Re: [galaxy-dev] Path to tool designation in tool config xml

2011-09-07 Thread Timothy Wu
Thanks, this helps. I was running with an interpreter and I didn't realize I had to had the full path in there. I was expecting that $PATH which contains the directory the script was located in to take care of it. Thanks you very much for the clarification. Timothy

[galaxy-dev] Providing Galaxy tool inputs as an (XML) file?

2011-09-07 Thread Peter Cock
Hi all, Some of my medium/long term plans for Galaxy involve running one tool which then generates input parameters (and perhaps input files) for another tool. This would be particularly powerful in combination with workflows. One example is phylogenetics where you might have a model selection

Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

2011-09-07 Thread CHAN Chee Seng
Hi, I also faced the same problem. I have a local galaxy and local ucsc genome browser mirror. The galaxy mirror is configured with the require_login equals to True. When I tried to display the data from galaxy to the local ucsc, I encountered the redirected to non-http(s): /root error as

[galaxy-dev] Tool Shed problems with browse repository files?

2011-09-07 Thread Peter Cock
Hi all, I've been having a few server errors and other problems browsing files for tool shed repositories, for example clicking to expand a folder sometimes gives a red exclamation icon with the text Load error! (error). Other times it does load but seems to merge several entries into single

Re: [galaxy-dev] value_label tool input param attribute doesn't work as documented

2011-09-07 Thread Leandro Hermida
Hi again, Sorry had to check what exactly was not working, the value_label attribute appears to not work when trying to reference a label from a dynamic_options driven input parameter. regards, Leandro On Wed, Aug 24, 2011 at 7:23 PM, Kanwei Li kan...@gmail.com wrote: Hi Leandro, I tested

Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

2011-09-07 Thread Nate Coraor
Whyte, Jeffrey wrote: Nate, For some reason, ~/galaxy-dist wasn't in my PATH. Here is the output when the script is run from the ~/galaxy-dist directory: [~/galaxy-dist] myuserid 03:50 PM python ./scripts/get_platforms.py macosx-10.6-intel-ucs2 [~/galaxy-dist] myuserid 03:50 PM

Re: [galaxy-dev] Path to tool designation in tool config xml

2011-09-07 Thread Nate Coraor
Timothy Wu wrote: Thanks, this helps. I was running with an interpreter and I didn't realize I had to had the full path in there. I was expecting that $PATH which contains the directory the script was located in to take care of it. Thanks you very much for the clarification. If the script is

Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

2011-09-07 Thread Nate Coraor
CHAN Chee Seng wrote: Hi, I also faced the same problem. I have a local galaxy and local ucsc genome browser mirror. The galaxy mirror is configured with the require_login equals to True. When I tried to display the data from galaxy to the local ucsc, I encountered the redirected to

Re: [galaxy-dev] Tool Shed problems with browse repository files?

2011-09-07 Thread Greg Von Kuster
Hello Peter, On Sep 7, 2011, at 6:47 AM, Peter Cock wrote: Hi all, I've been having a few server errors and other problems browsing files for tool shed repositories, for example clicking to expand a folder sometimes gives a red exclamation icon with the text Load error! (error). This is

Re: [galaxy-dev] Installation error

2011-09-07 Thread IT Support
Nate, You were right: I was using Python 2.4; should have checked. I changed the symlink in /opt/galaxy-python to point at a compiled version of Python 2.7. I then ran the run.sh script, only to get the same errors again. I've even tried Python 3.2. Any clues? I run ROCKS 5.3. Thanks!

Re: [galaxy-dev] Installation error

2011-09-07 Thread Malave, Michael
Nikhil, As the user who is running galaxy type $which python Something to remember is in $PATH the first folder that points to python wins. I actually use python 2.5.1 and it works perfectly. I also set the user environment ~/bin to search first (beginning of export

Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

2011-09-07 Thread Whyte, Jeffrey
That worked, Nate! Thank you very much. I really appreciate your efforts. Jeff From: Nate Coraor [n...@bx.psu.edu] Sent: Wednesday, September 07, 2011 10:33 AM To: Whyte, Jeffrey Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

[galaxy-dev] cuffcompare wrapper

2011-09-07 Thread Chorny, Ilya
Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below. Your code: for

Re: [galaxy-dev] GATK Unified Genotyper

2011-09-07 Thread Chorny, Ilya
Hi Daniel, I have been implementing the GATK unified genotyper and I was having some issues. Occasionally I would get an error that the Java virtual machine would not start. I got around that by adding the Xmx3g parameter to the command line. I also added the -nt 3 because otherwise it's

Re: [galaxy-dev] GATK Unified Genotyper

2011-09-07 Thread Daniel Blankenberg
Hi Ilya, The JVM can be quite a pain when determining the best way to determine max memory, however the underlying gatk_wrapper.py script was updated last week in 5970:20215fcf6da7 to allow using -Xmx or XX:DefaultMaxRAMFraction. Each of the GATK tools are currently already set to use

Re: [galaxy-dev] cuffcompare wrapper

2011-09-07 Thread Chorny, Ilya
Ok, I figured out why you need the symlink. Can you add an unlink after the process completes? i.e for i, arg in enumerate( args ): input_file_name = ./input%i % ( i+1 ) os.unlink(input_file_name) From: galaxy-dev-boun...@lists.bx.psu.edu

Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

2011-09-07 Thread Trevor Wennblom
On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote: This is normal since OS X has binary compatibility with older releases, the Python distributors build for an older platform rather than each individual platform. I see there's now an Intel-only build for 10.6+, I'll work on this ASAP. if it

Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

2011-09-07 Thread Nate Coraor
Trevor Wennblom wrote: On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote: This is normal since OS X has binary compatibility with older releases, the Python distributors build for an older platform rather than each individual platform. I see there's now an Intel-only build for 10.6+,

Re: [galaxy-dev] Tophat non Sanger input

2011-09-07 Thread Edward Kirton
seems unnecessary since illumina switched over to fastqsanger now. http://www.illumina.com/truseq/quality_101/quality_scores.ilmn On Wed, Aug 31, 2011 at 12:45 AM, Stephen Taylor stephen.tay...@imm.ox.ac.uk wrote: Hi, Is there any plans to enhance the tophat wrapper to accept non Sanger

Re: [galaxy-dev] Automatically removing items from history

2011-09-07 Thread Edward Kirton
i'm resurrecting this thread to see if there's any more support for the idea of deleting intermediate files in a workflow. i think this is an important feature to have. oftentimes a workflow creates many intermediate files no one will ever look at. and leaving it up to the user to cleanup their