Re: [galaxy-dev] number of dataset files within 000
Hi Shantanu The first 999 datasets will be stored in '000'. And the next one, ie: dataset_1000.dat, will be stored in '001', and so on. Regards, Hans On 6/23/11 5:44 AM, "Shantanu Pavgi" wrote: > Hi, > > The galaxy dataset files (file_path) are arranged within a subdirectory '000' > (database/files/000). Will galaxy create a new subdirectory for storing > datasets files after certain file count value is reached(say ~ 1000)? It may > not be a problem while using web interface, but I am wondering if this could > be a problem if user tries filesystem info commands from shell - e.g regular > ls command output. Also, curious to know if subdirectory name '000' signifies > something here? > > -- > Thanks, > Shantanu > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy Tool permission/Access
On 09/19/2011 04:35 PM, sohk...@notes.cc.sunysb.edu wrote:
> Hi,
>
> I am wondering if there is way to manage user access to Galaxy tools?
>
> I.E, certain users are restricted to use certain tools.
> Thanks.
Hi Sohail
We use a 'quick and dirty' solution by enforcing log-in and then taking
advantage of the reserved variables "$__user_email__"
(see: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax)
add "$__user_email__" to the command line, eg:
access_data.pl $dir $userEmail $output
and then use a little wrapper, or do the test in the script itself, eg:
my $priv_user = "geek\@fmi.ch";
my $file = $ARGV[0];
my $user = $ARGV[1];
unless ($user eq $priv_user) {
print "you don't have access to this data";
exit; }
open (FILE, "$file");
...
of coursde, instead of hard coding, you can expand this by using a little
database where you store all the 'privileged users'.
Regards, Hans
>
> -Sohail
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>http://lists.bx.psu.edu/
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-dev] Running galaxy on external hard drive
Hi Alessia Well, I am not a linux system expert, but I don't see a reason, why you can't run Galaxy from an external drive as long as it is mounted correctly and you have all the read and write permissions. The basic installation of Galaxy does not need any modification. The configuration files are created when you start the server for the first time with " sh run.sh ". Are you sure, you are using a 'clean' installation? or have you moved it around? I recommend you start again from scratch, following the steps explained on the wiki: http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy Regards, Hans On 10/31/11 10:10 PM, "Alessia D" wrote: > Hi Hans, > > Thanks for your reply.The error I am getting is "Can't open folder > /media/..." > But I guess my question was more in general if I can have Galaxy run from > an external drive so that it saves everything on it instead of /home, and > if so, how (modifications etc..) > > Thanks > > A > > > > > > > On Mon, Oct 31, 2011 at 11:25 AM, Hans-Rudolf Hotz wrote: > >> Hi Allessia >> >> >> It is difficult to help you without knowing what kind of error you've >> got. >> >> What is the error message you get? >> >> >> Regards, Hans >> >> >> >> On 10/31/2011 03:35 PM, Alessia D wrote: >> >>> Hi, >>> >>> I am very new to Galaxy and so far have only used the online interface. >>> However, I have an old Unix-running computer and I was hoping to run >>> Galaxy as a local instance. However, the computer has a very small hard >>> drive, that is already half full, so I was wondering if there is any way I >>> can run Galaxy by installing it on an external hard drive. I tried >>> already, and was able to install it properly and connect, but I get errors >>> when I try to upload data. >>> >>> Any help would be greatly appreciated. I don't have a lot of experience >>> with Unix systems, so it might be something easy to solve or impossible to >>> do, I have no idea. >>> >>> Thanks! >>> >>> Alessia >>> >>> >>> >>> >>> __**_ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] unable to display text output
Hi Mark Quick answer: It could be an issue with your browser. Have you tried looking at your date with a different web browser and/or on a different machine? Long answer: Could you please clarify, as I can't really follow your description of the problemyou say: it is working if you change the data format manually to 'txt', but it is not working if you specify it as 'txt' in the tool xml? And when you specify it as 'txt' in the tool xml do you get "format: txt," in the history display? Regards, Hans-Rudolf On Jul 22, 2013, at 3:27 PM, mailto:mark.r...@syngenta.com>> wrote: Hi All I’m trying to format one of the three outputs of my galaxy tool as plain text. Thus far no matter how I specify my output format in the tool xml file I have the same problem. When I click the eye icon it opens a save dialog rather that displaying the text output in the central frame. The preview shows the text output and if I follow through and save the output and open with wordpad it is fine. Also if I edit the attributes of the output and change it to “txt” (which is one of the formats I had tried specifying in the xml) it will render in the central frame but I would rather not have to do that. Both of my other outputs (a vcf and a tab-delimited file) are rendered in the central frame properly. How do I to fix this? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-user] Install Galaxy on Mac
Hi Edward I am moving your e-mail to 'galaxy-dev' since it's about a local Galaxy instance. I don't think there are any differences between installing Galaxy on Linux and Mac OS X. Hence you can follow the step-by-step instructions on the wiki (well, there are actually only two steps anyway...): http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy WRT checking the python version: just type 'python -V' on the command line, eg on my old MacBook: bash-3.2$ python -V Python 2.5.1 bash-3.2$ Hope this helps Regards, Hans On 08/10/2012 02:37 PM, Edward Turk wrote: > Hello, > Could someone provide instructions for installing galaxy on a Mac OS 10.7? The instructions provided by galaxy start off by asking me to check my python version, but I don't know how to do that. I figure someone has step-by-step instructions or a screen cast? > Thank you, > Edward > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > >http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > >http://lists.bx.psu.edu/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Galaxy-related job opening at the FMI in Basel, Switzerland
Hi I apologize for abusing the list for a job add: We are looking for a R/Bioconductor person which is familiar with Galaxy to help us expanding our sets of NGS tools in Galaxy, see http://www.fmi.ch/Careers/JobDetails.html?jobID=158 Please feel free to contact me for more details Regards, Hans-Rudolf Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
