[galaxy-dev] Error while writing data in tophat2

2013-02-15 Thread Sachit Adhikari
Galaxy is working fine in command line whereas in Galaxy at last i got this error: [2013-02-15 01:39:12] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 50

Re: [galaxy-dev] can't run instance for CloudMan

2013-02-15 Thread Quang Trinh
Hi Stefano, Can you try out what we put together: https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Thu, Feb 14, 2013 at 8:28 PM, stefano cardinale s.cardin...@berkeley.edu wrote: Hi, I am having a problem with running galaxy on the Amazon cloud. I have tried this several times over

[galaxy-dev] Fwd: Error while writing data in tophat2

2013-02-15 Thread Sachit Adhikari
-- Forwarded message -- From: Sachit Adhikari sachit.techner...@gmail.com Date: Fri, Feb 15, 2013 at 11:02 AM Subject: Error while writing data in tophat2 To: galaxy-dev@lists.bx.psu.edu Galaxy is working fine in command line whereas in Galaxy at last i got this error:

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
On Sep 12, 2012, at 1:00 PM, David Hoover wrote: Are there any environment variables that are honored by toolshed installed tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or $GALAXY_HOME, then uploaded it the test toolshed, then installed it automatically. Neither of

Re: [galaxy-dev] can't run instance for CloudMan

2013-02-15 Thread Dannon Baker
Stefano, Sounds like it's most likely that the security groups aren't configured correctly. What I'd recommend would be to launch your instance using http://usegalaxy.org/cloudlaunch which does all of those configuration steps for you automatically. -Dannon On Feb 14, 2013, at 8:28 PM,

Re: [galaxy-dev] hg19 reference gnome for Tophat2

2013-02-15 Thread Jeremy Goecks
Now try running the test data in Galaxy to see if you get the same results. You should probably try running from the history first and then try adding the test data as a built-in genome via the bowtie2_indexes.loc table Best, J. On Feb 15, 2013, at 12:18 AM, Sachit Adhikari wrote: Hi Jeremy,

Re: [galaxy-dev] Error while writing data in tophat2

2013-02-15 Thread Jeremy Goecks
This is not a known bug. For questions related to Tophat errors, you might try the Tophat mailing list: tophat.cuffli...@gmail.com Good luck, J. On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote: Galaxy is working fine in command line whereas in Galaxy at last i got this error:

Re: [galaxy-dev] Error while writing data in tophat2

2013-02-15 Thread Sachit Adhikari
Jeremy, But the tophat2 is running successfully in the command line. So, I guess it's related to Galaxy. Why am I getting this error in Galaxy? Is it because I don't have latest Galaxy? Is it file permission issue? I am using Tophat V2.0.7 and latest Bowtie2 version. On Fri, Feb 15, 2013 at 8:02

[galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread greg
Hi guys, I'm trying to run MACS in my local galaxy install (see screenshot: http://snag.gy/5QGUH.jpg) And I'm getting this error: Usage: macs -t tfile [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such

Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread James Taylor
The wrapper you are using is for MACS 1.3, there is a wrapper that is compatible with 1.4 in the toolshed. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Feb 15, 2013 at 9:26 AM, greg margeem...@gmail.com wrote: Hi guys, I'm trying to run MACS in my local galaxy

Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread greg
Thanks! So one question, when I go to install it from the toolshed I see two choices for a revision to select: 3:cdd9791c0afa 0:c1eeccec29d1 Which would I choose and why? Thanks, Greg On Fri, Feb 15, 2013 at 9:30 AM, James Taylor ja...@jamestaylor.org wrote: The wrapper you are using is for

Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread James Taylor
You likely want the newest version (3) On Feb 15, 2013 9:37 AM, greg margeem...@gmail.com wrote: Thanks! So one question, when I go to install it from the toolshed I see two choices for a revision to select: 3:cdd9791c0afa 0:c1eeccec29d1 Which would I choose and why? Thanks, Greg On

Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread greg
Hi guys, I'm getting an error when trying to install this from the toolshed? Let me know what I should do? Thanks, Greg Error - type 'exceptions.ValueError': too many values to unpack URL:

Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread Greg Von Kuster
Hello Greg, What version of Galaxy are you running - it is likely older than the December 20, 2012 Galaxy release. You'll have to upgrade to at least that release to use the main Galaxy tool shed. Greg Von Kuster On Feb 15, 2013, at 9:43 AM, greg wrote: Hi guys, I'm getting an error

Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread greg
Thanks. I'm trying to follow the instructions here to update the code: http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date But I'm getting this error: hg incoming Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from untrusted user galaxy, group scicomp Not

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

2013-02-15 Thread David Joly
I still haven't heard back from the Bio-Linux guys regarding how to update Galaxy within Bio-Linux... In the meantime, I tried to play with the Manage data libraries, in order to import large datasets. I modified the library_import_dir line in the universe_wsgi.ini. The first thing I can say is

Re: [galaxy-dev] New release : display problem

2013-02-15 Thread Mathieu Bahin
Hi, Enclosed is a dataset that I am not able to see anymore. I don't see any error in the log (but maybe I missed it !). To answer to Carlos, I have the problem with Firefox and Chrome. Cheers, Mathieu - Mail original - De: Dannon Baker dannon.ba...@gmail.com À: Mathieu Bahin

Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS

2013-02-15 Thread greg
Ok, I created a ~/.hgrc file and add this: [trusted] users=galaxy It seems to have fixed it. -Greg On Fri, Feb 15, 2013 at 9:50 AM, greg margeem...@gmail.com wrote: Thanks. I'm trying to follow the instructions here to update the code:

Re: [galaxy-dev] Install NGSRich in local galaxy

2013-02-15 Thread Hakeem Almabrazi
Thank you Greg, That what I tried to do initially but I could not find this tool the tool shed repository. Here is what I did, as an admin I went to Search and browse shed tool-Galaxy main tool shed Then I searched for ngsrich I could not find it. Then I looked under static category I still

[galaxy-dev] Confusion on Updating Code

2013-02-15 Thread greg
Hi guys, I'm trying to do my first update on my local galaxy install (it's been a few months at least since I installed) I'm trying to follow the instructions here to update the code: http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date My first question is how do I roll

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

2013-02-15 Thread Dannon Baker
It's really hard to say what's going on with those issues without more information about the particular version of galaxy (which unfortunately we'd get from `hg tip`, which won't work on your bio linux install) or proxy configuration, if any. I'm also not sure what the appropriate bio linux

Re: [galaxy-dev] Confusion on Updating Code

2013-02-15 Thread Nate Coraor
On Feb 15, 2013, at 10:45 AM, greg wrote: Hi guys, I'm trying to do my first update on my local galaxy install (it's been a few months at least since I installed) I'm trying to follow the instructions here to update the code:

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Greg Von Kuster
Hello Peter, please see my response at the end. On Feb 15, 2013, at 6:47 AM, Peter Cock wrote: On Sep 12, 2012, at 1:00 PM, David Hoover wrote: Are there any environment variables that are honored by toolshed installed tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or

Re: [galaxy-dev] New release : display problem

2013-02-15 Thread Dannon Baker
Well, (un)fortunately this file works for me in both firefox and chrome on the current galaxy-dist. Just to confirm -- when you click the eye, it doesn't download the file either, right -- nothing at all happens? In chrome, could you open the console (Tools - Javascript Console or Ctrl+Shift+J)

Re: [galaxy-dev] Install NGSRich in local galaxy

2013-02-15 Thread Greg Von Kuster
Hello Hakeem, When searching the tool shed from Galaxy, only repositories that are automatically installable into Galaxy will be located. Repositories are considered installable if they contain valid Galaxy utilities (tools, proprietary datatypes, repository dependency definitions, tool

Re: [galaxy-dev] Confusion on Updating Code

2013-02-15 Thread greg
Thanks! One followup, see below. -Greg On Fri, Feb 15, 2013 at 11:01 AM, Nate Coraor n...@bx.psu.edu wrote: On Feb 15, 2013, at 10:45 AM, greg wrote: Migrate: % sh manage_db.sh upgrade Pay attention to whatever the first revision you are migrating from is. Probably 109 if you were at

[galaxy-dev] Problems with rsync from datacache.g2.bx.psu.edu/indexes

2013-02-15 Thread Rodolfo Aramayo
Hi, I hope this is the right place to ask, I am trying to rsync from: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ and I am getting the error: @ERROR: chroot failed rsync error: error starting client-server protocol (code 5) at main.c(1534) [Receiver=3.0.9 I know I can rsync to any

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi guys, Reading the rest of the thread from December, Greg's new code did get checked in and should be working (I've not tried this yet). However, I can't help feeling that defining the two environment variables David

Re: [galaxy-dev] Confusion on Updating Code

2013-02-15 Thread Nate Coraor
On Feb 15, 2013, at 11:13 AM, greg wrote: Thanks! One followup, see below. -Greg On Fri, Feb 15, 2013 at 11:01 AM, Nate Coraor n...@bx.psu.edu wrote: On Feb 15, 2013, at 10:45 AM, greg wrote: Migrate: % sh manage_db.sh upgrade Pay attention to whatever the first revision you

Re: [galaxy-dev] Problems with rsync from datacache.g2.bx.psu.edu/indexes

2013-02-15 Thread Nate Coraor
On Feb 15, 2013, at 11:12 AM, Rodolfo Aramayo wrote: Hi, I hope this is the right place to ask, I am trying to rsync from: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ and I am getting the error: @ERROR: chroot failed rsync error: error starting client-server protocol

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Greg Von Kuster
Hi Peter, On Feb 15, 2013, at 11:14 AM, Peter Cock wrote: On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi guys, Reading the rest of the thread from December, Greg's new code did get checked in and should be working (I've not tried this yet). However, I can't

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: Usecase: Tool comes with a simple datafile (e.g. defining a search motif, say motif.dat) which is used by a script (say motif.py) via a normal Galaxy tool XML file (say motif.xml). Perhaps I can just put my data file

Re: [galaxy-dev] Install NGSRich in local galaxy

2013-02-15 Thread Hakeem Almabrazi
Thank you Greg, I will contact the owner of that software and see if we can get it installed. Regards From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Friday, February 15, 2013 10:13 AM To: Hakeem Almabrazi Cc: Galaxy Dev Subject: Re: [galaxy-dev] Install NGSRich in local galaxy Hello

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Greg Von Kuster
On Feb 15, 2013, at 11:45 AM, Peter Cock wrote: On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: Usecase: Tool comes with a simple datafile (e.g. defining a search motif, say motif.dat) which is used by a script (say motif.py) via a normal Galaxy tool XML file (say

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
On Fri, Feb 15, 2013 at 4:57 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Feb 15, 2013, at 11:45 AM, Peter Cock wrote: Actually for the example I am working on, the motif.py script would be the tool executable, called from motif.xml like this: command interpreter=pythonmotif.py $fasta_file

Re: [galaxy-dev] New release : display problem

2013-02-15 Thread Carlos Borroto
On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker dannon.ba...@gmail.com wrote: Well, (un)fortunately this file works for me in both firefox and chrome on the current galaxy-dist. Just to confirm -- when you click the eye, it doesn't download the file either, right -- nothing at all happens?

Re: [galaxy-dev] DustMasker tool for ncbi_blast_plus

2013-02-15 Thread Nicola Soranzo
Il giorno lun, 11/02/2013 alle 13.19 +, Peter Cock ha scritto: On Fri, Feb 8, 2013 at 4:30 PM, Nicola Soranzo sora...@crs4.it wrote: Il giorno mer, 06/02/2013 alle 20.01 +0100, Nicola Soranzo ha scritto: Hi Peter, I added these file formats mostly as placeholders for a future

Re: [galaxy-dev] DustMasker tool for ncbi_blast_plus

2013-02-15 Thread Peter Cock
On Fri, Feb 15, 2013 at 6:10 PM, Nicola Soranzo sora...@crs4.it wrote: Peter wrote: It seems to have confused the bitbucket page a little, but I have checked in your initial wrapper to my development repository (I use the tools branch):