From zain.alvi at student.shu.edu Tue Apr 7 11:51:27 2015 From: zain.alvi at student.shu.edu (Zain A Alvi) Date: Tue, 7 Apr 2015 15:51:27 +0000 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet Message-ID: <1428421887080.95011@student.shu.edu> Dear Sir or Madam, I hope this reaches you well. I am trying to add the Velvet (a custom version with Kmer value of 303, and another version that Velvet that was made up to 191) and VelvetOptimiser to path. In my findings with BioLinux 8's documentation, I found Velvet was pre-installed with BioLinux, which is great and useful. Unfortunately, the Kmer value is too low for our needs. I was wondering where exactly is the file to edit the path to this tool. I have tried export PATH=/dir/:$PATH , but I rather know where exactly is the file is located to edit. I have taken a look into $HOME/.bashrc (or ~/.bashrc) via gedit to no avail as well. Also I found the tools (Velvet and more tools) to be found in /usr/bin/ folder but they can't be replaced and they are found repeatedly in the X11 folders within them as well. I was wondering if you could kindly help in finding on correct folder and adding files to $PATH to alleviate this situation and have my higher kmer version of Velvet be used by VelvetOptimiser. Sincerely, Zain Alvi --- zain.alvi at student.shu.edu Ph. D. Candidate in Molecular Bioscience Seton Hall University Ph: (973) 710-7149 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Wed Apr 8 06:49:10 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 8 Apr 2015 11:49:10 +0100 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet In-Reply-To: <1428421887080.95011@student.shu.edu> References: <1428421887080.95011@student.shu.edu> Message-ID: <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> Hi, I think the quick answer is - you are probably running ZSH so edit ~/.zshrc and add the PATH setting there. The actual syntax for variable assignment in ZSH is the same as for BASH. Regarding paths for programs in general, this is a fairly fundamental question regarding modern Linux systems but I actually don't know anywhere that it is spelled out clearly and simply, so I'll give you my own summary: * Everything under /usr/ belongs to the package manager and you should only modify it by adding or removing packages (eg. with apt-get or the update manager) * The exception is /usr/local which belongs to you (as the system administrator) and overrides /usr. For example if you place a modified version of velvet in /usr/local/bin and then run "velvet" your own modified version will be called. This would also apply to the VelvetOptimiser. * A regular user (without sudo) can have a personal bin/ directory in their home directory and any executables in there will be added to the path automatically. But this does not override /usr/bin or /usr/local/bin, so you need to either give the executable a new name, like "velvet303" or else run it explicitly by typing "~/bin/velvet" or else add $HOME/bin at the start of your PATH. * The default shell in Bio-Linux is ZSH so you need to edit .zshrc to modify local behaviour and you can either modify the path or add aliases - eg.: * export PATH="$HOME/bin:$PATH" #(gives priority to programs in ~/bin) * alias velvet="~/mydir/velvet" #(overrides velvet but won't affect VelvetOptimiser as aliases aren't exported from the shell) I hope that makes sense. Cheers, TIM On Tue, 2015-04-07 at 16:51 +0100, Zain A Alvi wrote: > Dear Sir or Madam, > > > > I hope this reaches you well. I am trying to add the Velvet (a custom > version with Kmer value of 303, and another version that Velvet that > was made up to 191) and VelvetOptimiser to path. In my findings with > BioLinux 8's documentation, I found Velvet was pre-installed with > BioLinux, which is great and useful. Unfortunately, the Kmer value is > too low for our needs. > > > I was wondering where exactly is the file to edit the path to this > tool. I have tried export PATH=/dir/:$PATH , but I rather know where > exactly is the file is located to edit. I have taken a look into > $HOME/.bashrc (or ~/.bashrc) via gedit to no avail as well. > > > > Also I found the tools (Velvet and more tools) to be found > in /usr/bin/ folder but they can't be replaced and they are found > repeatedly in the X11 folders within them as well. > > > I was wondering if you could kindly help in finding on correct folder > and adding files to $PATH to alleviate this situation and have my > higher kmer version of Velvet be used by VelvetOptimiser. > > > > Sincerely, > > > Zain Alvi > > > --- > > zain.alvi at student.shu.edu > > Ph. D. Candidate in Molecular Bioscience > > Seton Hall University > > Ph: (973) 710-7149 > > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tony.travis at minke-informatics.co.uk Wed Apr 8 08:29:59 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Wed, 8 Apr 2015 13:29:59 +0100 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet In-Reply-To: <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <55251F47.4040905@minke-informatics.co.uk> On 08/04/15 11:49, Tim Booth wrote: > Hi, > > I think the quick answer is - you are probably running ZSH so edit > ~/.zshrc and add the PATH setting there. The actual syntax for variable > assignment in ZSH is the same as for BASH. Hi, Tim. Under Bio-Linux 8, you set up the environment for "zsh" in: /etc/zshrc Which sources 'profile' fragments in: /etc/zshrc.d/* Finally, "zsh" sources: ~/.zshrc However, the default order of files read by a "zsh" login shell is: /etc/zsh/zshenv ~/.zshenv /etc/zsh/zprofile ~/.zprofile /etc/zsh/zshrc (sources /etc/zsh/zshrc.d/* in Bio-Linux) ~/.zshrc /etc/zsh/zlogin ~/.zlogin Common practice is only to source the start-up files once, at login, regardless of the shell you are using. We had a discussion about this recently because I had put some of my "bash" 'profile' fragments in: /etc/profile.d/* This is similar to what your "zsh" files do under Bio-Linux in: /etc/zsh/zshrc.d/* The environment of an interactive shell is inherited from the login shell that spawned it, except in the case of a Unity/MATE GUI terminal, in which case you have to edit the terminal preferences (once) to make the terminal run as a login shell - Is that why you prefer "zshrc*"? I note that the official Ubuntu "base-files" package contains: /etc/profile.d And, you have put some 'profile' fragments in there from packages: bio-linux-cd-hit bio-linux-blast Does this signal a change of heart about Bio-Linux supporting "bash"? If so, it might it be worth considering "zsh" and "bash" sourcing the same start-up files in order to create the same environment for both (with adjustments based on the SHELL environment variable if needed). > Regarding paths for programs in general, this is a fairly fundamental > question regarding modern Linux systems but I actually don't know > anywhere that it is spelled out clearly and simply, so I'll give you my > own summary: The Filesystem Hierarchy Standard is a widely used reference: http://www.pathname.com/fhs/ HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Wed Apr 8 08:34:36 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Wed, 8 Apr 2015 13:34:36 +0100 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <55251F47.4040905@minke-informatics.co.uk> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk> Message-ID: <5525205C.9080409@minke-informatics.co.uk> On 08/04/15 13:29, Tony Travis wrote: > [...] > Under Bio-Linux 8, you set up the environment for "zsh" in: > > /etc/zshrc > > Which sources 'profile' fragments in: > > /etc/zshrc.d/* Hi, Tim. Sorry, I meant: /etc/zsh/zshrc /etc/zsh/zshrc.d/* Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From zain.alvi at student.shu.edu Wed Apr 8 12:11:51 2015 From: zain.alvi at student.shu.edu (Zain A Alvi) Date: Wed, 8 Apr 2015 16:11:51 +0000 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <5525205C.9080409@minke-informatics.co.uk> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk>, <5525205C.9080409@minke-informatics.co.uk> Message-ID: <1428509512578.98742@student.shu.edu> Hi Tim and Tony, Thank you so much for the detailed explanation of how $PATH work with Bio-Linux and how environments are set up in Bio-Linux. I tried to setup the paths to VelvetOptimiser and new Velvets in ZSH (~/.zshrc) and I've gotten command not found for VelvetOptimiser. The lines that I added the are following two lines: export PATH=$PATH:/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/ export PATH=$PATH:/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/ The first one is for VelvetOptimiser and the second one is for Velveth and Velvetg that was created for Kmer length of 303. If I try % VelvetOptimiser.pl then the output states fg: no current job I have follow up question in regards to aliases. VelvetOptimiser is designed specifically for look for Velveth and Velvetg and run them as it goes through each of the kmers. I am worried that it will seek the built in/old Velveth/g instead of the new compiled velveth/g. It seeks the name velveth and velvetg respectively when it is executed in terminal. I've added the following alias terms in ~/.zshrc alias velveth="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velveth_folder" alias velvetg="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velvetg_folder" If I type velveth or velvetg , I would receive an error of you do not have permission, which is strange as I am the administrator. I remember not being root could cause this occur. Could that be the reason here? Now the strange part, is if I do sudo velveth then enter my password. Terminal will execute the built in/old velvet instead of the new one, which is strange. Is there method for VelvetOptimiser to seek the correct Velvet and without forcing sudo or having it override velvets that are built in. Unfortunately renaming the newly compiled velvets is not an option as I far I can see so far. Thank you again for the great help. I really appreciate it. Kind regards, Zain ________________________________________ From: Tony Travis Sent: Wednesday, April 8, 2015 8:34 AM To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction On 08/04/15 13:29, Tony Travis wrote: > [...] > Under Bio-Linux 8, you set up the environment for "zsh" in: > > /etc/zshrc > > Which sources 'profile' fragments in: > > /etc/zshrc.d/* Hi, Tim. Sorry, I meant: /etc/zsh/zshrc /etc/zsh/zshrc.d/* Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Wed Apr 8 14:04:09 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 8 Apr 2015 19:04:09 +0100 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <1428509512578.98742@student.shu.edu> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk> , <5525205C.9080409@minke-informatics.co.uk> <1428509512578.98742@student.shu.edu> Message-ID: <1428516249.5355.105.camel@wllt1771.nerc-wallingford.ac.uk> Hi Zain, All of the behaviour you are seeing makes sense to me. You are suffering from some fundamental misunderstandings about how the shell handles aliases vs. environment variables and what the permissions errors actually mean. No use of sudo will help you in this situation! We cover most of this in an interactive session when I teach introductory Linux courses with my colleagues, but unfortunately the printed notes on the topic in our tutorial are not very good. Therefore I'd strongly recommend you get a book on Linux that covers learning the quirks of the command line and take a little time to work through it. I'll give some brief pointers below but they probably won't answer all your questions: > export PATH= $PATH:/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/ This adds to the end of the path, so it won't override anything already in the system. Put the ":$PATH" bit on the end of the line. See: http://rute.2038bug.com/node7.html.gz#SECTION007180000000000000000 > If I try % VelvetOptimiser.pl then the output states fg: no current job The error relates to the '%' sign, which represents your shell prompt not a thing for you to type. See: http://en.wikibooks.org/wiki/Guide_to_Unix/Explanations/Shell_Prompt#Appearance_of_the_prompt > I have follow up question in regards to aliases. VelvetOptimiser is > designed specifically for look for Velveth and Velvetg and run them as > it goes through each of the kmers. I am worried that it will seek the > built in/old Velveth/g instead of the new compiled velveth/g. It > seeks the name velveth and velvetg respectively when it is executed in > terminal. Aliases won't help you here because they only affect commands you type directly in the interactive shell, so stick to manipulating the PATH which is an environmental setting and therefore inherited. See: https://help.ubuntu.com/community/EnvironmentVariables#Inheritance > I've added the following alias terms in ~/.zshrc > > alias velveth="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velveth_folder" > alias velvetg="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velvetg_folder" > > If I type velveth or velvetg , I would receive an error of you do not have permission, which is strange as I am the administrator. I remember not being root could cause this occur. Could that be the reason here? Try typing the name of any directory you can think of - eg: /media/biolinux301 You'll get "permission denied" every time. Unfortunately there are various situations where you can trigger a "permission denied" error when it has nothing to do with the permissions of your user account. (Tony will undoubtedly point out that BASH returns a better error message in this specific case.) Aliases need to refer to the actual binary file, not the directory, but as I said above they won't help you here. > Now the strange part, is if I do sudo velveth then enter my password. Terminal will execute the built in/old velvet instead of the new one, which is strange. It's expected behaviour. Sudo uses a standard PATH whatever your current setting is - run "sudo less /etc/sudoers" and look for the "secure_path" line. Sudo also resets other settings in your environment, unless you tell it not too. But you don't need "sudo" here, as I explained above. Best, TIM From zain.alvi at student.shu.edu Wed Apr 8 15:56:41 2015 From: zain.alvi at student.shu.edu (Zain A Alvi) Date: Wed, 8 Apr 2015 19:56:41 +0000 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <1428516249.5355.105.camel@wllt1771.nerc-wallingford.ac.uk> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk> , <5525205C.9080409@minke-informatics.co.uk> <1428509512578.98742@student.shu.edu>, <1428516249.5355.105.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <1428523002802.4625@student.shu.edu> Hi Tim, Thank you for the great advice. I have been self teaching myself most of the ins and out of Linux/Ubuntu from online tutorials since the days of PS3 had Ubuntu support. I was wondering what books would you recommend? I have set the following up with the following aliases and environmental variables in ~/.zshrc: export PATH=/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/:$PATH alias velveth="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velveth_folder/velveth" alias velvetg="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velvetg_folder/velvetg" I was following the VelvetOptimiser manual for the ~/.bashrc as an example. export PATH=$PATH:$HOME/VelvetOptimiser-2.2.4 Source: https://raw.githubusercontent.com/Victorian-Bioinformatics-Consortium/VelvetOptimiser/master/INSTALL and https://raw.githubusercontent.com/Victorian-Bioinformatics-Consortium/VelvetOptimiser/master/README Anyway, VelvetOptimiser and Velveth/g are able to work independently when trying to access them through the terminal. Unfortunately, VelvetOptimiser still executes the old built in Velveth (Kmer31 build) instead of referring to the newly compiled Kmer303 velveth version when trying assembly the genome. Thank you again for all great help. Kind regards, Zain ________________________________________ From: Tim Booth Sent: Wednesday, April 8, 2015 2:04 PM To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction Hi Zain, All of the behaviour you are seeing makes sense to me. You are suffering from some fundamental misunderstandings about how the shell handles aliases vs. environment variables and what the permissions errors actually mean. No use of sudo will help you in this situation! We cover most of this in an interactive session when I teach introductory Linux courses with my colleagues, but unfortunately the printed notes on the topic in our tutorial are not very good. Therefore I'd strongly recommend you get a book on Linux that covers learning the quirks of the command line and take a little time to work through it. I'll give some brief pointers below but they probably won't answer all your questions: > export PATH= $PATH:/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/ This adds to the end of the path, so it won't override anything already in the system. Put the ":$PATH" bit on the end of the line. See: http://rute.2038bug.com/node7.html.gz#SECTION007180000000000000000 > If I try % VelvetOptimiser.pl then the output states fg: no current job The error relates to the '%' sign, which represents your shell prompt not a thing for you to type. See: http://en.wikibooks.org/wiki/Guide_to_Unix/Explanations/Shell_Prompt#Appearance_of_the_prompt > I have follow up question in regards to aliases. VelvetOptimiser is > designed specifically for look for Velveth and Velvetg and run them as > it goes through each of the kmers. I am worried that it will seek the > built in/old Velveth/g instead of the new compiled velveth/g. It > seeks the name velveth and velvetg respectively when it is executed in > terminal. Aliases won't help you here because they only affect commands you type directly in the interactive shell, so stick to manipulating the PATH which is an environmental setting and therefore inherited. See: https://help.ubuntu.com/community/EnvironmentVariables#Inheritance > I've added the following alias terms in ~/.zshrc > > alias velveth="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velveth_folder" > alias velvetg="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velvetg_folder" > > If I type velveth or velvetg , I would receive an error of you do not have permission, which is strange as I am the administrator. I remember not being root could cause this occur. Could that be the reason here? Try typing the name of any directory you can think of - eg: /media/biolinux301 You'll get "permission denied" every time. Unfortunately there are various situations where you can trigger a "permission denied" error when it has nothing to do with the permissions of your user account. (Tony will undoubtedly point out that BASH returns a better error message in this specific case.) Aliases need to refer to the actual binary file, not the directory, but as I said above they won't help you here. > Now the strange part, is if I do sudo velveth then enter my password. Terminal will execute the built in/old velvet instead of the new one, which is strange. It's expected behaviour. Sudo uses a standard PATH whatever your current setting is - run "sudo less /etc/sudoers" and look for the "secure_path" line. Sudo also resets other settings in your environment, unless you tell it not too. But you don't need "sudo" here, as I explained above. Best, TIM _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From zain.alvi at student.shu.edu Wed Apr 8 19:42:17 2015 From: zain.alvi at student.shu.edu (Zain A Alvi) Date: Wed, 8 Apr 2015 23:42:17 +0000 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <1428523002802.4625@student.shu.edu> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk> , <5525205C.9080409@minke-informatics.co.uk> <1428509512578.98742@student.shu.edu>, <1428516249.5355.105.camel@wllt1771.nerc-wallingford.ac.uk>, <1428523002802.4625@student.shu.edu> Message-ID: <1428536531370.7520@student.shu.edu> Hi Tim and Tony, I hope everything is well. I just had an idea for a temporary solution, would going into root via terminal and then re-downloading and re-compiling velvet with the higher Kmer value in the usr/bin folder. Do you think that this would make VelvetOptimiser to work properly with the higher compiled Velvet? But my main question would be, how are we able to keep the older version in usr/bin and force VelvetOptimiser to use the newly compiled version of the software in some other location. Kind regards, Zain ________________________________________ From: Zain A Alvi Sent: Wednesday, April 8, 2015 3:56 PM To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction Hi Tim, Thank you for the great advice. I have been self teaching myself most of the ins and out of Linux/Ubuntu from online tutorials since the days of PS3 had Ubuntu support. I was wondering what books would you recommend? I have set the following up with the following aliases and environmental variables in ~/.zshrc: export PATH=/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/:$PATH alias velveth="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velveth_folder/velveth" alias velvetg="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velvetg_folder/velvetg" I was following the VelvetOptimiser manual for the ~/.bashrc as an example. export PATH=$PATH:$HOME/VelvetOptimiser-2.2.4 Source: https://raw.githubusercontent.com/Victorian-Bioinformatics-Consortium/VelvetOptimiser/master/INSTALL and https://raw.githubusercontent.com/Victorian-Bioinformatics-Consortium/VelvetOptimiser/master/README Anyway, VelvetOptimiser and Velveth/g are able to work independently when trying to access them through the terminal. Unfortunately, VelvetOptimiser still executes the old built in Velveth (Kmer31 build) instead of referring to the newly compiled Kmer303 velveth version when trying assembly the genome. Thank you again for all great help. Kind regards, Zain ________________________________________ From: Tim Booth Sent: Wednesday, April 8, 2015 2:04 PM To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction Hi Zain, All of the behaviour you are seeing makes sense to me. You are suffering from some fundamental misunderstandings about how the shell handles aliases vs. environment variables and what the permissions errors actually mean. No use of sudo will help you in this situation! We cover most of this in an interactive session when I teach introductory Linux courses with my colleagues, but unfortunately the printed notes on the topic in our tutorial are not very good. Therefore I'd strongly recommend you get a book on Linux that covers learning the quirks of the command line and take a little time to work through it. I'll give some brief pointers below but they probably won't answer all your questions: > export PATH= $PATH:/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/ This adds to the end of the path, so it won't override anything already in the system. Put the ":$PATH" bit on the end of the line. See: http://rute.2038bug.com/node7.html.gz#SECTION007180000000000000000 > If I try % VelvetOptimiser.pl then the output states fg: no current job The error relates to the '%' sign, which represents your shell prompt not a thing for you to type. See: http://en.wikibooks.org/wiki/Guide_to_Unix/Explanations/Shell_Prompt#Appearance_of_the_prompt > I have follow up question in regards to aliases. VelvetOptimiser is > designed specifically for look for Velveth and Velvetg and run them as > it goes through each of the kmers. I am worried that it will seek the > built in/old Velveth/g instead of the new compiled velveth/g. It > seeks the name velveth and velvetg respectively when it is executed in > terminal. Aliases won't help you here because they only affect commands you type directly in the interactive shell, so stick to manipulating the PATH which is an environmental setting and therefore inherited. See: https://help.ubuntu.com/community/EnvironmentVariables#Inheritance > I've added the following alias terms in ~/.zshrc > > alias velveth="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velveth_folder" > alias velvetg="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velvetg_folder" > > If I type velveth or velvetg , I would receive an error of you do not have permission, which is strange as I am the administrator. I remember not being root could cause this occur. Could that be the reason here? Try typing the name of any directory you can think of - eg: /media/biolinux301 You'll get "permission denied" every time. Unfortunately there are various situations where you can trigger a "permission denied" error when it has nothing to do with the permissions of your user account. (Tony will undoubtedly point out that BASH returns a better error message in this specific case.) Aliases need to refer to the actual binary file, not the directory, but as I said above they won't help you here. > Now the strange part, is if I do sudo velveth then enter my password. Terminal will execute the built in/old velvet instead of the new one, which is strange. It's expected behaviour. Sudo uses a standard PATH whatever your current setting is - run "sudo less /etc/sudoers" and look for the "secure_path" line. Sudo also resets other settings in your environment, unless you tell it not too. But you don't need "sudo" here, as I explained above. Best, TIM _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tony.travis at minke-informatics.co.uk Thu Apr 9 05:27:49 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 9 Apr 2015 10:27:49 +0100 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <1428536531370.7520@student.shu.edu> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk> , <5525205C.9080409@minke-informatics.co.uk> <1428509512578.98742@student.shu.edu>, <1428516249.5355.105.camel@wllt1771.nerc-wallingford.ac.uk>, <1428523002802.4625@student.shu.edu> <1428536531370.7520@student.shu.edu> Message-ID: <55264615.6060807@minke-informatics.co.uk> On 09/04/15 00:42, Zain A Alvi wrote: > Hi Tim and Tony, > > I hope everything is well. I just had an idea for a temporary > solution, would going into root via terminal and then re-downloading > and re-compiling velvet with the higher Kmer value in the usr/bin > folder. Do you think that this would make VelvetOptimiser to work > properly with the higher compiled Velvet? > > But my main question would be, how are we able to keep the older > version in usr/bin and force VelvetOptimiser to use the newly > compiled version of the software in some other location. Hi, Zain. As Tim said, you need to understand how the shell finds commands using the PATH. Here is a quick summary of how to compile and install a custom version of Velvet in /usr/local/bin: > wget http://www.ebi.ac.uk/~zerbino/velvet/velvet_latest.tgz > tar xzf velvet_latest.tgz > cd velvet_1.2.10/ > make velveth velvetg MAXKMERLENGTH=191 > cp -ai velvetg velveth /usr/local/bin Check your PATH contains "/usr/local/bin" and it is before /usr/bin: > printenv PATH > /usr/local/hyb-master/bin:/home/ajt/bin:/usr/local/hyb-master/bin:/home/ajt/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/cd-hit:/usr/lib/cd-hit Check which version of "velvet[hg]" the shell finds: > which -a velveth > /usr/local/bin/velveth > /usr/bin/velveth > which -a velvetg > /usr/local/bin/velvetg > /usr/bin/velvetg Test e.g. velveth > velveth > velveth - simple hashing program > Version 1.2.10 > > Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk) > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > Compilation settings: > CATEGORIES = 2 > MAXKMERLENGTH = 191 > Look in VelvetOpt/[gh]wrap.pm to see how "VelvetOptimiser" calls the "velveth" and "velvetg" binaries: > VelvetOptimiser-2.2.5$ ls VelvetOpt > Assembly.pm gwrap.pm hwrap.pm Utils.pm It just uses the first "velveth" and "velvetg" it finds on the PATH. HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From t.fedrizzi at unitn.it Thu Apr 9 06:13:12 2015 From: t.fedrizzi at unitn.it (Tarcisio Fedrizzi) Date: Thu, 9 Apr 2015 12:13:12 +0200 Subject: [Bio-Linux] Qiime 1.9 dependencies problem Message-ID: Hello, I write you because I have a problem with the dependencies of qiime. I'm using ubuntu server 14.04 lts and I've added the repos for biolinux 8: deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main The problem with qiime 1.9 is that the package r-cran-optparse is included neither in ubuntu nor in biolinux. I report this especially because the trusty release is an LTS and maybe there are other users that want to keep this release of ubuntu. Thank you very much. Best regards, Tarcisio Fedrizzi. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu Apr 9 08:01:59 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 9 Apr 2015 13:01:59 +0100 Subject: [Bio-Linux] Qiime 1.9 dependencies problem In-Reply-To: References: Message-ID: <1428580919.5355.116.camel@wllt1771.nerc-wallingford.ac.uk> Hi Tarcisio, Thanks for the bug report. The package is on the C2D4U PPA which is activated by default on Bio-Linux machines which is why I didn't spot this problem before. I've copied the package over to the Bio-Linux PPA, so this problem should now be fixed, and you should be able to use QIIME without any further changes to your APT sources configuration. Is it working for you now? Cheers, TIM On Thu, 2015-04-09 at 11:13 +0100, Tarcisio Fedrizzi wrote: > Hello, > > I write you because I have a problem with the dependencies of qiime. > > I'm using ubuntu server 14.04 lts and I've added the repos for > biolinux 8: > > deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux deb > http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main > deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main > > > The problem with qiime 1.9 is that the package r-cran-optparse is > included neither in ubuntu nor in biolinux. I report this especially > because the trusty release is an LTS and maybe there are other users > that want to keep this release of ubuntu. > > > Thank you very much. > > Best regards, > > Tarcisio Fedrizzi. > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From t.fedrizzi at unitn.it Thu Apr 9 09:17:20 2015 From: t.fedrizzi at unitn.it (Tarcisio Fedrizzi) Date: Thu, 9 Apr 2015 15:17:20 +0200 Subject: [Bio-Linux] Qiime 1.9 dependencies problem In-Reply-To: <1428580919.5355.116.camel@wllt1771.nerc-wallingford.ac.uk> References: <1428580919.5355.116.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: Hi Tim, the problem is fixed! Thank you. Cheers, Tarcisio. On Thu, Apr 9, 2015 at 2:01 PM, Tim Booth wrote: > Hi Tarcisio, > > Thanks for the bug report. The package is on the C2D4U PPA which is > activated by default on Bio-Linux machines which is why I didn't spot > this problem before. > > I've copied the package over to the Bio-Linux PPA, so this problem > should now be fixed, and you should be able to use QIIME without any > further changes to your APT sources configuration. Is it working for > you now? > > Cheers, > > TIM > > On Thu, 2015-04-09 at 11:13 +0100, Tarcisio Fedrizzi wrote: > > Hello, > > > > I write you because I have a problem with the dependencies of qiime. > > > > I'm using ubuntu server 14.04 lts and I've added the repos for > > biolinux 8: > > > > deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux deb > > http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main > > deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main > > > > > > The problem with qiime 1.9 is that the package r-cran-optparse is > > included neither in ubuntu nor in biolinux. I report this especially > > because the trusty release is an LTS and maybe there are other users > > that want to keep this release of ubuntu. > > > > > > Thank you very much. > > > > Best regards, > > > > Tarcisio Fedrizzi. > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://environmentalomics.org/bio-linux > +44 1491 69 2297 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tauqeer9 at gmail.com Sun Apr 12 03:29:34 2015 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Sun, 12 Apr 2015 03:29:34 -0400 Subject: [Bio-Linux] undo mv command Message-ID: Hi Tim I Just made a mistake while installing a program on my Bio-linux. I was trying to move something from the bin of a program to /usr/local/bin/, but I typed the following command by mistake. $ sudo mv /bin/* /usr/local/bin/ How can i get everything back in the /bin directory? Pleas help. Thanks Tauqeer -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From zain.alvi at student.shu.edu Sun Apr 12 16:49:43 2015 From: zain.alvi at student.shu.edu (Zain A Alvi) Date: Sun, 12 Apr 2015 20:49:43 +0000 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <55264615.6060807@minke-informatics.co.uk> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk> , <5525205C.9080409@minke-informatics.co.uk> <1428509512578.98742@student.shu.edu>, <1428516249.5355.105.camel@wllt1771.nerc-wallingford.ac.uk>, <1428523002802.4625@student.shu.edu> <1428536531370.7520@student.shu.edu>, <55264615.6060807@minke-informatics.co.uk> Message-ID: <1428871771847.19163@student.shu.edu> Hi Tim and Tony, Thank you Tim and Tony for bearing with me. I really appreciate the detailed explanation on how Velveth/g and VelvetOptimiser seeks Velvet through the PATHs. I finally understand your points about looking into path order and on how to add those into ~/.zshrc for new apps. I apologize for all the trouble. On a side note. I had to sudo cp -ai velvetg velveth /usr/local/bin as I was receiving Permission Errors. Is this normal even when I am admin and not root in Bio-Linux/Ubunut? I know to access root you have to go through sudo su and it should be rarely used. If I ever want to add other applications, I would then continue adding/copying them into /usr/local/bin and adding the paths to ~/.zshrc Is there any way to change the order for $PATH? For example if I do something like: > echo $PATH It would return: >/usr/local/bin before usr/bin and then any other $PATH that I might add in ~/.zshrc. What if I wanted to create separate location to store the installed applications. How would I force biolinux to go there before going to /usr/local/bin or usr/bin? I know we can always add locations at the end? What do we have to do to add locations in the beginning for the $PATH. The main concern is that we only about 5 GB free on the partition has BioLinux installed. Whereas we have about 3.8 TB free (800 GB - SSD and 3 TB - 3.5" Hard Drive). Thank you again for all the help. I sincerely appreciate it. Kind regards, Zain ________________________________________ From: Tony Travis Sent: Thursday, April 9, 2015 5:27 AM To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction On 09/04/15 00:42, Zain A Alvi wrote: > Hi Tim and Tony, > > I hope everything is well. I just had an idea for a temporary > solution, would going into root via terminal and then re-downloading > and re-compiling velvet with the higher Kmer value in the usr/bin > folder. Do you think that this would make VelvetOptimiser to work > properly with the higher compiled Velvet? > > But my main question would be, how are we able to keep the older > version in usr/bin and force VelvetOptimiser to use the newly > compiled version of the software in some other location. Hi, Zain. As Tim said, you need to understand how the shell finds commands using the PATH. Here is a quick summary of how to compile and install a custom version of Velvet in /usr/local/bin: > wget http://www.ebi.ac.uk/~zerbino/velvet/velvet_latest.tgz > tar xzf velvet_latest.tgz > cd velvet_1.2.10/ > make velveth velvetg MAXKMERLENGTH=191 > cp -ai velvetg velveth /usr/local/bin Check your PATH contains "/usr/local/bin" and it is before /usr/bin: > printenv PATH > /usr/local/hyb-master/bin:/home/ajt/bin:/usr/local/hyb-master/bin:/home/ajt/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/cd-hit:/usr/lib/cd-hit Check which version of "velvet[hg]" the shell finds: > which -a velveth > /usr/local/bin/velveth > /usr/bin/velveth > which -a velvetg > /usr/local/bin/velvetg > /usr/bin/velvetg Test e.g. velveth > velveth > velveth - simple hashing program > Version 1.2.10 > > Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk) > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > Compilation settings: > CATEGORIES = 2 > MAXKMERLENGTH = 191 > Look in VelvetOpt/[gh]wrap.pm to see how "VelvetOptimiser" calls the "velveth" and "velvetg" binaries: > VelvetOptimiser-2.2.5$ ls VelvetOpt > Assembly.pm gwrap.pm hwrap.pm Utils.pm It just uses the first "velveth" and "velvetg" it finds on the PATH. HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tauqeer9 at gmail.com Sun Apr 12 21:29:46 2015 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Sun, 12 Apr 2015 21:29:46 -0400 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: References: Message-ID: Hi Tim This is related to my earlier email (pls see below). I tried to retrieve all the files which I had accidentally moved back to "/bin" and it seems that everything is working now. I am attaching with this email the ls output of the current "/bin" directory. I have 3 extra files which I am not sure if they are part of the "/bin" or "/usr/local/bin", these are- seq_cache_populate.pl formatrpsdb htsjdk-1.119.jar Also, is there anyway to confirm that the "/bin" now has all the original files? Thanks Tauqeer ---------- Forwarded message ---------- From: Tauqeer Alam Date: Sun, Apr 12, 2015 at 3:29 AM Subject: undo mv command To: Bio-Linux help and discussion Hi Tim I Just made a mistake while installing a program on my Bio-linux. I was trying to move something from the bin of a program to /usr/local/bin/, but I typed the following command by mistake. $ sudo mv /bin/* /usr/local/bin/ How can i get everything back in the /bin directory? Pleas help. Thanks Tauqeer -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- bash bsd-csh bunzip2 busybox bzcat bzcmp bzdiff bzegrep bzexe bzfgrep bzgrep bzip2 bzip2recover bzless bzmore cat chacl chgrp chmod chown chvt cp cpio csh dash date dbus-cleanup-sockets dbus-daemon dbus-uuidgen dd df dir dmesg dnsdomainname domainname dumpkeys echo ed egrep false fgconsole fgrep findmnt fuser fusermount getfacl grep gunzip gzexe gzip hostname ip kbd_mode kill kmod ksh ksh93 less lessecho lessfile lesskey lesspipe ln loadkeys login loginctl lowntfs-3g ls lsblk lsmod mkdir mknod mktemp more mount mountpoint mt mt-gnu mv nano nc nc.openbsd netcat netstat nisdomainname ntfs-3g ntfs-3g.probe ntfs-3g.secaudit ntfs-3g.usermap ntfscat ntfsck ntfscluster ntfscmp ntfsdump_logfile ntfsfix ntfsinfo ntfsls ntfsmftalloc ntfsmove ntfstruncate ntfswipe open openvt ping ping6 plymouth plymouth-upstart-bridge ps pwd rbash readlink red rm rmdir rnano running-in-container run-parts rzsh sed setfacl setfont setupcon sh sh.distrib sleep ss static-sh stty su sync tailf tar tcsh tempfile touch true udevadm ulockmgr_server umount uname uncompress unicode_start vdir vmmouse_detect which whiptail ypdomainname zcat zcmp zdiff zegrep zfgrep zforce zgrep zless zmore znew zsh zsh5 From tony.travis at minke-informatics.co.uk Mon Apr 13 07:34:13 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 13 Apr 2015 12:34:13 +0100 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: References: Message-ID: <552BA9B5.60800@minke-informatics.co.uk> On 13/04/15 02:29, Tauqeer Alam wrote: > Hi Tim > This is related to my earlier email (pls see below). I tried to retrieve > all the files which I had accidentally moved back to "/bin" and it seems > that everything is working now. I am attaching with this email the ls > output of the current "/bin" directory. I have 3 extra files which I am > not sure if they are part of the "/bin" or "/usr/local/bin", these are- > > seq_cache_populate.pl > formatrpsdb > htsjdk-1.119.jar > > Also, is there anyway to confirm that the "/bin" now has all the > original files? Hi, Tauqeer. You could install "debsums", which you can use to verify that all the files installed from a .deb are present: sudo apt-get install debsums sudo debsums -ac HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Mon Apr 13 08:00:40 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 13 Apr 2015 13:00:40 +0100 Subject: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction In-Reply-To: <1428871771847.19163@student.shu.edu> References: <1428421887080.95011@student.shu.edu> <1428490150.5355.34.camel@wllt1771.nerc-wallingford.ac.uk> <55251F47.4040905@minke-informatics.co.uk> , <5525205C.9080409@minke-informatics.co.uk> <1428509512578.98742@student.shu.edu>, <1428516249.5355.105.camel@wllt1771.nerc-wallingford.ac.uk>, <1428523002802.4625@student.shu.edu> <1428536531370.7520@student.shu.edu>, <55264615.6060807@minke-informatics.co.uk> <1428871771847.19163@student.shu.edu> Message-ID: <552BAFE8.6020406@minke-informatics.co.uk> On 12/04/15 21:49, Zain A Alvi wrote: > [...] > On a side note. I had to sudo cp -ai velvetg velveth /usr/local/bin > as I was receiving Permission Errors. Is this normal even when I am > admin and not root in Bio-Linux/Ubunut? I know to access root you > have to go through sudo su and it should be rarely used. Hi, Zain. Yes, it's normal: Ubuntu discourages use of the "root" account for external logins because this is a serious security hole. The 'Administrator' accounts are accounts with permission to use "sudo". Ordinary user accounts are not permitted to use the "sudo" command. BTW, it is redundant to use: sudo su It's better to use; sudo -i This gives you a "root" shell with the same environment as if you had logged in as "root", but without exposing your computer to e.g. 'brute-force' attacks, which target external SSH logins on the "root" account. > If I ever want to add other applications, I would then continue > adding/copying them into /usr/local/bin and adding the paths to > ~/.zshrc > > Is there any way to change the order for $PATH? You can edit the PATH variable and export it, but it is best to keep your changes to a mimimum: Either by adding another directory before the current PATH e.g.: export PATH=/before_path:$PATH Or, after the current PATH e.g.: export PATH=$PATH:/after_path You have to 'rehash' the PATH unless you start a new shell: hash -r HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tbooth at ceh.ac.uk Mon Apr 13 09:12:56 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 13 Apr 2015 14:12:56 +0100 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: References: Message-ID: <1428930776.2822.72.camel@wllt1771.nerc-wallingford.ac.uk> Hi Tauqeer, Tony's debsums suggestion is good, but I'd already written this by the time I saw his reply, so here's my alternative in case you need it... I did a similar thing to myself a few years ago, but in this case it was "rm" rather than "mv". Well done on getting back to a usable system. The good news is that you can use 'dpkg' to check that everything is back correctly because it has a registry of all the files installed in /usr/bin, assuming you didn't add them via some other means. $ dpkg -S /usr/bin | sed 's/, /\n/g;s/: .*//' | xargs dpkg -L | grep ^/usr/bin/ | sort > /tmp/files_expected and $ find /usr/bin -mindepth 1 | sort > /tmp/files_found Now, to find files that dpkg thinks should be in /usr/bin but are actually missing, compare the two lists: $ grep -vFf /tmp/files_found /tmp/files_expected This first list should be empty. If not, use 'dpkg -S /usr/bin/foo' to discover the package that is missing a file and re-install that package. $ grep -vFf /tmp/files_expected /tmp/files_found This second list shouldn't be empty, but it will normally contain only symlinks. Check like so: $ grep -vFf /tmp/files_expected /tmp/files_found | xargs ls --color=always -l As for the files you listed, /usr/bin/formatrpsdb is part of the BLAST package, so reinstall 'blast2' just to be sure. I don't recognise the others, and I'd not expect any .jar file to be living in either /usr/bin or /usr/local/bin. Cheers, TIM On Mon, 2015-04-13 at 02:29 +0100, Tauqeer Alam wrote: > Hi Tim > This is related to my earlier email (pls see below). I tried to > retrieve all the files which I had accidentally moved back to "/bin" > and it seems that everything is working now. I am attaching with this > email the ls output of the current "/bin" directory. I have 3 extra > files which I am not sure if they are part of the "/bin" or > "/usr/local/bin", these are- > > > seq_cache_populate.pl > formatrpsdb > htsjdk-1.119.jar > > > Also, is there anyway to confirm that the "/bin" now has all the > original files? > > > Thanks > > > Tauqeer > > > > > ---------- Forwarded message ---------- > > From: Tauqeer Alam > Date: Sun, Apr 12, 2015 at 3:29 AM > Subject: undo mv command > To: Bio-Linux help and discussion > > > Hi Tim > I Just made a mistake while installing a program on my Bio-linux. I > was trying to move something from the bin of a program > to /usr/local/bin/, but I typed the following command by mistake. > > > $ sudo mv /bin/* /usr/local/bin/ > > > > How can i get everything back in the /bin directory? Pleas help. > > > Thanks > > > Tauqeer > > > -- > ********************************************* > Md Tauqeer Alam, Ph.D > Division of Infectious Diseases > Emory University School of Medicine > 615 Michael Street, Atlanta, GA 30322, USA > tauqeer9 at gmail.com > > > > > > -- > ********************************************* > Md Tauqeer Alam, Ph.D > Division of Infectious Diseases > Emory University School of Medicine > 615 Michael Street, Atlanta, GA 30322, USA > tauqeer9 at gmail.com > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tony.travis at minke-informatics.co.uk Mon Apr 13 10:28:14 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 13 Apr 2015 15:28:14 +0100 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: <1428930776.2822.72.camel@wllt1771.nerc-wallingford.ac.uk> References: <1428930776.2822.72.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <552BD27E.2050203@minke-informatics.co.uk> On 13/04/15 14:12, Tim Booth wrote: > [...] > As for the files you listed, /usr/bin/formatrpsdb is part of the BLAST > package, so reinstall 'blast2' just to be sure. I don't recognise the > others, and I'd not expect any .jar file to be living in either /usr/bin > or /usr/local/bin. > [...] Hi, Tim. These are from Samtools. seq_cache_populate.pl: > https://github.com/samtools/samtools/blob/b7ac1e2819ab85d5950eb2ce02434aa422fe39ed/misc/seq_cache_populate.pl htsjdk-1.119.jar: > https://github.com/samtools/htsjdk/tree/1.119 [A version of Samtools could have been installed manually] HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tauqeer9 at gmail.com Mon Apr 13 19:30:41 2015 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Mon, 13 Apr 2015 19:30:41 -0400 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: <552BD27E.2050203@minke-informatics.co.uk> References: <1428930776.2822.72.camel@wllt1771.nerc-wallingford.ac.uk> <552BD27E.2050203@minke-informatics.co.uk> Message-ID: Thanks Tony and Tim. Yes, I had installed new version of samtools recently (after un-installing the older one through Ubuntu Software Center), so I will leave those three files in the /usr/local/bin/. I first tried Tony's suggestions of using "sudo debsums -ac" command to find out if there are any missing files in my "/bin". I got the following output. I understand the lines related to Brother printer which I once tried to install (un-successfully). I also have chromium browser installed. Do I have to install any of these missing files and how do I do that? :~$ sudo debsums -ac debsums: missing file /etc/firefox/profile/localstore.rdf (from bio-linux-themes-v8 package) debsums: missing file /etc/firefox/profile/bookmarks.html (from bio-linux-themes-v8 package) debsums: missing file /etc/firefox/profile/prefs.js (from bio-linux-themes-v8 package) debsums: missing file /etc/default/chromium-browser (from chromium-browser package) /etc/default/cups /etc/grub.d/10_linux /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWrc /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWfunc debsums: missing file /usr/share/doc/hl2270dwlpr/copyright (from hl2270dwlpr package) debsums: missing file /usr/share/doc/hl2270dwlpr/changelog.Debian.gz (from hl2270dwlpr package) debsums: missing file /usr/share/doc/ia32-libs-multiarch/changelog.gz (from ia32-libs-multiarch package) /boot/vmlinuz-3.13.0-43-generic /etc/NetworkManager/NetworkManager.conf I really appreciate your help. Best Tauqeer On Mon, Apr 13, 2015 at 10:28 AM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 13/04/15 14:12, Tim Booth wrote: > > [...] > > As for the files you listed, /usr/bin/formatrpsdb is part of the BLAST > > package, so reinstall 'blast2' just to be sure. I don't recognise the > > others, and I'd not expect any .jar file to be living in either /usr/bin > > or /usr/local/bin. > > [...] > > Hi, Tim. > > These are from Samtools. > > seq_cache_populate.pl: > > > > https://github.com/samtools/samtools/blob/b7ac1e2819ab85d5950eb2ce02434aa422fe39ed/misc/seq_cache_populate.pl > > htsjdk-1.119.jar: > > > https://github.com/samtools/htsjdk/tree/1.119 > > [A version of Samtools could have been installed manually] > > HTH, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Apr 14 05:00:37 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 14 Apr 2015 10:00:37 +0100 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: References: <1428930776.2822.72.camel@wllt1771.nerc-wallingford.ac.uk> <552BD27E.2050203@minke-informatics.co.uk> Message-ID: <1429002037.2822.98.camel@wllt1771.nerc-wallingford.ac.uk> Hi Tauqeer, I can't see any actual problems there at all, so I'd just leave it. I get way more warnings than that if I run debsums on my own machine. TIM On Tue, 2015-04-14 at 00:30 +0100, Tauqeer Alam wrote: > Thanks Tony and Tim. > > > Yes, I had installed new version of samtools recently (after > un-installing the older one through Ubuntu Software Center), so I will > leave those three files in the /usr/local/bin/. > > > I first tried Tony's suggestions of using "sudo debsums -ac" command > to find out if there are any missing files in my "/bin". > I got the following output. I understand the lines related to Brother > printer which I once tried to install (un-successfully). I also have > chromium browser installed. Do I have to install any of these missing > files and how do I do that? > > > :~$ sudo debsums -ac > debsums: missing file /etc/firefox/profile/localstore.rdf (from > bio-linux-themes-v8 package) > debsums: missing file /etc/firefox/profile/bookmarks.html (from > bio-linux-themes-v8 package) > debsums: missing file /etc/firefox/profile/prefs.js (from > bio-linux-themes-v8 package) > debsums: missing file /etc/default/chromium-browser (from > chromium-browser package) > /etc/default/cups > /etc/grub.d/10_linux > /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWrc > /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWfunc > debsums: missing file /usr/share/doc/hl2270dwlpr/copyright (from > hl2270dwlpr package) > debsums: missing file /usr/share/doc/hl2270dwlpr/changelog.Debian.gz > (from hl2270dwlpr package) > debsums: missing file /usr/share/doc/ia32-libs-multiarch/changelog.gz > (from ia32-libs-multiarch package) > /boot/vmlinuz-3.13.0-43-generic > /etc/NetworkManager/NetworkManager.conf > > > I really appreciate your help. > > > Best > > > Tauqeer > > > > > > > > On Mon, Apr 13, 2015 at 10:28 AM, Tony Travis > wrote: > On 13/04/15 14:12, Tim Booth wrote: > > [...] > > As for the files you listed, /usr/bin/formatrpsdb is part of > the BLAST > > package, so reinstall 'blast2' just to be sure. I don't > recognise the > > others, and I'd not expect any .jar file to be living in > either /usr/bin > > or /usr/local/bin. > > [...] > > Hi, Tim. > > These are from Samtools. > > seq_cache_populate.pl: > > > > https://github.com/samtools/samtools/blob/b7ac1e2819ab85d5950eb2ce02434aa422fe39ed/misc/seq_cache_populate.pl > > htsjdk-1.119.jar: > > > https://github.com/samtools/htsjdk/tree/1.119 > > [A version of Samtools could have been installed manually] > > HTH, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company > No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, > Scotland (UK) > tel. +44(0)19755 63548 > http://minke-informatics.co.uk > mob. +44(0)7985 078324 > mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > > -- > ********************************************* > Md Tauqeer Alam, Ph.D > Division of Infectious Diseases > Emory University School of Medicine > 615 Michael Street, Atlanta, GA 30322, USA > tauqeer9 at gmail.com > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tony.travis at minke-informatics.co.uk Tue Apr 14 05:16:08 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 14 Apr 2015 10:16:08 +0100 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: References: <1428930776.2822.72.camel@wllt1771.nerc-wallingford.ac.uk> <552BD27E.2050203@minke-informatics.co.uk> Message-ID: <552CDAD8.6050802@minke-informatics.co.uk> On 14/04/15 00:30, Tauqeer Alam wrote: > [...] Do I have to install any of these missing > files and how do I do that? > > :~$ sudo debsums -ac > debsums: missing file /etc/firefox/profile/localstore.rdf (from > bio-linux-themes-v8 package) > debsums: missing file /etc/firefox/profile/bookmarks.html (from > bio-linux-themes-v8 package) > debsums: missing file /etc/firefox/profile/prefs.js (from > bio-linux-themes-v8 package) > debsums: missing file /etc/default/chromium-browser (from > chromium-browser package) > /etc/default/cups > /etc/grub.d/10_linux > /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWrc > /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWfunc > debsums: missing file /usr/share/doc/hl2270dwlpr/copyright (from > hl2270dwlpr package) > debsums: missing file /usr/share/doc/hl2270dwlpr/changelog.Debian.gz > (from hl2270dwlpr package) > debsums: missing file /usr/share/doc/ia32-libs-multiarch/changelog.gz > (from ia32-libs-multiarch package) > /boot/vmlinuz-3.13.0-43-generic > /etc/NetworkManager/NetworkManager.conf Hi, Tauqeer. No, I don't think any of your missing/changed files are a result of accidentally moving files from /bin/* to /usr/local/bin/* and back. Here's the output from the same command on my laptop "beluga": > ajt at beluga:~$ sudo debsums -ac > [sudo] password for ajt: > /opt/avg/av/var/data/incavi.avm > /opt/avg/av/cfg/updatecomps.cfg > /opt/avg/av/lib/libavgcore.so > debsums: missing file /etc/firefox/profile/localstore.rdf (from bio-linux-themes-v8 package) > debsums: missing file /etc/firefox/profile/bookmarks.html (from bio-linux-themes-v8 package) > debsums: missing file /etc/firefox/profile/prefs.js (from bio-linux-themes-v8 package) > /etc/boinc-client/global_prefs_override.xml > /etc/default/chaosvpn > /etc/tinc/chaosvpn.conf > /etc/default/crda > /etc/cups/cupsd.conf > /etc/cups/cups-browsed.conf > /etc/default/cups > /etc/gnome/defaults.list > /etc/fuse.conf > /etc/dconf/db/gdm > /etc/grub.d/10_linux > debsums: missing file /usr/share/doc/ia32-libs-multiarch/changelog.gz (from ia32-libs-multiarch package) > /etc/iproute2/ematch_map > /etc/dhcp/dhcpd.conf > debsums: missing file /etc/gtk-2.0/im-multipress.conf (from libgtk2.0-common package) > debsums: no md5sums for libjson0:amd64 > debsums: no md5sums for libjson0:i386 > /etc/sane.d/dll.conf > /etc/sane.d/dll.conf > /etc/mime.types > /etc/modprobe.d/blacklist-framebuffer.conf > /etc/init.d/networking > /etc/logrotate.d/postgresql-common > /etc/sysctl.conf > /var/lib/smartmontools/drivedb/drivedb.h > /etc/update-motd.d/91-release-upgrade > /etc/cron.daily/upgrade-system > /etc/upgrade-system.conf I've installed some packages that you don't have and changed various config files, but I've also got some of the same "missing file" warnings as you. Tim might be interested in fixing some of these :-) Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tauqeer9 at gmail.com Tue Apr 14 22:28:10 2015 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Tue, 14 Apr 2015 22:28:10 -0400 Subject: [Bio-Linux] Fwd: undo mv command In-Reply-To: <552CDAD8.6050802@minke-informatics.co.uk> References: <1428930776.2822.72.camel@wllt1771.nerc-wallingford.ac.uk> <552BD27E.2050203@minke-informatics.co.uk> <552CDAD8.6050802@minke-informatics.co.uk> Message-ID: Hi Tony and Tim I really appreciate your help and as you have advised I am not going to change anything else. My computer is working fine. Thanks again! Tauqeer On Tue, Apr 14, 2015 at 5:16 AM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 14/04/15 00:30, Tauqeer Alam wrote: > > [...] Do I have to install any of these missing > > files and how do I do that? > > > > :~$ sudo debsums -ac > > debsums: missing file /etc/firefox/profile/localstore.rdf (from > > bio-linux-themes-v8 package) > > debsums: missing file /etc/firefox/profile/bookmarks.html (from > > bio-linux-themes-v8 package) > > debsums: missing file /etc/firefox/profile/prefs.js (from > > bio-linux-themes-v8 package) > > debsums: missing file /etc/default/chromium-browser (from > > chromium-browser package) > > /etc/default/cups > > /etc/grub.d/10_linux > > /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWrc > > /usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWfunc > > debsums: missing file /usr/share/doc/hl2270dwlpr/copyright (from > > hl2270dwlpr package) > > debsums: missing file /usr/share/doc/hl2270dwlpr/changelog.Debian.gz > > (from hl2270dwlpr package) > > debsums: missing file /usr/share/doc/ia32-libs-multiarch/changelog.gz > > (from ia32-libs-multiarch package) > > /boot/vmlinuz-3.13.0-43-generic > > /etc/NetworkManager/NetworkManager.conf > > Hi, Tauqeer. > > No, I don't think any of your missing/changed files are a result of > accidentally moving files from /bin/* to /usr/local/bin/* and back. > > Here's the output from the same command on my laptop "beluga": > > > ajt at beluga:~$ sudo debsums -ac > > [sudo] password for ajt: > > /opt/avg/av/var/data/incavi.avm > > /opt/avg/av/cfg/updatecomps.cfg > > /opt/avg/av/lib/libavgcore.so > > debsums: missing file /etc/firefox/profile/localstore.rdf (from > bio-linux-themes-v8 package) > > debsums: missing file /etc/firefox/profile/bookmarks.html (from > bio-linux-themes-v8 package) > > debsums: missing file /etc/firefox/profile/prefs.js (from > bio-linux-themes-v8 package) > > /etc/boinc-client/global_prefs_override.xml > > /etc/default/chaosvpn > > /etc/tinc/chaosvpn.conf > > /etc/default/crda > > /etc/cups/cupsd.conf > > /etc/cups/cups-browsed.conf > > /etc/default/cups > > /etc/gnome/defaults.list > > /etc/fuse.conf > > /etc/dconf/db/gdm > > /etc/grub.d/10_linux > > debsums: missing file /usr/share/doc/ia32-libs-multiarch/changelog.gz > (from ia32-libs-multiarch package) > > /etc/iproute2/ematch_map > > /etc/dhcp/dhcpd.conf > > debsums: missing file /etc/gtk-2.0/im-multipress.conf (from > libgtk2.0-common package) > > debsums: no md5sums for libjson0:amd64 > > debsums: no md5sums for libjson0:i386 > > /etc/sane.d/dll.conf > > /etc/sane.d/dll.conf > > /etc/mime.types > > /etc/modprobe.d/blacklist-framebuffer.conf > > /etc/init.d/networking > > /etc/logrotate.d/postgresql-common > > /etc/sysctl.conf > > /var/lib/smartmontools/drivedb/drivedb.h > > /etc/update-motd.d/91-release-upgrade > > /etc/cron.daily/upgrade-system > > /etc/upgrade-system.conf > > I've installed some packages that you don't have and changed various > config files, but I've also got some of the same "missing file" warnings > as you. Tim might be interested in fixing some of these :-) > > Bye, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ian.Donaldson at manchester.ac.uk Tue Apr 21 06:18:25 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Tue, 21 Apr 2015 10:18:25 +0000 Subject: [Bio-Linux] GALAXY version and failure to install a tool from the toolshed Message-ID: <7E756F18289AF64B967C333AC3BF7021018241067F@MBXP02.ds.man.ac.uk> Hi, We have been trying to prepare a suite of tools to use on our production GALAXY instance and on a Bio-Linux 8 VM instance (for the purpose of running tutorials). The tool in the link below installs correctly on our GALAXY (a clone of galaxy-dist from bitbucket, changeset 16062:a7ae7afffa8f ), but does not install correctly in Bio-Linux. https://testtoolshed.g2.bx.psu.edu/view/pjbriggs/macs21/9f6d5cae9181 All we can say at the moment is that the older version handles the installation differently... Is it possible to update the version of GALAXY in Bio-Linux, or there some other work around to get the tool installed? Thank you, Ian -------------- next part -------------- An HTML attachment was scrubbed... URL: From kissaj at miamioh.edu Tue Apr 21 14:47:10 2015 From: kissaj at miamioh.edu (Andor J Kiss) Date: Tue, 21 Apr 2015 14:47:10 -0400 Subject: [Bio-Linux] QIIME 1.9 biom cmd issue Message-ID: <1429642030.6894.4.camel@methy1> Hi, Trying to run the command biom summarize-table and I'm getting an error: biom [ 2:47PM] usage: biom [] The currently available commands are: add-metadata Add metadata to a BIOM table convert Convert to/from the BIOM table format normalize-table Normalize a BIOM table show-install-info Provide information about the biom-format installation subset-table Subset a BIOM table validate-table Validate a BIOM-formatted file The following commands could not be loaded: summarize-table Error: cannot import name write_or_print_list_of_strings Any ideas on how to fix? Thanks, -- __________________________________________________________________ Andor J Kiss, Supervisor Center for Bioinformatics and Functional Genomics 086 Pearson Hall ~ Miami University 700 East High Street Oxford, Ohio 45056 USA eMAIL: kissaj at MiamiOH.edu Telephone: +1 (513) 529-4280 Fax: +1 (513) 529-2431 URL (CBFG): http://www.cas.miamioh.edu/cbfg/ URL (CBFG Services): https://www.scienceexchange.com/labs/center-for-bioinformatics-functional-genomics URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Wed Apr 22 06:01:18 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 22 Apr 2015 11:01:18 +0100 Subject: [Bio-Linux] GALAXY version and failure to install a tool from the toolshed In-Reply-To: <7E756F18289AF64B967C333AC3BF7021018241067F@MBXP02.ds.man.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021018241067F@MBXP02.ds.man.ac.uk> Message-ID: <1429696878.9233.34.camel@wllt1771.nerc-wallingford.ac.uk> Hi Ian, I'm wary of upgrading the Galaxy package, because unless it gets a whole load of testing it tends to break people's exiting configurations and workflows. I'll do it at some point, but not soon. Certainly some stuff from the Tool Shed is still installing fine, so I'm wondering if it might be possible to persuade this package to install and just add it in to the galaxy-tools-bl package. All Tool Shed installation actually does, despite the big song-and-dance you see in the web interface, is to copy a few files into a directory. This would be much easier for me to do than upgrading Galaxy. Do you think it would solve your problem? How are you installing the actual macs21 tool? Bio-Linux still has only macs20 just now but I could upgrade it. If the version of Galaxy on Bio-Linux is giving you trouble and you are happy with your BitBucket installation then you could always try removing galaxy-server from the VM image and cloning the configuration you have working. On Bio-Linux I tried to make Galaxy set-up "smart" and "foolproof" but the downside of that is that if something goes wrong, or needs manual updating, it can be very confusing, so if my version is doing more harm than good you don't have to use it. Cheers, TIM On Tue, 2015-04-21 at 11:18 +0100, Ian Donaldson wrote: > Hi, > > We have been trying to prepare a suite of tools to use on our > production GALAXY instance and on a Bio-Linux 8 VM instance (for the > purpose of running tutorials). The tool in the link below installs > correctly on our GALAXY (a clone of galaxy-dist from bitbucket, > changeset 16062:a7ae7afffa8f ), but does not install correctly in > Bio-Linux. > > https://testtoolshed.g2.bx.psu.edu/view/pjbriggs/macs21/9f6d5cae9181 > > All we can say at the moment is that the older version handles the > installation differently... Is it possible to update the version of > GALAXY in Bio-Linux, or there some other work around to get the tool > installed? > > Thank you, > Ian > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tbooth at ceh.ac.uk Wed Apr 22 12:53:48 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 22 Apr 2015 17:53:48 +0100 Subject: [Bio-Linux] QIIME 1.9 biom cmd issue In-Reply-To: <1429642030.6894.4.camel@methy1> References: <1429642030.6894.4.camel@methy1> Message-ID: <1429721628.9233.60.camel@wllt1771.nerc-wallingford.ac.uk> Hi Andor, Looks like I neglected to update the "pyqi" library when I updated QIIME. I've now pushed an updated package and the obvious error message is gone. Could you please see if that fixes it for you? Cheers, TIM On Tue, 2015-04-21 at 19:47 +0100, Andor J Kiss wrote: > Hi, > > Trying to run the command biom summarize-table and I'm getting an > error: > > biom > [ 2:47PM] > usage: biom [] > > The currently available commands are: > add-metadata Add metadata to a BIOM table > convert Convert to/from the BIOM table format > normalize-table Normalize a BIOM table > show-install-info Provide information about the biom-format > installation > subset-table Subset a BIOM table > validate-table Validate a BIOM-formatted file > > The following commands could not be loaded: > summarize-table Error: cannot import name > write_or_print_list_of_strings > > Any ideas on how to fix? > > Thanks, > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From kissaj at miamioh.edu Wed Apr 22 14:49:19 2015 From: kissaj at miamioh.edu (Andor J Kiss) Date: Wed, 22 Apr 2015 14:49:19 -0400 Subject: [Bio-Linux] QIIME 1.9 biom cmd issue In-Reply-To: <1429721628.9233.60.camel@wllt1771.nerc-wallingford.ac.uk> References: <1429642030.6894.4.camel@methy1> <1429721628.9233.60.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <1429728559.25962.24.camel@methy1> will do - thanks! -- __________________________________________________________________ Andor J Kiss, Supervisor Center for Bioinformatics and Functional Genomics 086 Pearson Hall ~ Miami University 700 East High Street Oxford, Ohio 45056 USA eMAIL: kissaj at MiamiOH.edu Telephone: +1 (513) 529-4280 Fax: +1 (513) 529-2431 URL (CBFG): http://www.cas.miamioh.edu/cbfg/ URL (CBFG Services): https://www.scienceexchange.com/labs/center-for-bioinformatics-functional-genomics URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss On Wed, 2015-04-22 at 17:53 +0100, Tim Booth wrote: > Hi Andor, > > Looks like I neglected to update the "pyqi" library when I updated > QIIME. I've now pushed an updated package and the obvious error message > is gone. Could you please see if that fixes it for you? > > Cheers, > > TIM > > On Tue, 2015-04-21 at 19:47 +0100, Andor J Kiss wrote: > > Hi, > > > > Trying to run the command biom summarize-table and I'm getting an > > error: > > > > biom > > [ 2:47PM] > > usage: biom [] > > > > The currently available commands are: > > add-metadata Add metadata to a BIOM table > > convert Convert to/from the BIOM table format > > normalize-table Normalize a BIOM table > > show-install-info Provide information about the biom-format > > installation > > subset-table Subset a BIOM table > > validate-table Validate a BIOM-formatted file > > > > The following commands could not be loaded: > > summarize-table Error: cannot import name > > write_or_print_list_of_strings > > > > Any ideas on how to fix? > > > > Thanks, > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From kissaj at miamioh.edu Wed Apr 22 15:06:16 2015 From: kissaj at miamioh.edu (Andor J Kiss) Date: Wed, 22 Apr 2015 15:06:16 -0400 Subject: [Bio-Linux] QIIME 1.9 biom cmd issue In-Reply-To: <1429721628.9233.60.camel@wllt1771.nerc-wallingford.ac.uk> References: <1429642030.6894.4.camel@methy1> <1429721628.9233.60.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <1429729576.25962.28.camel@methy1> Hi Tim, That solved it! Thanks, -- __________________________________________________________________ Andor J Kiss, Supervisor Center for Bioinformatics and Functional Genomics 086 Pearson Hall ~ Miami University 700 East High Street Oxford, Ohio 45056 USA eMAIL: kissaj at MiamiOH.edu Telephone: +1 (513) 529-4280 Fax: +1 (513) 529-2431 URL (CBFG): http://www.cas.miamioh.edu/cbfg/ URL (CBFG Services): https://www.scienceexchange.com/labs/center-for-bioinformatics-functional-genomics URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss On Wed, 2015-04-22 at 17:53 +0100, Tim Booth wrote: > Hi Andor, > > Looks like I neglected to update the "pyqi" library when I updated > QIIME. I've now pushed an updated package and the obvious error message > is gone. Could you please see if that fixes it for you? > > Cheers, > > TIM > > On Tue, 2015-04-21 at 19:47 +0100, Andor J Kiss wrote: > > Hi, > > > > Trying to run the command biom summarize-table and I'm getting an > > error: > > > > biom > > [ 2:47PM] > > usage: biom [] > > > > The currently available commands are: > > add-metadata Add metadata to a BIOM table > > convert Convert to/from the BIOM table format > > normalize-table Normalize a BIOM table > > show-install-info Provide information about the biom-format > > installation > > subset-table Subset a BIOM table > > validate-table Validate a BIOM-formatted file > > > > The following commands could not be loaded: > > summarize-table Error: cannot import name > > write_or_print_list_of_strings > > > > Any ideas on how to fix? > > > > Thanks, > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mpozud00 at gmail.com Thu Apr 23 05:00:06 2015 From: mpozud00 at gmail.com (MARTA POZUELO DEL RIO) Date: Thu, 23 Apr 2015 11:00:06 +0200 Subject: [Bio-Linux] Biolinux QIIME 1.9.0 release errors Message-ID: Good morning, After having installed the new release of qiime in my biolinux, and starting to use the pipeline I used for QIIME 1.8.0, I get the following errors in two scripts for the moment, even when calling the help options. 1. For pick_otus.py script: File "/usr/local/bin/pick_otus.py", line 18, in from qiime.util import get_tmp_filename ImportError: cannot import name get_tmp_filename 2. For split_libraries_fastq.py script: Traceback (most recent call last): File "/usr/local/bin/split_libraries_fastq.py", line 25, in from qiime.quality import phred_to_ascii33, phred_to_ascii64 For the second case, I've seen that this module disappears in QIIME 1.9.0, the script quality.py does not exist any more. So having a look at the scripts included in the packages for biolinux release, I've found that the version of these scripts used comes from QIIME 1.6.0. Hope this will be solved as soon as possible! Thanks in advance. Marta -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu Apr 23 07:16:24 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 23 Apr 2015 12:16:24 +0100 Subject: [Bio-Linux] Biolinux QIIME 1.9.0 release errors In-Reply-To: References: Message-ID: <1429787784.29817.38.camel@wllt1771.nerc-wallingford.ac.uk> Hi Marta, This seems to be an issue with old files being on your machine after the update. As you say, these seem to be a relic from QIIME 1.6, and should not be there. To help me diagnose the problem, could you please run the following four commands: dpkg -S /usr/local/bin/pick_otus.py dpkg -S /usr/local/bin/split_libraries_fastq.py apt-cache policy qiime apt-cache policy bio-linux-qiime And send me the results. Thanks, TIM On Thu, 2015-04-23 at 10:00 +0100, MARTA POZUELO DEL RIO wrote: > Good morning, > > > After having installed the new release of qiime in my biolinux, and > starting to use the pipeline I used for QIIME 1.8.0, I get the > following errors in two scripts for the moment, even when calling the > help options. > > > 1. For pick_otus.py script: > > File "/usr/local/bin/pick_otus.py", line 18, in > from qiime.util import get_tmp_filename > ImportError: cannot import name get_tmp_filename > > > 2. For split_libraries_fastq.py script: > > Traceback (most recent call last): > File "/usr/local/bin/split_libraries_fastq.py", line 25, in > from qiime.quality import phred_to_ascii33, phred_to_ascii64 > > > > > For the second case, I've seen that this module disappears in QIIME > 1.9.0, the script quality.py does not exist any more. So having a look > at the scripts included in the packages for biolinux release, I've > found that the version of these scripts used comes from QIIME 1.6.0. > > > Hope this will be solved as soon as possible! > > > Thanks in advance. > > > Marta > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From Ian.Donaldson at manchester.ac.uk Thu Apr 23 10:03:36 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Thu, 23 Apr 2015 14:03:36 +0000 Subject: [Bio-Linux] GALAXY version and failure to install a tool from the toolshed In-Reply-To: <1429696878.9233.34.camel@wllt1771.nerc-wallingford.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021018241067F@MBXP02.ds.man.ac.uk>, <1429696878.9233.34.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <7E756F18289AF64B967C333AC3BF7021018241095B@MBXP02.ds.man.ac.uk> Dear Tim, Thanks for your detailed reply! The essence of the problem is that our MACS2 tool has a few dependencies that need to be installed in order, which is something the Bio-Linux version cannot do and newer versions can. My aim is to give a set of ChIP-seq tutorials and allow people to run the analyses themselves using Galaxy in Bio-Linux. Bio-Linux Galaxy is great as it works out of the box, however several tweaks are needed already, so I don't think getting people to reinstall Galaxy is an option. The MACS2 tool installs MACS2.1.0 including numpy. Pre-installing MACS2.1.0 seems to be an option, as even if the installation fails MACS2 would still be available. However I do not know how this effects the distribution of the VM. Regards, Ian ________________________________________ From: Tim Booth [tbooth at ceh.ac.uk] Sent: 22 April 2015 11:01 To: Bio-Linux help and discussion Cc: Peter Briggs Subject: Re: [Bio-Linux] GALAXY version and failure to install a tool from the toolshed Hi Ian, I'm wary of upgrading the Galaxy package, because unless it gets a whole load of testing it tends to break people's exiting configurations and workflows. I'll do it at some point, but not soon. Certainly some stuff from the Tool Shed is still installing fine, so I'm wondering if it might be possible to persuade this package to install and just add it in to the galaxy-tools-bl package. All Tool Shed installation actually does, despite the big song-and-dance you see in the web interface, is to copy a few files into a directory. This would be much easier for me to do than upgrading Galaxy. Do you think it would solve your problem? How are you installing the actual macs21 tool? Bio-Linux still has only macs20 just now but I could upgrade it. If the version of Galaxy on Bio-Linux is giving you trouble and you are happy with your BitBucket installation then you could always try removing galaxy-server from the VM image and cloning the configuration you have working. On Bio-Linux I tried to make Galaxy set-up "smart" and "foolproof" but the downside of that is that if something goes wrong, or needs manual updating, it can be very confusing, so if my version is doing more harm than good you don't have to use it. Cheers, TIM On Tue, 2015-04-21 at 11:18 +0100, Ian Donaldson wrote: > Hi, > > We have been trying to prepare a suite of tools to use on our > production GALAXY instance and on a Bio-Linux 8 VM instance (for the > purpose of running tutorials). The tool in the link below installs > correctly on our GALAXY (a clone of galaxy-dist from bitbucket, > changeset 16062:a7ae7afffa8f ), but does not install correctly in > Bio-Linux. > > https://testtoolshed.g2.bx.psu.edu/view/pjbriggs/macs21/9f6d5cae9181 > > All we can say at the moment is that the older version handles the > installation differently... Is it possible to update the version of > GALAXY in Bio-Linux, or there some other work around to get the tool > installed? > > Thank you, > Ian > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Fri Apr 24 09:11:02 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 24 Apr 2015 14:11:02 +0100 Subject: [Bio-Linux] [Biolinux] QIIME 1.9.0 release errors info required In-Reply-To: References: Message-ID: <1429881062.29817.101.camel@wllt1771.nerc-wallingford.ac.uk> Hi Marta, No worries. I suspected that this was the case but I wanted to be sure the package installation was right before I told you to start removing things. Good luck with your data analysis. Cheers, TIM On Fri, 2015-04-24 at 13:08 +0100, MARTA POZUELO DEL RIO wrote: > Hi Tim, > > > Sorry to bother you. We have found out that a previous partner had > copied qiime 1.6.0 scripts in our /usr/local/bin folder, so, removing > them from it, qiime now takes scripts > from /usr/lib/qiime/bin/pick_otus.py where the new scripts have been > installed. So the problem is solved. > > > Thanks very much for your time. > > > Marta > > > 2015-04-24 13:23 GMT+02:00 MARTA POZUELO DEL RIO : > Hi Tim, > > > I've run the commands you asked me for on my computer and > these are the results: > > dpkg -S /usr/local/bin/pick_otus.py > dpkg-query: no path found matching > pattern /usr/local/bin/pick_otus.py > > dpkg -S /usr/local/bin/split_libraries_fastq.py > dpkg-query: no path found matching > pattern /usr/local/bin/split_libraries_fastq.py > > apt-cache policy qiime > qiime: > Installed: 1.9.0+dfsg-0biolinux5 > Candidate: 1.9.0+dfsg-0biolinux5 > Version table: > *** 1.9.0+dfsg-0biolinux5 0 > 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ > trusty/main amd64 Packages > 100 /var/lib/dpkg/status > 1.8.0+dfsg-2 0 > 500 http://gb.archive.ubuntu.com/ubuntu/ > trusty/universe amd64 Packages > > apt-cache policy bio-linux-qiime > bio-linux-qiime: > Installed: 2:1bl-10 > Candidate: 2:1bl-10 > Version table: > *** 2:1bl-10 0 > 500 http://nebc.nerc.ac.uk/bio-linux/ > unstable/bio-linux amd64 Packages > 100 /var/lib/dpkg/status > > > > When calling qiime and running print_qiime_config_all I also > get this: > > QIIME library version: 1.9.0 > QIIME script version: 1.6.0 > > > > When opening these scripts contained in folder /usr/local/bin, > they are from version 1.6.0, but when checking the package > installed (/usr/lib/python2.7/dist-packages/qiime/), these > scripts are from version 1.9.0. > > > Hope this will help. > > > > Thanks, > > > Marta > > > > > > > > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tbooth at ceh.ac.uk Mon Apr 27 04:47:17 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 27 Apr 2015 09:47:17 +0100 Subject: [Bio-Linux] (no subject) In-Reply-To: References: Message-ID: <1430124437.29817.138.camel@wllt1771.nerc-wallingford.ac.uk> Hi Roy, If you want to run a BLAST search without downloading the database you can use the -remote flag, so: blastp -query PROTEIN_SEQ.fa -db nr -out PROTEIN_SEQ.blast -remote But because this uses the processing power on the NCBI servers it will potentially be a lot slower than downloading the database for yourself, so if you are processing a whole lot of sequences you should probably download the database files from FTP first. Cheers, TIM On Sat, 2015-04-25 at 18:53 +0100, Roy Lee wrote: > > > > > > >My name is Roy Lee. With Hunter College in New York city. > > >When I am running a blast search from the command line for a > protein fasta > > >file, I keep getting asked where the nr reference database is. May > you please > > >let me know what I need to do to access that database on my blast > search? I > > >don\'t think I should be downloading a 15GB database onto my ubuntu > VM. > > > > > >I\'m in the ubuntu terminal , so far, I\'ve written > > > > > >$ blastp -query PROTEIN SEQ.fa -db $blastdb/nr -out PROTEIN > SEQ.blast > > > > > > > > >I keep getting the error message that the nr database is > non-existent. Would > > >you happen to know where this database is? Thanks. > > >Thanks for your help. > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From rlee03 at gmail.com Sat Apr 25 13:53:56 2015 From: rlee03 at gmail.com (Roy Lee) Date: Sat, 25 Apr 2015 13:53:56 -0400 Subject: [Bio-Linux] (no subject) Message-ID: > > > >My name is Roy Lee. With Hunter College in New York city. > >When I am running a blast search from the command line for a protein fasta > >file, I keep getting asked where the nr reference database is. May you please > >let me know what I need to do to access that database on my blast search? I > >don\'t think I should be downloading a 15GB database onto my ubuntu VM. > > > >I\'m in the ubuntu terminal , so far, I\'ve written > > > >$ blastp -query PROTEIN SEQ.fa -db $blastdb/nr -out PROTEIN SEQ.blast > > > > > >I keep getting the error message that the nr database is non-existent. Would > >you happen to know where this database is? Thanks. > >Thanks for your help. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paumarc at gmail.com Thu Apr 30 08:04:06 2015 From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=) Date: Thu, 30 Apr 2015 14:04:06 +0200 Subject: [Bio-Linux] problems with mysql Message-ID: Hello everybody i have a problem with mysql, i tired to change the persmiossions to acces to it remotelly, to this objective i loged as a root > mysql -u root -p and i ejecute GRANT ALL ON *.* TO myuser@'remote_ip' IDENTIFIED BY 'my_password'; Now mysql fails to restart what can i do? p Pau Marc Mu?oz Torres skype: pau_marc http://www.linkedin.com/in/paumarc http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Thu Apr 30 08:18:46 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 30 Apr 2015 13:18:46 +0100 Subject: [Bio-Linux] problems with mysql In-Reply-To: References: Message-ID: <55421DA6.3010602@minke-informatics.co.uk> On 30/04/15 13:04, Pau Marc Mu?oz Torres wrote: > GRANT ALL ON *.* TO myuser@'remote_ip' IDENTIFIED BY 'my_password'; Hi, Pau. I'm not sure "privileges" is optional in a GRANT - I would have used: > grant all privileges on *.* to 'root'@'remote_ip' with grant option; However, I think it is a BIG security hole to expose MySQL on the public Internet - Please beware of doing that :-( If you're locked out, try: > stop mysql > mysqld_safe --skip-grant-tables& > mysql > use mysql; > update user set password=PASSWORD("")where User='root'; > flush privileges; > quit That's got me out of quite a few dark holes in the past :-) HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From paumarc at gmail.com Thu Apr 30 08:28:41 2015 From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=) Date: Thu, 30 Apr 2015 14:28:41 +0200 Subject: [Bio-Linux] problems with mysql In-Reply-To: <55421DA6.3010602@minke-informatics.co.uk> References: <55421DA6.3010602@minke-informatics.co.uk> Message-ID: thanks tony Pau Marc Mu?oz Torres skype: pau_marc http://www.linkedin.com/in/paumarc http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ 2015-04-30 14:18 GMT+02:00 Tony Travis : > On 30/04/15 13:04, Pau Marc Mu?oz Torres wrote: > > GRANT ALL ON *.* TO myuser@'remote_ip' IDENTIFIED BY 'my_password'; > > Hi, Pau. > > I'm not sure "privileges" is optional in a GRANT - I would have used: > > > grant all privileges on *.* to 'root'@'remote_ip' with grant option; > > However, I think it is a BIG security hole to expose MySQL on the public > Internet - Please beware of doing that :-( > > If you're locked out, try: > > > stop mysql > > mysqld_safe --skip-grant-tables& > > mysql > > use mysql; > > update user set password=PASSWORD("")where User='root'; > > flush privileges; > > quit > > That's got me out of quite a few dark holes in the past :-) > > HTH, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... 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