September 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Galaxy Tool permission/Access
by Hotz, Hans-Rudolf 20 Sep '11

20 Sep '11

On 09/19/2011 04:35 PM, sohkhan(a)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: <command interpreter="perl"> access_data.pl $dir $userEmail $output </command> and then use a little wrapper, or do the test in the script itself, eg: my $priv_user = "geek\(a)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/

1 0

Writing Galaxy Extensions involving Workflows
by Oren Livne 19 Sep '11

19 Sep '11

Dear All, I am a software developer, new to Galaxy. Is there a detailed document about the Galaxy code architecture, API, what runners are, and how to write a runner that has access to the workflow object model? I could not find this information on the Galaxy Wiki. I am especially interested in integrating Galaxy with an external scheduler software (I am aware of Galaxy's scheduling capabilities but we'd like to use our own). My goal is to intercept Galaxy workflow run events and send workflows to my scheduler.I could not find this information on the Galaxy Wiki. Thank you so much in advance, Oren Livne

1 0

Error Using Intersect Tool on Genomic Intervals
by Chamith Fonseka 19 Sep '11

19 Sep '11

Hello, I am trying to use Galaxy to intersect different sets of genomic intervals. When I do this, I get the following error. Skipped 10 invalid lines of 1st dataset, 1st line #20: "chr10 131694149 131694408", problem: 536870912 is larger than the size of this BitSet (536870912). I have tried using different sets of intervals, in both interval and BED format and used the two queries in different order in the intersect tool, but I cannot seem to resolve the problem. The error message will differ in the number of "invalid lines" skipped, but when I check the intervals they appear to be alright. Could anyone help? Thank you very much, Chamith Fonseka

1 0

Query related to BLAST
by Jennifer Jackson 19 Sep '11

19 Sep '11

Hi Kumar, I am going to forward this question to the Galaxy Development discussion list for others to offer input, but here are the basics: Wiki: http://galaxyproject.org/wiki/Admin/Tools/External%20Display%20Applications… Archived mailing list responses on this topic: http://gmod.827538.n3.nabble.com/galaxy-dev-adding-another-UCSC-mirror-to-d… http://gmod.827538.n3.nabble.com/UCSC-genome-browser-tt1911708.html#a2039796 http://gmod.827538.n3.nabble.com/Re-Genome-UCSC-browser-access-from-Galaxy-… Other configuration help: http://galaxyproject.org/wiki/Admin http://galaxyproject.org/wiki/Admin/Config/Apache%20Proxy http://galaxyproject.org/wiki/Admin/Data%20Integration http://galaxyproject.org/wiki/Config/Performance/Production%20Server Hopefully this helps! Best, Jen Galaxy team On 9/19/11 4:24 AM, kumar Saurabh wrote: > Dear Jen, > > Thank you for the reply. I have one more query. > > Currently, Galaxy tool is integrated with the UCSC genome browser and > that is the way it operates. You can retrieve any region from the human > and other available genome (Available with UCSC) and analyze the data or > create the workflows. We can even upload the data in various file formats. > > I was wondering if there is any option available or is it possible to > integrate the Galaxy tool with our own customised genome browser/genome > databases? I just would like to confirm if its possible to integrate the > local version of galaxy with our own genome browsers. If yes, can we > also connect it to multiple genome browsers? > > Best regards, > Kumar > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

1 0

MACS.html download error
by Susan Newman 19 Sep '11

19 Sep '11

Hi, I am running the public instance of Galaxy. I've successfully run multiple histories using MACS. Recently, I am unable to download the MACS.html file. The MACS steps have run successfully and they are green. When I click on the diskette icon to download I get this message "Unable to remove temporary download and archive file directory". In addition, I am sharing the history with another user. He sees a server error when he clicks any of the file links to the .xls files when he uses the eye icon to view the MACS.html data within Galaxy. I am able to use the links within my own Galaxy account. Thanks for your assistance, Susan Susan S. Newman, Laboratory Manager Genomics Core Facility, L2012 Pennington Biomedical Research Center 6400 Perkins Road Baton Rouge, LA 70808 225-763-0255 (o) 225-763-0257 (lab) http://gcf.pbrc.edu

1 0

Quick question regarding dist and central
by michael burrell (TSL) 19 Sep '11

19 Sep '11

Good afternoon, Just a quick question, is it possible to switch an installed version of galaxy from the central repository to the dist repo? Thanks Michael.

2 1

Galaxy Tool permission/Access
by sohkhan＠notes.cc.sunysb.edu 19 Sep '11

19 Sep '11

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. -Sohail

1 0

Galaxy test quotas
by Candace Seeve 19 Sep '11

19 Sep '11

I've deleted all of my histories and datasets and the status bar in the top right corner indicates that I am using 67% of my quotas. Is there any way to remove all data and jobs to return to 0%? Thanks.

3 2

outputting different numbers of files based on variables?
by Nikhil Joshi 16 Sep '11

16 Sep '11

Hi all, Is it possible to output a different number of files based on variables that the use has chosen? I have a program that will output different numbers of files based upon the input data. So, for example, if the user wants to use a single-end fastq file, the program outputs only one file, however, if the user chooses paired-end fastq files, it outputs three files. Is there any way to get that to work in just one tool? I could make separate tools for single vs. paired end, but I'd rather not. - Nik.

4 5

update for library
by Belinda M. Giardine 16 Sep '11

16 Sep '11

I have the files ready for an update to the Putative SNP phenotypes library. All the new files use hg19 coordinates. They should go either into a new library or put subdirectories under the first where you chose the build. What is the best way to add the metadata to these files? The files are located on draco.bx.psu.edu under /scratch/giardine/galaxyLib/. As I work on a poster for the ASHG and HGVS meetings I may think of more files to add. Belinda

1 0