From jaa53 at cornell.edu Thu May 4 11:11:14 2006 From: jaa53 at cornell.edu (Jose A. Andres) Date: Thu, 4 May 2006 11:11:14 -0400 (EDT) Subject: [Bio-Linux] USB flash-drive on Bio-linux Message-ID: <49220.132.236.111.198.1146755474.squirrel@webmail.cornell.edu> Hi I am a new (i.e. naive) user of Bio-linux and I've been trying to read some files from my Flashdrive but couldn't get into it On the Konsole (as manager) I typed... mount /media/usbkey mount: can't find /media/usbkey in etc/fstab or etc/mac.. I sudo nano /etec/fstad and added the following line... /dev/sda/ /media/usbkey vfat user,rw 0 0 Then, I tried the mount commad again... However, got the following error mount: /dev/sda/ already mounted or /media/usbkey busy. Please check that the disk is entered correctly. I've also tried to get into the flashdrive with Konqueror --->Devices---->sda, but obviously got the same error. Any suggestions? Thanks a lot in advance! /Jose From a.j.pemberton at bham.ac.uk Thu May 4 11:50:49 2006 From: a.j.pemberton at bham.ac.uk (Tony Pemberton) Date: Thu, 4 May 2006 16:50:49 +0100 Subject: [Bio-Linux] USB flash-drive on Bio-linux In-Reply-To: <49220.132.236.111.198.1146755474.squirrel@webmail.cornell.edu> Message-ID: Jose, Looking at the messages in your text, have you checked to see if the drive *is* already mounted as suggested by the error message when you tried to mount /dev/sda? To check a mount just df - lists all mounted filesystems and their usage -----Original Message----- From: bio-linux-bounces at envgen.nox.ac.uk [mailto:bio-linux-bounces at envgen.nox.ac.uk]On Behalf Of Jose A. Andres Sent: 04 May 2006 16:11 To: bio-linux at envgen.nerc-oxford.ac.uk Subject: [Bio-Linux] USB flash-drive on Bio-linux Hi I am a new (i.e. naive) user of Bio-linux and I've been trying to read some files from my Flashdrive but couldn't get into it On the Konsole (as manager) I typed... mount /media/usbkey mount: can't find /media/usbkey in etc/fstab or etc/mac.. I sudo nano /etec/fstad and added the following line... /dev/sda/ /media/usbkey vfat user,rw 0 0 Then, I tried the mount commad again... However, got the following error mount: /dev/sda/ already mounted or /media/usbkey busy. Please check that the disk is entered correctly. I've also tried to get into the flashdrive with Konqueror --->Devices---->sda, but obviously got the same error. Any suggestions? Thanks a lot in advance! /Jose _______________________________________________ Bio-linux mailing list Bio-linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From jaa53 at cornell.edu Thu May 4 11:56:56 2006 From: jaa53 at cornell.edu (Jose A. Andres) Date: Thu, 4 May 2006 11:56:56 -0400 (EDT) Subject: [Bio-Linux] USB flash-drive on Bio-linux In-Reply-To: References: <49220.132.236.111.198.1146755474.squirrel@webmail.cornell.edu> Message-ID: <49287.132.236.111.198.1146758216.squirrel@webmail.cornell.edu> Tony, Thanks for your quick answer to my naive question if I type df I only see /dev/sda1 mounted on / tmpfs mounted on /dev/shm So seems that I am not able to mount the flashdrive (which is formatted in DOS (can this be the source of error?) Thanks again, /Jose > Jose, > > Looking at the messages in your text, have you checked to > see if the drive *is* already mounted as suggested by the > error message when you tried to mount /dev/sda? To check > a mount just > > df > > - lists all mounted filesystems and their usage > > > -----Original Message----- > From: bio-linux-bounces at envgen.nox.ac.uk > [mailto:bio-linux-bounces at envgen.nox.ac.uk]On Behalf Of Jose A. Andres > Sent: 04 May 2006 16:11 > To: bio-linux at envgen.nerc-oxford.ac.uk > Subject: [Bio-Linux] USB flash-drive on Bio-linux > > > Hi > > I am a new (i.e. naive) user of Bio-linux and I've been trying to read > some files from my Flashdrive but couldn't get into it > > On the Konsole (as manager) I typed... > > mount /media/usbkey > > mount: can't find /media/usbkey in etc/fstab or etc/mac.. > > I sudo nano /etec/fstad and added the following line... > > /dev/sda/ /media/usbkey vfat user,rw 0 0 > > Then, I tried the mount commad again... > > However, got the following error > > mount: /dev/sda/ already mounted or /media/usbkey busy. Please check that > the disk is entered correctly. > > I've also tried to get into the flashdrive with Konqueror > --->Devices---->sda, but obviously got the same error. > > Any suggestions? > > Thanks a lot in advance! > > /Jose > > > > _______________________________________________ > 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 tbooth at ceh.ac.uk Thu May 4 12:13:47 2006 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 04 May 2006 17:13:47 +0100 Subject: [Bio-Linux] USB flash-drive on Bio-linux In-Reply-To: <49287.132.236.111.198.1146758216.squirrel@webmail.cornell.edu> References: <49220.132.236.111.198.1146755474.squirrel@webmail.cornell.edu> <49287.132.236.111.198.1146758216.squirrel@webmail.cornell.edu> Message-ID: <1146759227.16490.181.camel@ivpcp044.nox.ac.uk> Hi Jose, Your machine has SCSI drives, so your main hard drive is /dev/sda, your second drive is /dev/sdb and the first thing you hotplug will end up as /dev/sdc. Therefore the correct line for /etc/fstab is: /dev/sdc1 /media/usbkey vfat user,noauto 0 0 Does that work for you? Also some USB keys just don't want to play ball and come up as /dev/sdc (no number 1 on the end) or else need repartitioning from scratch to work on Linux. Cheers, TIM ps. There is a system called HAL which will one day soon make all this stuff go away, but at the moment you only get it with Ubuntu Linux. On Thu, 2006-05-04 at 11:56 -0400, Jose A. Andres wrote: > Tony, > Thanks for your quick answer to my naive question > > if I type df I only see > /dev/sda1 mounted on / > tmpfs mounted on /dev/shm > > So seems that I am not able to mount the flashdrive (which is formatted > in DOS (can this be the source of error?) > From a.j.pemberton at bham.ac.uk Fri May 5 04:51:27 2006 From: a.j.pemberton at bham.ac.uk (Tony Pemberton) Date: Fri, 5 May 2006 09:51:27 +0100 Subject: [Bio-Linux] USB flash-drive on Bio-linux In-Reply-To: <49287.132.236.111.198.1146758216.squirrel@webmail.cornell.edu> Message-ID: Jose, I think I see the problem. I just checked my system. Is your system using sata or scsi disks? If so and this looks to be the case /dev/sda1 is the root partition of your hard drive as detailed below /dev/sda1 mounted on / On my system I have an entry in /etc/fstab for the usb key: /dev/sdc1 /media/usbkey vfat rw,user,noauto 0 0 I notice when I plug my key into the usb port that the lamp above the key slot flashes. This does not auto mount the key, but I have an icon on the desktop "USB key" - when I click on it, that mounts the key and gives me a graphical directory view of the top directory on the key. You need to discover which device (/dev/sdc1 ?) is configured for your usb key. I have tried the "Info Center", but the USB devices section does not help in this regard. Perhaps someone else on the list can shed light on this. Once you have discovered the device you could try adding the entry to your fstab as above - perhaps try /dev/sdc1 For sure it will not be /dev/sda1 Regards, Tony Pemberton -----Original Message----- From: bio-linux-bounces at envgen.nox.ac.uk [mailto:bio-linux-bounces at envgen.nox.ac.uk]On Behalf Of Jose A. Andres Sent: 04 May 2006 16:57 To: Bio-Linux help and discussion Subject: RE: [Bio-Linux] USB flash-drive on Bio-linux Tony, Thanks for your quick answer to my naive question if I type df I only see /dev/sda1 mounted on / tmpfs mounted on /dev/shm So seems that I am not able to mount the flashdrive (which is formatted in DOS (can this be the source of error?) Thanks again, /Jose > Jose, > > Looking at the messages in your text, have you checked to > see if the drive *is* already mounted as suggested by the > error message when you tried to mount /dev/sda? To check > a mount just > > df > > - lists all mounted filesystems and their usage > > > -----Original Message----- > From: bio-linux-bounces at envgen.nox.ac.uk > [mailto:bio-linux-bounces at envgen.nox.ac.uk]On Behalf Of Jose A. Andres > Sent: 04 May 2006 16:11 > To: bio-linux at envgen.nerc-oxford.ac.uk > Subject: [Bio-Linux] USB flash-drive on Bio-linux > > > Hi > > I am a new (i.e. naive) user of Bio-linux and I've been trying to read > some files from my Flashdrive but couldn't get into it > > On the Konsole (as manager) I typed... > > mount /media/usbkey > > mount: can't find /media/usbkey in etc/fstab or etc/mac.. > > I sudo nano /etec/fstad and added the following line... > > /dev/sda/ /media/usbkey vfat user,rw 0 0 > > Then, I tried the mount commad again... > > However, got the following error > > mount: /dev/sda/ already mounted or /media/usbkey busy. Please check that > the disk is entered correctly. > > I've also tried to get into the flashdrive with Konqueror > --->Devices---->sda, but obviously got the same error. > > Any suggestions? > > Thanks a lot in advance! > > /Jose > > > > _______________________________________________ > 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 > _______________________________________________ Bio-linux mailing list Bio-linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From H.J.NEWBURY at bham.ac.uk Fri May 5 04:51:21 2006 From: H.J.NEWBURY at bham.ac.uk (John Newbury) Date: Fri, 5 May 2006 09:51:21 +0100 Subject: [Bio-Linux] USB flash-drive on Bio-linux Message-ID: <8BAA42D1298CA341BA5E80F938E76F9B031D66@BIOEX2.adf.bham.ac.uk> Tony I seem to be getting messages about Bio-Linux that are not very appropriate to me. Is there a 'reply to all' problem? John > -----Original Message----- > From: bio-linux-bounces at envgen.nox.ac.uk > [mailto:bio-linux-bounces at envgen.nox.ac.uk] On Behalf Of Tony > Pemberton > Sent: 05 May 2006 09:51 > To: Bio-Linux help and discussion > Subject: RE: [Bio-Linux] USB flash-drive on Bio-linux > > Jose, > > I think I see the problem. I just checked my system. Is your > system using sata or scsi disks? If so and this looks to be the case > > /dev/sda1 is the root partition of your hard drive as detailed below > > /dev/sda1 mounted on / > > On my system I have an entry in /etc/fstab for the usb key: > > /dev/sdc1 /media/usbkey vfat rw,user,noauto 0 0 > > I notice when I plug my key into the usb port that the lamp > above the key slot flashes. This does not auto mount the key, > but I have an icon on the desktop "USB key" - when I click on > it, that mounts the key and gives me a graphical directory > view of the top directory on the key. > > You need to discover which device (/dev/sdc1 ?) is > configured for your usb key. I have tried the "Info Center", > but the USB devices section does not help in this regard. > Perhaps someone else on the list can shed light on this. Once > you have discovered the device you could try adding the entry > to your fstab as above - perhaps try /dev/sdc1 > > For sure it will not be /dev/sda1 > > Regards, > > Tony Pemberton > > -----Original Message----- > From: bio-linux-bounces at envgen.nox.ac.uk > [mailto:bio-linux-bounces at envgen.nox.ac.uk]On Behalf Of Jose A. Andres > Sent: 04 May 2006 16:57 > To: Bio-Linux help and discussion > Subject: RE: [Bio-Linux] USB flash-drive on Bio-linux > > > Tony, > Thanks for your quick answer to my naive question > > if I type df I only see > /dev/sda1 mounted on / > tmpfs mounted on /dev/shm > > So seems that I am not able to mount the flashdrive (which > is formatted in DOS (can this be the source of error?) > > Thanks again, > > /Jose > > > Jose, > > > > Looking at the messages in your text, have you checked to > see if the > > drive *is* already mounted as suggested by the error > message when you > > tried to mount /dev/sda? To check a mount just > > > > df > > > > - lists all mounted filesystems and their usage > > > > > > -----Original Message----- > > From: bio-linux-bounces at envgen.nox.ac.uk > > [mailto:bio-linux-bounces at envgen.nox.ac.uk]On Behalf Of > Jose A. Andres > > Sent: 04 May 2006 16:11 > > To: bio-linux at envgen.nerc-oxford.ac.uk > > Subject: [Bio-Linux] USB flash-drive on Bio-linux > > > > > > Hi > > > > I am a new (i.e. naive) user of Bio-linux and I've been > trying to read > > some files from my Flashdrive but couldn't get into it > > > > On the Konsole (as manager) I typed... > > > > mount /media/usbkey > > > > mount: can't find /media/usbkey in etc/fstab or etc/mac.. > > > > I sudo nano /etec/fstad and added the following line... > > > > /dev/sda/ /media/usbkey vfat user,rw 0 0 > > > > Then, I tried the mount commad again... > > > > However, got the following error > > > > mount: /dev/sda/ already mounted or /media/usbkey busy. > Please check > > that the disk is entered correctly. > > > > I've also tried to get into the flashdrive with Konqueror > > --->Devices---->sda, but obviously got the same error. > > > > Any suggestions? > > > > Thanks a lot in advance! > > > > /Jose > > > > > > > > _______________________________________________ > > 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 > > > > > _______________________________________________ > 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 ajt at rri.sari.ac.uk Fri May 5 06:48:39 2006 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Fri, 05 May 2006 11:48:39 +0100 Subject: [Bio-Linux] USB flash-drive on Bio-linux In-Reply-To: <1146759227.16490.181.camel@ivpcp044.nox.ac.uk> References: <49220.132.236.111.198.1146755474.squirrel@webmail.cornell.edu> <49287.132.236.111.198.1146758216.squirrel@webmail.cornell.edu> <1146759227.16490.181.camel@ivpcp044.nox.ac.uk> Message-ID: <445B2D87.4020506@rri.sari.ac.uk> Tim Booth wrote: > [...] > ps. There is a system called HAL which will one day soon make all this > stuff go away, but at the moment you only get it with Ubuntu Linux. Hello, Tim. Actually, it's in Sarge and Etch too. I've upgraded my Bio-Linux desktop (kitcat.rri.sari.ac.uk) to use Debian 'testing' as the base distribution instead of 'stable). I tried installing the Bio-Linux deb packages under 'Dapper Drake' 6.06 beta 2, but it crashed and burned because "xlibs" is not installable - bio-linux-base-directories depends on xlibs >= 4.3.0. There is quite a lot of discussion about xlibs vs. xlibs-dev on the Ubuntu forums. In fact, both xlibs and xlibs-dev are supposed to be 'transitional' packages for migration from Debian 3.0 to 3.1. Has anyone else got Bio-Linux working under Ubuntu? FYI, Here's 'hal' running on kitcat: [root at kitcat: ~]# apt-show-versions -a hal hal 0.5.7-1 install ok installed hal 0.4.7-3sarge1 stable hal 0.5.7-1 testing No unstable version hal/testing uptodate 0.5.7-1 [root at kitcat: ~]# uname -a Linux kitcat 2.6.8-2-686-smp #1 SMP Tue Aug 16 12:08:30 UTC 2005 i686 GNU/Linux [root at kitcat: ~]# lshal | more Dumping 57 device(s) from the Global Device List: ------------------------------------------------- udi = '/org/freedesktop/Hal/devices/computer' info.callouts.add = {'hal-system-storage-cleanup-mountpoints'} (stri ng list) org.freedesktop.Hal.Device.SystemPowerManagement.method_execpaths = {'hal-system-power-suspend', 'hal-system-power-hibernate', 'hal-system -power-shutdown', 'hal-system-power-reboot', 'hal-system-power-set-pow er-save'} (string list) org.freedesktop.Hal.Device.SystemPowerManagement.method_signatures = {'i', '', '', '', 'b'} (string list) org.freedesktop.Hal.Device.SystemPowerManagement.method_names = {'Su spend', 'Hibernate', 'Shutdown', 'Reboot', 'SetPowerSave'} (string lis [...] Best wishes, Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 From jaa53 at cornell.edu Fri May 5 11:03:04 2006 From: jaa53 at cornell.edu (Jose A. Andres) Date: Fri, 5 May 2006 11:03:04 -0400 (EDT) Subject: [Bio-Linux] phred/phrap/consed installation on Bio-linux In-Reply-To: <445B2D87.4020506@rri.sari.ac.uk> References: <49220.132.236.111.198.1146755474.squirrel@webmail.cornell.edu> <49287.132.236.111.198.1146758216.squirrel@webmail.cornell.edu> <1146759227.16490.181.camel@ivpcp044.nox.ac.uk> <445B2D87.4020506@rri.sari.ac.uk> Message-ID: <49224.132.236.111.198.1146841384.squirrel@webmail.cornell.edu> Hi all, (Thanks in advance for all your help) I'd like to install phred/phrap/consed into bio-linux4 but since I am not funded by the NEBC, I have to do it from the original files I got from Phil's Green lab. I should be able to do it, but I am a bit confuse with the symlinks (and another couple of things) and I'd like to get some extra advice from the community (if possible). I realise how busy we all are and I'd really appreciate any suggestions and comments.THANKS!! Cheers, /Jose Here is what I am planning: # reading from a flash-drive... mount /media/usbkey # storing source code on /usr/local/src sudo mkdir -p /usr/local/src/phred #moving stuff around... sudo mv /media/usbkey/ /usr/local/src/phred #uncompressing the file ... uncompress phred-dist-020425.c-acd.tar.Z tar xvf phred-dist-020425.c-acd.tar # I've read somewhere (do not remember exactly where) that to compile phred with the correct optimization I need to edit one line of the make file (Soooo.... nano Makefile ("remove # from the LXFLAGS = -DX86_GCC_LINUX line and save). #then... ./make #now I need to copy the executable of this version (to keep the bio-linux standards) into the right place. I am assuming /usr/software/phred/phred_020425). Am I right? or shall I put it into /usr/local/bioinf?? Sooo I create the new dir sudo mkdir -p /usr/software/phred/phred_020425 (or # and copy the executable there sudo cp phred /usr/software/phred/phred_020425 # As I said I am a bit confuse cause both /usr/software and /usr/local/bioinf seem to have the same stuff in... !!!!!! Do I have to also copy the make the dir /usr/local/bioinf/phred/phred_02004425 and cp the Phred executable there? !!!!!! do I have to make a symlink? if so, shall I make it in the same place? That is sudo ln -s /usr/software/phred/phred_020425 /usr/software/phred/phred !!!!!!! or in the /usr/local/bioinf/ or both? sudo ln -s /usr/software/phred/phred_020425 /usr/local/bioinf/phred # Any suggestions? # I shall move the phred parameter file to the right location.Something like this? sudo cp phredpar.dat /usr/local/bioinf/phred/phred/prhredpar.dat #set the enviroment.. nano -w /usr/local/bioinf/config_files/bioenvrc (Add and save..) export PHRED_PARAMETER_FILE=/usr/local/bioinf/phred/phred/phredpar.dat; export PATH=$PATH:/usr/local/bioinf/blast/blast: /usr/local/bioinf/netblast/netblast: /usr/local/bioinf/phred/phred: /usr/local/bioinf/phrap/phrap:/usr/sbin #installing WOULD THIS WORK??? IF so I shall also be able to install phrap and consed in a very similar way... THANKS EVERYONE!!!!!!!!!!!!!!!!!! From keith.jolley at medawar.ox.ac.uk Fri May 5 11:22:58 2006 From: keith.jolley at medawar.ox.ac.uk (Keith Jolley) Date: Fri, 5 May 2006 16:22:58 +0100 Subject: [Bio-Linux] phred/phrap/consed installation on Bio-linux In-Reply-To: <49224.132.236.111.198.1146841384.squirrel@webmail.cornell.edu> Message-ID: <006801c67057$ca4dcd80$0401a8c0@mistral> I've instructions for installing phred and phrap on Bio-Linux on http://pubmlst.org/software/bio-linux/stars/config/. You may find that useful. Cheers Keith > -----Original Message----- > From: bio-linux-bounces at envgen.nox.ac.uk [mailto:bio-linux- > bounces at envgen.nox.ac.uk] On Behalf Of Jose A. Andres > Sent: 05 May 2006 16:03 > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] phred/phrap/consed installation on Bio-linux > > Hi all, > > (Thanks in advance for all your help) > > I'd like to install phred/phrap/consed into bio-linux4 but since I am not > funded by the NEBC, I have to do it from the original files I got from > Phil's Green lab. I should be able to do it, but I am a bit confuse with > the symlinks (and another couple of things) and I'd like to get some > extra advice from the community (if possible). > > I realise how busy we all are and I'd really appreciate any suggestions > and comments.THANKS!! > > Cheers, > > /Jose > > Here is what I am planning: > > # reading from a flash-drive... > > mount /media/usbkey > > # storing source code on /usr/local/src > > sudo mkdir -p /usr/local/src/phred > > #moving stuff around... > > sudo mv /media/usbkey/ /usr/local/src/phred > > #uncompressing the file ... > > uncompress phred-dist-020425.c-acd.tar.Z > tar xvf phred-dist-020425.c-acd.tar > > # I've read somewhere (do not remember exactly where) that to compile > phred with the correct optimization I need to edit one line of the make > file > (Soooo.... > > nano Makefile ("remove # from the LXFLAGS = -DX86_GCC_LINUX line and > save). > > #then... > > ./make > > #now I need to copy the executable of this version (to keep the bio-linux > standards) into the right place. I am assuming > > /usr/software/phred/phred_020425). Am I right? or shall I put it into > /usr/local/bioinf?? Sooo I create the new dir > > > sudo mkdir -p /usr/software/phred/phred_020425 (or > > # and copy the executable there > > sudo cp phred /usr/software/phred/phred_020425 > > # As I said I am a bit confuse cause both /usr/software and > /usr/local/bioinf seem to have the same stuff in... > > !!!!!! Do I have to also copy the make the dir > /usr/local/bioinf/phred/phred_02004425 and cp the Phred executable there? > > !!!!!! do I have to make a symlink? if so, shall I make it in the same > place? That is > > sudo ln -s /usr/software/phred/phred_020425 /usr/software/phred/phred > > !!!!!!! or in the /usr/local/bioinf/ or both? > > sudo ln -s /usr/software/phred/phred_020425 /usr/local/bioinf/phred > > # Any suggestions? > > # I shall move the phred parameter file to the right location.Something > like this? > > sudo cp phredpar.dat /usr/local/bioinf/phred/phred/prhredpar.dat > > #set the enviroment.. > > nano -w /usr/local/bioinf/config_files/bioenvrc > > (Add and save..) > > export PHRED_PARAMETER_FILE=/usr/local/bioinf/phred/phred/phredpar.dat; > export PATH=$PATH:/usr/local/bioinf/blast/blast: > /usr/local/bioinf/netblast/netblast: /usr/local/bioinf/phred/phred: > /usr/local/bioinf/phrap/phrap:/usr/sbin > > #installing > > WOULD THIS WORK??? IF so I shall also be able to install phrap and consed > in a very similar way... > > THANKS EVERYONE!!!!!!!!!!!!!!!!!! > > > > > _______________________________________________ > 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 Fri May 5 11:27:39 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Fri, 05 May 2006 16:27:39 +0100 Subject: [Bio-Linux] phred/phrap/consed installation on Bio-linux Message-ID: Hi Jose, It sounds like you already have licenses for phred and phrap. If so, we can provide you with Bio-Linux packages for them, which will be much easier to install. Can you please write to the helpdesk address: helpdesk at envgen.nox.ac.uk to confirm that you have licenses and then we can help you from there. We haven't packaged consed for Bio-Linux yet, so at the moment there is not much we can say except that if you follow the instructions given by the authors, it is possible to get it running on Bio-Linux. I am planning on making a package for consed, but I probably won't have time for this until June at the earliest. I know that others in the community have managed to install Consed on Bio-Linux successfully, but their feedback was that it wasn't a fun task. If you write to the helpdesk about phred and phrap, please let us know (in general terms) what you are trying to do with these tools so that we can let you know of any other programs on Bio-Linux that might be of help to you. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* >>> jaa53 at cornell.edu 05/05/2006 16:03 >>> Hi all, (Thanks in advance for all your help) I'd like to install phred/phrap/consed into bio-linux4 but since I am not funded by the NEBC, I have to do it from the original files I got from Phil's Green lab. I should be able to do it, but I am a bit confuse with the symlinks (and another couple of things) and I'd like to get some extra advice from the community (if possible). I realise how busy we all are and I'd really appreciate any suggestions and comments.THANKS!! Cheers, /Jose Here is what I am planning: # reading from a flash-drive... mount /media/usbkey # storing source code on /usr/local/src sudo mkdir -p /usr/local/src/phred #moving stuff around... sudo mv /media/usbkey/ /usr/local/src/phred #uncompressing the file ... uncompress phred-dist-020425.c-acd.tar.Z tar xvf phred-dist-020425.c-acd.tar # I've read somewhere (do not remember exactly where) that to compile phred with the correct optimization I need to edit one line of the make file (Soooo.... nano Makefile ("remove # from the LXFLAGS = -DX86_GCC_LINUX line and save). #then... ./make #now I need to copy the executable of this version (to keep the bio-linux standards) into the right place. I am assuming /usr/software/phred/phred_020425). Am I right? or shall I put it into /usr/local/bioinf?? Sooo I create the new dir sudo mkdir -p /usr/software/phred/phred_020425 (or # and copy the executable there sudo cp phred /usr/software/phred/phred_020425 # As I said I am a bit confuse cause both /usr/software and /usr/local/bioinf seem to have the same stuff in... !!!!!! Do I have to also copy the make the dir /usr/local/bioinf/phred/phred_02004425 and cp the Phred executable there? !!!!!! do I have to make a symlink? if so, shall I make it in the same place? That is sudo ln -s /usr/software/phred/phred_020425 /usr/software/phred/phred !!!!!!! or in the /usr/local/bioinf/ or both? sudo ln -s /usr/software/phred/phred_020425 /usr/local/bioinf/phred # Any suggestions? # I shall move the phred parameter file to the right location.Something like this? sudo cp phredpar.dat /usr/local/bioinf/phred/phred/prhredpar.dat #set the enviroment.. nano -w /usr/local/bioinf/config_files/bioenvrc (Add and save..) export PHRED_PARAMETER_FILE=/usr/local/bioinf/phred/phred/phredpar.dat; export PATH=$PATH:/usr/local/bioinf/blast/blast: /usr/local/bioinf/netblast/netblast: /usr/local/bioinf/phred/phred: /usr/local/bioinf/phrap/phrap:/usr/sbin #installing WOULD THIS WORK??? IF so I shall also be able to install phrap and consed in a very similar way... THANKS EVERYONE!!!!!!!!!!!!!!!!!! _______________________________________________ Bio-linux mailing list Bio-linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From ajt at rri.sari.ac.uk Fri May 5 11:31:08 2006 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Fri, 05 May 2006 16:31:08 +0100 Subject: [Bio-Linux] phred/phrap/consed installation on Bio-linux In-Reply-To: <49224.132.236.111.198.1146841384.squirrel@webmail.cornell.edu> References: <49220.132.236.111.198.1146755474.squirrel@webmail.cornell.edu> <49287.132.236.111.198.1146758216.squirrel@webmail.cornell.edu> <1146759227.16490.181.camel@ivpcp044.nox.ac.uk> <445B2D87.4020506@rri.sari.ac.uk> <49224.132.236.111.198.1146841384.squirrel@webmail.cornell.edu> Message-ID: <445B6FBC.4000606@rri.sari.ac.uk> Jose A. Andres wrote: > Hi all, > > (Thanks in advance for all your help) > > I'd like to install phred/phrap/consed into bio-linux4 but since I am not > funded by the NEBC, I have to do it from the original files I got from > Phil's Green lab. I should be able to do it, but I am a bit confuse with > the symlinks (and another couple of things) and I'd like to get some > extra advice from the community (if possible). Hello, Jose. I'm using phred/phrap/consed with Bio-Linux4, but Consed is not supported (Bio-Linux uses GAP4). If you have already registered your use of phred/phrap/consed then you should email NEBC and ask for their deb packages to install phred/phrap in Bio-Linux. These packages cannot be distributed freely, so you have to register your use as you have done. I originally installed phred/phrap/consed from the same files that you downloaded, but I've now replaced the phred/phrap component with files from NEBC because I want to use GAP4 under Bio-Linux. However, I'm still using Consed at the moment because I find it a lot easier to use! I'm assembling a ~2Mb microbial genome - what are you using it for? Best wishes, Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 From keith.jolley at medawar.ox.ac.uk Fri May 5 11:32:51 2006 From: keith.jolley at medawar.ox.ac.uk (Keith Jolley) Date: Fri, 5 May 2006 16:32:51 +0100 Subject: [Bio-Linux] phred/phrap/consed installation on Bio-linux In-Reply-To: <49224.132.236.111.198.1146841384.squirrel@webmail.cornell.edu> Message-ID: <006901c67059$2b96ef30$0401a8c0@mistral> Your confusion stems from the fact that /usr/local/bioinf and /usr/software are equivalent. If you 'ls -l' from /usr you'll see that software is a symlink to local/bioinf, so you could use either. Keith > -----Original Message----- > From: bio-linux-bounces at envgen.nox.ac.uk [mailto:bio-linux- > bounces at envgen.nox.ac.uk] On Behalf Of Jose A. Andres > Sent: 05 May 2006 16:03 > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] phred/phrap/consed installation on Bio-linux > > Hi all, > > (Thanks in advance for all your help) > > I'd like to install phred/phrap/consed into bio-linux4 but since I am not > funded by the NEBC, I have to do it from the original files I got from > Phil's Green lab. I should be able to do it, but I am a bit confuse with > the symlinks (and another couple of things) and I'd like to get some > extra advice from the community (if possible). > > I realise how busy we all are and I'd really appreciate any suggestions > and comments.THANKS!! > > Cheers, > > /Jose > > Here is what I am planning: > > # reading from a flash-drive... > > mount /media/usbkey > > # storing source code on /usr/local/src > > sudo mkdir -p /usr/local/src/phred > > #moving stuff around... > > sudo mv /media/usbkey/ /usr/local/src/phred > > #uncompressing the file ... > > uncompress phred-dist-020425.c-acd.tar.Z > tar xvf phred-dist-020425.c-acd.tar > > # I've read somewhere (do not remember exactly where) that to compile > phred with the correct optimization I need to edit one line of the make > file > (Soooo.... > > nano Makefile ("remove # from the LXFLAGS = -DX86_GCC_LINUX line and > save). > > #then... > > ./make > > #now I need to copy the executable of this version (to keep the bio-linux > standards) into the right place. I am assuming > > /usr/software/phred/phred_020425). Am I right? or shall I put it into > /usr/local/bioinf?? Sooo I create the new dir > > > sudo mkdir -p /usr/software/phred/phred_020425 (or > > # and copy the executable there > > sudo cp phred /usr/software/phred/phred_020425 > > # As I said I am a bit confuse cause both /usr/software and > /usr/local/bioinf seem to have the same stuff in... > > !!!!!! Do I have to also copy the make the dir > /usr/local/bioinf/phred/phred_02004425 and cp the Phred executable there? > > !!!!!! do I have to make a symlink? if so, shall I make it in the same > place? That is > > sudo ln -s /usr/software/phred/phred_020425 /usr/software/phred/phred > > !!!!!!! or in the /usr/local/bioinf/ or both? > > sudo ln -s /usr/software/phred/phred_020425 /usr/local/bioinf/phred > > # Any suggestions? > > # I shall move the phred parameter file to the right location.Something > like this? > > sudo cp phredpar.dat /usr/local/bioinf/phred/phred/prhredpar.dat > > #set the enviroment.. > > nano -w /usr/local/bioinf/config_files/bioenvrc > > (Add and save..) > > export PHRED_PARAMETER_FILE=/usr/local/bioinf/phred/phred/phredpar.dat; > export PATH=$PATH:/usr/local/bioinf/blast/blast: > /usr/local/bioinf/netblast/netblast: /usr/local/bioinf/phred/phred: > /usr/local/bioinf/phrap/phrap:/usr/sbin > > #installing > > WOULD THIS WORK??? IF so I shall also be able to install phrap and consed > in a very similar way... > > THANKS EVERYONE!!!!!!!!!!!!!!!!!! > > > > > _______________________________________________ > Bio-linux mailing list > Bio-linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From ajt at rri.sari.ac.uk Mon May 8 19:23:47 2006 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Tue, 09 May 2006 00:23:47 +0100 Subject: [Bio-Linux] bio-linux-emboss breaks debsums Message-ID: <445FD303.4030601@rri.sari.ac.uk> I've noticed that "debsums" (used to verify the installation of Debian packages) is broken after installing bio-linux-emboss under Debian Sarge/Etch. The "debsums" package is not a standard part of Bio-Linux4, but it's a useful way of verifying system integrity. Unfortunately, a problem in the bio-linux-emboss package results in diagnostic errors being produced when subsequently installing *any* other packages! This is caused by trailing spaces in the filename: "/usr/local/bioinf/EMBOSS/EMBOSS-3.0.0/test/data/structure/scop.all " ^ > ajt at wildcat:% debsums -ac bio-linux-emboss_3.0.0-3_i386.deb > debsums: can't open scop.all (No such file or directory) > Can't return to /tmp/YGGGLV8DjO/bio-linux-emboss/usr/local/bioinf/EMBOSS/EMBOSS-3.0.0/test/data/structure from /tmp/YGGGLV8DjO (No such file or directory) at /usr/share/perl/5.8/File/Temp.pm line 858 > END failed--call queue aborted. The "debsums" program is a Perl script, and the perl library function open() automatically processes filenames to remove leading/trailing spaces. However, the "scop.all " file is created _with_ a trailing space when bio-linux-emboss is installed. I've extracted the contents of the NEBC package "bio-linux-emboss_3.0.0-3_i386.deb" and confirmed that the file in the package does indeed have a trailing space in its name. Renaming the file "scop.all" (i.e. without a trailing space), then rebuilding and installing the updated package cures this problem, but there is also a problem with at least one other file in the package: /var/lib/menu-xdg/applications/menu-xdg/jemboss.desktop I've confirmed that this file is in the bio-linux-emboss package but it doesn't seem to be created when the package is installed, and I'm not sure why... Any ideas? Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 From btiwari at ceh.ac.uk Tue May 9 04:46:20 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Tue, 09 May 2006 09:46:20 +0100 Subject: [Bio-Linux] bio-linux-emboss breaks debsums Message-ID: Hi Tony Thanks for the report and investigating the causes of the problem. The file scop.all is part of the EMBOSS release itself rather than something I have put in. I have updated the package, removing the space at the end of the filename. Can you install the latest bio-linux-emboss package and see what happens? I wasn't sure what he problem was that you saw with the jemboss.desktop file. There didn't seem to be a space at the end of that filename. The jemboss.desktop file becomes X-Debian-Apps-Science-jemboss.desktop. This is on my machine. Can you check again to see if it is on yours? cheers, Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* >>> ajt at rri.sari.ac.uk 09/05/2006 00:23 >>> I've noticed that "debsums" (used to verify the installation of Debian packages) is broken after installing bio-linux-emboss under Debian Sarge/Etch. The "debsums" package is not a standard part of Bio-Linux4, but it's a useful way of verifying system integrity. Unfortunately, a problem in the bio-linux-emboss package results in diagnostic errors being produced when subsequently installing *any* other packages! This is caused by trailing spaces in the filename: "/usr/local/bioinf/EMBOSS/EMBOSS-3.0.0/test/data/structure/scop.all " ^ > ajt at wildcat:% debsums -ac bio-linux-emboss_3.0.0-3_i386.deb > debsums: can't open scop.all (No such file or directory) > Can't return to /tmp/YGGGLV8DjO/bio-linux-emboss/usr/local/bioinf/EMBOSS/EMBOSS-3.0.0/test/data/structure from /tmp/YGGGLV8DjO (No such file or directory) at /usr/share/perl/5.8/File/Temp.pm line 858 > END failed--call queue aborted. The "debsums" program is a Perl script, and the perl library function open() automatically processes filenames to remove leading/trailing spaces. However, the "scop.all " file is created _with_ a trailing space when bio-linux-emboss is installed. I've extracted the contents of the NEBC package "bio-linux-emboss_3.0.0-3_i386.deb" and confirmed that the file in the package does indeed have a trailing space in its name. Renaming the file "scop.all" (i.e. without a trailing space), then rebuilding and installing the updated package cures this problem, but there is also a problem with at least one other file in the package: /var/lib/menu-xdg/applications/menu-xdg/jemboss.desktop I've confirmed that this file is in the bio-linux-emboss package but it doesn't seem to be created when the package is installed, and I'm not sure why... Any ideas? Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 _______________________________________________ Bio-linux mailing list Bio-linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From jaa53 at cornell.edu Tue May 9 18:18:04 2006 From: jaa53 at cornell.edu (Jose A. Andres) Date: Tue, 9 May 2006 18:18:04 -0400 (EDT) Subject: [Bio-Linux] chown problems? In-Reply-To: <445FD303.4030601@rri.sari.ac.uk> References: <445FD303.4030601@rri.sari.ac.uk> Message-ID: <41332.132.236.111.235.1147213084.squirrel@webmail.cornell.edu> Hi All! I've decided to mount an external hard drive on our bio-linux machine so everyone can store there their raw data (mostly traces) I already done that (/media/usbdrive) the /etc/fstab line looks like /dev/sdd1 /media/usbdrive auto rw,user,auto 0 0 There only one partition of the drive and on it I made a data-storage directory with 5 different subdirectories for the users... (ls -l on /media/usbdrive/data-storage/ total 160 drwxr-xr-x 3 manager manager 32768 2006-05-09 16:19 user1 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user2 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user3 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user4 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user5 As you see manager is both the owner and the group. I 've tried to change this (log as manager) using Konkeror and sudo chown e.g. sudo chown user1 /media/usbdrive/data-storage/user1 but I got the following error chown: changing ownership of `/media/usbdrive/data-storage/user1': Operation not permitted That's also true even if I log on as root!! Any ideas on how to change the onwership of the files? Thanks! /Jose From gary.barker at bristol.ac.uk Tue May 9 18:35:00 2006 From: gary.barker at bristol.ac.uk (Gary Barker) Date: Tue, 9 May 2006 23:35:00 0100 Subject: [Bio-Linux] chown problems? Message-ID: <200605092232.k49MWs5A024997@envgen.nox.ac.uk> Is the external drive formatted as ext3, FAT, NTFS? Would the latter two formats present file permission problems? Gary Gary Barker PhD Bioinfomatician University of Bristol UK. "Jose A. Andres" wrote: __________ >Hi All! > >I've decided to mount an external hard drive on our bio-linux machine so >everyone can store there their raw data (mostly traces) > >I already done that (/media/usbdrive) the /etc/fstab line looks like > >/dev/sdd1 /media/usbdrive auto rw,user,auto 0 0 > >There only one partition of the drive and on it I made a data-storage >directory with 5 different subdirectories for the users... > >(ls -l on /media/usbdrive/data-storage/ >total 160 >drwxr-xr-x 3 manager manager 32768 2006-05-09 16:19 user1 >drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user2 >drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user3 >drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user4 >drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user5 > >As you see manager is both the owner and the group. I 've tried to change >this (log as manager) using Konkeror and sudo chown >e.g. sudo chown user1 /media/usbdrive/data-storage/user1 > >but I got the following error >chown: changing ownership of `/media/usbdrive/data-storage/user1': >Operation not permitted > >That's also true even if I log on as root!! > >Any ideas on how to change the onwership of the files? > >Thanks! > >/Jose > > >_______________________________________________ >Bio-linux mailing list >Bio-linux at envgen.nox.ac.uk >http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From nsb at ceh.ac.uk Tue May 9 18:41:13 2006 From: nsb at ceh.ac.uk (Nicolas Bertrand) Date: Tue, 09 May 2006 23:41:13 +0100 Subject: [Bio-Linux] chown problems? Message-ID: Hi Jose, It could be that the USB hard drive is formatted as a Fat32 filesystem (vfat to a linux machine). Such filesystem does not support permissions. you could 1. mount the drive so all users have read and write permissions : edit /etc/fstab as follows: /dev/sdd1 /media/usbdrive vfat rw,umask=000 0 0 -- not good if you require some access control on the raw data. 2. backup your data and reformat the drive with a file system that support permissions (e.g. ext2) utility to use to reformat filesystem is mkfs e.g. mkfs -t ext2 /dev/sdd1 man mkfs for more info. -- please note that a windows or macosx machine won't be able to access the data on that partition out of the box -- Hope this helps, Nic -- CEH Environmental Informatics Programme ================================== South Down Way Randonnee Challenge Winchester to Eastbourne 1 DAY 100 miles Offroad 10 000 ft of Climbing In comparison... Oxford - Cambridge = 85 miles on the road. Please dig deep to support the Britsh Heart Foundation: http://www.bhf.org.uk/sponsorship/sponsorpage.aspx?User=nicolasbertrand&SponsorshipPageID=10484 >>> jaa53 at cornell.edu 09/05/2006 23:18 >>> Hi All! I've decided to mount an external hard drive on our bio-linux machine so everyone can store there their raw data (mostly traces) I already done that (/media/usbdrive) the /etc/fstab line looks like /dev/sdd1 /media/usbdrive auto rw,user,auto 0 0 There only one partition of the drive and on it I made a data-storage directory with 5 different subdirectories for the users... (ls -l on /media/usbdrive/data-storage/ total 160 drwxr-xr-x 3 manager manager 32768 2006-05-09 16:19 user1 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user2 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user3 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user4 drwxr-xr-x 2 manager manager 32768 2006-05-09 16:18 user5 As you see manager is both the owner and the group. I 've tried to change this (log as manager) using Konkeror and sudo chown e.g. sudo chown user1 /media/usbdrive/data-storage/user1 but I got the following error chown: changing ownership of `/media/usbdrive/data-storage/user1': Operation not permitted That's also true even if I log on as root!! Any ideas on how to change the onwership of the files? Thanks! /Jose _______________________________________________ Bio-linux mailing list Bio-linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From NEBC at wpo.nerc.ac.uk Tue May 16 07:09:47 2006 From: NEBC at wpo.nerc.ac.uk (NEBC) Date: Tue, 16 May 2006 12:09:47 +0100 Subject: [Bio-Linux] Introduction to Bio-Linux 4.0 Training course - CEH Oxford - 2nd June 2006 Message-ID: Dear Colleagues, There are three places remaining on the above Bio-Linux course on 2nd June, so we are keeping open the registration page on our website in case anyone would like to attend but thought they may have missed the deadline. The course will be held at CEH Oxford and will run from 10:30am until 5:00pm. This is a one day course designed to introduce new users to the Bio-Linux system. The course is divided into two sections: Introduction to Linux and Introduction to Bioinformatics on Bio-Linux. The course is designed so that people can work at their own pace and discover the facilities available on Bio-Linux. Instructors from the NEBC will be on hand to answer Bio-Linux-related questions as well as to discuss any data management or bioinformatics analysis requirements you may have. You or anyone on your NERC EG or PG&P grant can register for this course using our web registration form at: http://envgen.nox.ac.uk/cgi-bin/showcourses.cgi All course notes and sample files are already available at: http://envgen.nox.ac.uk/envgen/training/archives/000530.html best wishes, The NEBC Team NERC Environmental Bioinformatics Centre, (formerly EGTDC), Centre for Ecology & Hydrology Mansfield Road, Oxford, OX1 3SR UK Tel: +44 (0) 1865 281976 Fax: +44 (0) 1865 281 696 http://nebc.nox.ac.uk/ Email: admin at nebc.ac.uk This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed.