifs //psbnas01.fvms.ugent.be/biocomp > /mnt/biocomp -o user=kebil,domain=FVMS > Password: # for sudo > Password: # for mounting the share > [kebil@psbpc057 ~]$ ll /mnt/biocomp/ > total 32 > drwxrwxrwx 1 root root 4096 2008-08-13 10:01 cbd > drwxrwxrwx 1 root root 4096 2008-09-02 14:34 doc > drwxrwxrwx 1 root root 4096 2008-09-05 10:03 mounts > drwxrwxrwx 1 root root 8192 2008-10-08 14:26 projects > drwxrwxrwx 1 root root 4096 2008-10-16 00:00 ~snapshot > drwxrwxrwx 1 root root 8192 2008-10-08 12:01 users > [kebil@psbpc057 ~]$ id > uid=1153(kebil) gid=345(biocomp) groups=345(biocomp) > > en op midas > [kebil@midas ~]$ id > uid=1153(kebil) gid=345(biocomp) groups=345(biocomp),410(dev),442(psbdev) > > User id's zijn dezelfde, maar de mount is nog steeds als root gemount. > > Ik probeerde ook een entry toe te voegen in fstab zodanig dat ik geen sudo > of dergelijke zou moeten doen: > //psbnas01.fvms.ugent.be/biocomp /mnt/biocomp cifs > noauto,rw,users,suid,username=kebil,password=xxxxxx,domain=FVMS 0 0 > > Maar ik blijf errors krijgen > [kebil@psbpc057 ~]$ mount /mnt/biocomp/ > mount error: permission denied or not superuser and mount.cifs not installed > SUID > > mount.cifs heeft weldegelijk +s en /mnt/biocomp is 775. > Met sudo gaat het dan wel weer errorloos, maar de gemounte share is nog > steeds onder root gemount. > > -Kenny >

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[Binari] java classpath - pain in the ass.
by Sofie Van Landeghem 16 Oct '08

16 Oct '08

I'm always having problems with the java class path, I think I just don't really understand how it works (well, I do in theory, but that doesn't seem to help). Suppose you have an external library L, used by both project X and project Y. Project Y also uses the built jar of project X. What would be best practice for the location of library L, without me having to copy it? I think the problem is that in Netbeans, by creating the dependency between Y and X, you don't have to create an extra dependency between L and Y (it propagates). However, when running on command line, you then have a problem, and Y can't find L. sigh. Any tips? Sofie -- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be

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[Binari] french fries aftermath
by Sebastian Proost 16 Oct '08

16 Oct '08

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[Binari] Red Queen Race
by Kenny Billiau 14 Oct '08

14 Oct '08

I knew it was from Alice in Wonderland :) "Well, in our country," said Alice, still panting a little, "you'd generally get to somewhere else - if you run very fast for a long time, as we've been doing." "A slow sort of country!" said the Queen. "Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!" http://en.wikipedia.org/wiki/Red_Queen's_race -- ================================================================== Kenny Billiau Web Developer 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 kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] No load on midas ..
by Kenny Billiau 14 Oct '08

14 Oct '08

.. is this because Seppe is gone? [kebil@midas ~]$ uptime 11:41:08 up 6 days, 22:48, 48 users, load average: 0.07, 0.04, 0.01 -- ================================================================== Kenny Billiau Web Developer 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 kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] Perly perly
by Michiel Van Bel 14 Oct '08

14 Oct '08

ok people, i've got some really weird problem with perl DBI, and I cannot find out what the hell I'm doing wrong. The code is below. The executed query is a simple count, which should always return a value. You can also see the "#TESTING"-part, which returns the count immediately for testing purposes. If the "TESTING"-part is not commented out: - %test_sd returns the actual value that is stored in the database (0 or higher). Checked manually. Not a problem. If the "TESTING"-part is commented out: a) $test_count is not zero: not a problem, the program just skips the content of the if-clause b) $test_count is zero: program crashes (just says: 'error: n'). That's it :s So, anybody can see what's wrong here? Michiel my $query_count = "SELECT count(`msa`.`aln`) as count FROM `msa` WHERE `msa`.`gf_id` ='".$gf_id."' ;"; my $rt_count = $dbh->prepare($query_count); my $dbi_ret_count = $rt_count->execute(); if(!$dbi_ret_count){ my %retval = ("error"=>"No valid database connection"); return \%retval; } my @res_count = $rt_count->fetchrow_array; my $test_count = @res_count[0]; my %test_sd = ("count result"=>$test_count); #TESTING return \%test_sd; #TESTING if($test_count==0){ my %retval = ("error"=>"no gf data"); return \%retval; } -- ================================================================== Michiel Van Bel PhD student 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 mibel(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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[Binari] Traveling through hyperspace ain't like dusting crops, boy!
by Thomas Van Parys 14 Oct '08

14 Oct '08

I have the sad duty to inform you all of the fact that the Millennium Falcon has been taken down by the TIE fighters. Seems like he didn't succeed in making the jump into hyperspace. The Jedi must have felt that one. T. PS. First Post! -- ================================================================== 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.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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