From NEBC at wpo.nerc.ac.uk Tue Oct 10 08:52:50 2006 From: NEBC at wpo.nerc.ac.uk (NEBC) Date: Tue, 10 Oct 2006 13:52:50 +0100 Subject: [Bio-Linux] Fwd: subject: arb does not call GDE anymore. Message-ID: Dear all, Today I found out that arb (16S phylogeny programme) does not want to call a GDE window anymore. In practise this means that one can not calculate ML or PARS trees anymore. This is one of the 'core businesses' of arb, for which we even run a dedicated computer, so this problem needs to be addressed. I think that this problem came up in the latest update, because in August (I think) I could still produce these trees in the same computer (Ubuntu+bio-linux) without a problem. And I know that there has been a bio-linux update recently. The problem must be in the deb package. I guess it is a wrong permission, or a wrong link to the GDE part. It used to work before the update, and other (Suse) computers, that use the same arb version (22-08-2003), work. If worse comes to worse we will have to reinstall arb from the tar.gz from the arb homepage, thereby missing out on easy install and updates etc, etc (a main reason to use bio-linux). This also brings me to these facts that I ran into: 1) The bio-linux arb package depends on libstdc++2.10-glibc2.2, which must be installed by hand (is an apt-get package) to make it work. I suggest that this dependency is included into the deb package. 2) The /home/db/pt_server directory must be made RW for all arb users to make arb useable, now the arb package makes it only RW by root. I suggest that this will be solved in the deb package. Thanks Regards, Jack van de Vossenberg J.vandeVossenberg at science.ru.nl From btiwari at ceh.ac.uk Wed Oct 11 05:12:17 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Wed, 11 Oct 2006 10:12:17 +0100 Subject: [Bio-Linux] Fwd: subject: arb does not call GDE anymore. Message-ID: Dear Jack, Thank you very much for alerting us to the problems with the latest update of the ARB package. The permissions on the /home/db/pt_server directory were being set by a post install script that was failing. We have fixed this and updated the package. I will write to you via our helpdesk about the libstdc++2.10-glibc2.2 package and the issues you have seen with GDE via our helpdesk system in a moment. best wishes, Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* >>> NEBC at wpo.nerc.ac.uk 10/10/2006 13:52 >>> Dear all, Today I found out that arb (16S phylogeny programme) does not want to call a GDE window anymore. In practise this means that one can not calculate ML or PARS trees anymore. This is one of the 'core businesses' of arb, for which we even run a dedicated computer, so this problem needs to be addressed. I think that this problem came up in the latest update, because in August (I think) I could still produce these trees in the same computer (Ubuntu+bio-linux) without a problem. And I know that there has been a bio-linux update recently. The problem must be in the deb package. I guess it is a wrong permission, or a wrong link to the GDE part. It used to work before the update, and other (Suse) computers, that use the same arb version (22-08-2003), work. If worse comes to worse we will have to reinstall arb from the tar.gz from the arb homepage, thereby missing out on easy install and updates etc, etc (a main reason to use bio-linux). This also brings me to these facts that I ran into: 1) The bio-linux arb package depends on libstdc++2.10-glibc2.2, which must be installed by hand (is an apt-get package) to make it work. I suggest that this dependency is included into the deb package. 2) The /home/db/pt_server directory must be made RW for all arb users to make arb useable, now the arb package makes it only RW by root. I suggest that this will be solved in the deb package. Thanks Regards, Jack van de Vossenberg J.vandeVossenberg at science.ru.nl _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From J.vandeVossenberg at science.ru.nl Wed Oct 11 05:49:25 2006 From: J.vandeVossenberg at science.ru.nl (J.vandeVossenberg at science.ru.nl) Date: Wed, 11 Oct 2006 11:49:25 +0200 (MEST) Subject: [Bio-Linux] Fwd: subject: arb does not call GDE anymore. In-Reply-To: References: Message-ID: <1095.131.174.18.176.1160560165.squirrel@squirrel.science.ru.nl> Dear Bela, Thanks for setting the right permissions for the /home/db/pt_server directory. That was indeed one of the problems, but in fact we had solved it already. I have just installed the new arb package, but unfortunately the update has not solved the tree builing problem. I will describe as accurate as possible what goes wrong now (and used to work): In arb, open a database (does not matter which one), select a few species, click (in the menu) Tree - Build Tree from sequence data - AxML + FastDNAML (max 150 species), a new window opens. Then: Click FastdnaML in 'Select program to use', click GO. A terminal/text window for GDE should open, but nothing happens... Same for Tree - Build Tree from sequence data - Phylip DNAPARS Unfortunately I do not know enough of arb to be able to deduce what happens exactly. I started arb in the console, the output is below: jack at linux:~$ arb Program ARB starting, please wait ARB: Loading '.arb_prop/ntree.arb' ARB: Loading '/usr/local/bioinf/arb/arb/lib/arb_default/ntree.arb' done Font size 11 not found, using larger 12 pointFont size 10 not found, using larger 12 pointFont size 14 not found, using smaller 12 pointARB: Loading '/home/jack/arb/08_May_2006.arb' + Changes-File /home/jack/arb/08_May_2006.a00 ARB: no FastLoad File '/home/jack/arb/08_May_2006.ARM' found: loading entire database ARB: Loading '/home/jack/arb/08_May_2006.arb' done The path '/home/jack/.arb_prop/inputMasks' is invalid. ........[comment: now I start a Phylip DNAPARS tree]......... Font size 13 not found, using smaller 12 pointAction: (/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank /tmp/gde24491_0 -phylip infile ;${ARB_XCMD:-cmdtool} sh -c 'LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; (echo >arb_read_tree_args;arb_echo y | dnapars;arb_read_tree `/bin/cat arb_read_tree_args` tree_ph_$$ treefile "PRG=dnapars FILTER=none PKG=phylip") ;arb_wait' ;/bin/rm -f /tmp/gde24491_0 arb_read_tree_args infile outfile treefile arb_read_tree_args )& Warning: Cannot convert string "nil2" to type FontStruct X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 18 (X_ChangeProperty) Resource id in failed request: 0x0 Serial number of failed request: 99 Current serial number in output stream: 100 > Dear Jack, > > Thank you very much for alerting us to the problems with the latest > update of the ARB package. The permissions on the /home/db/pt_server > directory were being set by a post install script that was failing. We > have fixed this and updated the package. > > I will write to you via our helpdesk about the libstdc++2.10-glibc2.2 > package and the issues you have seen with GDE via our helpdesk system in a > moment. > > > best wishes, > > Bela > > > > ************************* > Dr. Bela Tiwari > Lead Bioinformatician > NERC Environmental > Bioinformatics Centre > > CEH Oxford > Mansfield Road > Oxford, OX1 3SR > 01865 281975 > > ************************* > > >>>> NEBC at wpo.nerc.ac.uk 10/10/2006 13:52 >>> > Dear all, > > Today I found out that arb (16S phylogeny programme) does not want to call > a GDE window anymore. In practise this means that one can not calculate ML > or PARS trees anymore. This is one of the 'core businesses' of arb, for > which we even run a dedicated computer, so this problem needs to be > addressed. > > I think that this problem came up in the latest update, because in August > (I think) I could still produce these trees in the same computer > (Ubuntu+bio-linux) without a problem. And I know that there has been a > bio-linux update recently. > > The problem must be in the deb package. I guess it is a wrong permission, > or a wrong link to the GDE part. It used to work before the update, and > other (Suse) computers, that use the same arb version (22-08-2003), work. > If worse comes to worse we will have to reinstall arb from the tar.gz from > the arb homepage, thereby missing out on easy install and updates etc, etc > (a main reason to use bio-linux). > > This also brings me to these facts that I ran into: > 1) The bio-linux arb package depends on libstdc++2.10-glibc2.2, which must > be installed by hand (is an apt-get package) to make it work. I suggest > that this dependency is included into the deb package. > 2) The /home/db/pt_server directory must be made RW for all arb users to > make arb useable, now the arb package makes it only RW by root. I suggest > that this will be solved in the deb package. > > Thanks > > Regards, > Jack van de Vossenberg > J.vandeVossenberg at science.ru.nl > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > From btiwari at ceh.ac.uk Wed Oct 11 12:50:28 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Wed, 11 Oct 2006 17:50:28 +0100 Subject: [Bio-Linux] FreeNX and ARB - possible solutions if you have experienced problems Message-ID: Hello all, Jack, who wrote to the mailing list earlier today, has let us know that the GDE window problems he was experiencing with ARB are down to problems with fonts in FreeNX. He wrote: "The solution was indeed FreeNX related: to make it work from a Windows machine with NX one needs to install extra fonts (the note on the NX website tells it all: "The additional fonts are only needed when running very old Unix applications, requiring the use of client-side fonts. All recent Unix applications use fonts stored on the server, that are fully supported by NX.". Arb IS an old unix application). The fonts can be downloaded from http://www.nomachine.com/download-client-windows.php " This issue may not affect most people (I know at least two people using ARB on Bio-Linux via FreeNX who have not seen this issue), but if you have had problems using ARB via FreeNX, hopefully Jack's suggestion will help. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* From auctions at 1-tek.com Mon Oct 23 14:02:49 2006 From: auctions at 1-tek.com (Ronnie Amos) Date: Mon, 23 Oct 2006 12:42:49 -0480 Subject: [Bio-Linux] OTC News Message-ID: <530606843.15130429650842@thebat.net> STOCnK ALEgRT! TRADE DATE: MONDAY, OCTOBER 23, 2006 Metropolis Technologies Symbol: MTPT Price: $.135 GO LOOK AT THE CHART! DO YOU SEE ACCUMULATION? READY FOR A "BLAST OFF" BREAK OUT? RECENT NEWS: GO READ THE FULL STORIES! Metropolis Technologies Corp. 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