Re: [galaxy-dev] RNAseq Map with Top Hat job in queue 4 days, 'waiting to run"

Hello Theresa, Local jobs should run fairly quickly. But the NGS queue was stalled, then believed to be moving earlier (incorrectly by me), but now under review again. The grey queued jobs will eventually execute, so I wouldn't delete them quite yet. http://wiki.galaxyproject.org/Support#Data

Re: [galaxy-dev] bwa indexing not automatic?

Jennifer - Yes, I installed Galaxy that same day with: 1 % hg clone https://bitbucket.org/galaxy/galaxy-dist/ 2

[galaxy-dev] RNAseq Map with Top Hat job in queue 4 days, 'waiting to run"

Greetings, I would like to map some RNAseq data in Top hat in Galaxy Main- I only have 2 files but both have have been in queue 'waiting to run' since last Thursday (9/26)? I have a data meeting this Thursday and am gonna get trounced can you advise? history is below is there another galaxy I

[galaxy-dev] bwa indexing not automatic?

Hi Joshua, Just to double check, you are running the latest stable distribution? There are a few different BWA wrappers in the tool shed, maybe you are using a different one than previously? Using a custom reference genome from the history with bwa is possible with the wrapper with the owner

Re: [galaxy-dev] How can I get a txt output file from R

The previous code doesn't work in the command line, but this yes: file=file("output.txt","w")source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")close(file) Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw") pdf=file("relatorio.pdf","w") ## I changed here texi2dvi("/home

Re: [galaxy-dev] Test Toolshed Biopython package dependency Atlas fails to install (Was: Re: UnboundLocalError: local variable 'prior_installation_required' referenced before assignment)

On Sun, Sep 29, 2013 at 10:43 PM, Guest, Simon wrote: > At Fri, 27 Sep 2013 00:23:37 -0500, > John Chilton wrote: >> >> Simon, >> >> What is the advantage of putting that XML definition in the tool shed? >> It is not 100% true because of prior_install_required dependencies, >> but for the most par

Re: [galaxy-dev] How can I get a txt output file from R

Hi, > > > > file=file("output.txt","w") > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R") > close(file) > > Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw") > ##generate the relatorio.tex file based on the output.txt file > > pdf=file("${relatorio}","w") ##I

Re: [galaxy-dev] How can I get a txt output file from R

Hi, I need one more help. The code that I cite before now is this: ... file=file("output.txt","w")source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")close(file)Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw") ##generate the relatorio.tex file based on the output.txt

Re: [galaxy-dev] Dynamic data library

Hi Nathan, Dannon answered similar question few days ago: There's an import mechanism in libraries that'll allow you to simply link > to the file on disk without copy/upload. I believe the > "example_watch_folder.py" sample script (in the distribution) does just > this via the API, if you want a

[galaxy-dev] Dynamic data library

Hello, we've set up a local Galaxy instance in our genotyping and next-gen sequencing lab with local Apache LDAP (AD) integration, NFS mounts to a large NAS, and cluster integration coming. Do to the high volume of samples and staff that will be using the system, I want to set up data libraries

Re: [galaxy-dev] How can I get a txt output file from R

Surely not, but I had some doubts about this. No more. Thank you > Subject: Re: [galaxy-dev] How can I get a txt output file from R > From: bjoern.gruen...@gmail.com > To: ramao_tiago_tibur...@hotmail.com > CC: galaxy-...@bx.psu.edu > Date: Mon, 30 Sep 2013 20:01:41 +0200 > > Am Montag, den 30.09

Re: [galaxy-dev] How can I get a txt output file from R

Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski: > Thank you, you solved my problem. Maybe you can help with one more > thing, Can I interact in the middle of an workflow execution ? For > example: I have a workflow with ten steps and after I started this, I > want to select options a

[galaxy-dev] October Galaxy Update Newsletter is out

Hello all, The October 2013 Galaxy Update is out : *Highlights:* - A record *six new public servers * - 44 new papers

[galaxy-dev] Problem with get data/uploading file.

Hi, guys, Recently I found the Upload File tool under the Get Data category runs forever on my locally installed Galaxy system. It worked fine for a long time, but now it's not working anymore. Have you guys experienced similar things? Thanks, Luobin __

Re: [galaxy-dev] How can I get a txt output file from R

Thank you, you solved my problem. Maybe you can help with one more thing, Can I interact in the middle of an workflow execution ? For example: I have a workflow with ten steps and after I started this, I want to select options always before each step (like a software instalation). Is it possible

Re: [galaxy-dev] How can I get a txt output file from R

Hi Ramon, > Code: > > > ... > r_wrapper.sh $script_file > > ... > > > > > ... > > file=file("output.txt","w") Do not hardcode a filepath here, you need to reference the template variable from your output section (name="outpu

[galaxy-dev] How can I get a txt output file from R

Code:...r_wrapper.sh $script_file... ... file=file("output.txt","w") source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R") close(file) ... ... I

Re: [galaxy-dev] pbkdf2 encryption - disabling does not work

Jan, I just ran it on pure galaxy-dist (https://bitbucket.org/galaxy/galaxy-dist) and it runs OK. I recommend you updating your Galaxy instance towards tip of the galaxy-dist. Martin On Thu, Sep 26, 2013 at 3:54 PM, Jan Hapala wrote: > I could not find a "Galaxy version" in the application bu

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

Hi Joachim, I had such problems if my XML file is invalid. Than I get immediately the 'installed:' text and can click install again, without any change. Also I would really recommend to reset your toolshed. These "white ghosts" can have unpredictable effects. If you can upload your tools to the

Re: [galaxy-dev] problems with toolshed package update process

Hi Greg, Yes, we have an older Mercurial installation (2.0.2 !) . We will try a newer version. Thanks! Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: vrijdag 13 september 2013 13:56 To: Lukasse, Pieter Cc: Kuijt, Eric; 'galaxy-...@bx.psu.edu' Subject: Re: problems with toolshed p

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

Still having a hard time and some strange situations. It is almost too much to report via email. Basically, the tool_dependencies.xml get recognised sometimes. Please, watch this video to see what I mean (1'30''), and pause as you like: https://dl.dropboxusercontent.com/u/18352887/toolshedissu

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

Am Montag, den 30.09.2013, 14:02 +0100 schrieb Peter Cock: > On Mon, Sep 30, 2013 at 1:58 PM, Dave Bouvier wrote: > > Peter, > > > > It looks like there may be a version conflict between package_numpy and > > either a system numpy or the Galaxy numpy egg. I'll investigate and keep you > > updated

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

On Mon, Sep 30, 2013 at 1:58 PM, Dave Bouvier wrote: > Peter, > > It looks like there may be a version conflict between package_numpy and > either a system numpy or the Galaxy numpy egg. I'll investigate and keep you > updated on my progress. > >--Dave B. Thanks Dave, If Tool authors can ass

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/30/2013 02:15 PM, Greg Von Kuster wrote: Hello Joachim, What version of Galaxy / Tool Shed code are you using? [galaxy@galaxy galaxy-dist]$ hg tip changeset: 10411:c42567f43aa7 On Sep 30, 2013, at 8:05

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

Peter, It looks like there may be a version conflict between package_numpy and either a system numpy or the Galaxy numpy egg. I'll investigate and keep you updated on my progress. --Dave B. On 09/30/2013 05:08 AM, Peter Cock wrote: On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote: I

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

Joachim, For sourceforge URLs, you can safely omit the question mark and everything after it, since that's part of the browser download load balancing process. When downloading with wget, curl, or python's urllib, downloads.sourceforge.net does its own behind-the-scenes load balancing. As for

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

See attachment. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/30/2013 02:15 PM, Peter Cock wrote: On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB | wrote: Hi Greg, Sorry to dig up this unsolved thread from a few months back. Recap of the bug: I h

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

Hi all, Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such fil

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

Hello Joachim, What version of Galaxy / Tool Shed code are you using? On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB | wrote: > Hi Greg, > > > Sorry to dig up this unsolved thread from a few months back. > > Recap of the bug: I have developed a small tool. I have put it in my local > To

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB | wrote: > Hi Greg, > > > Sorry to dig up this unsolved thread from a few months back. > > Recap of the bug: I have developed a small tool. I have put it in my local > Toolshed, and installed it. After applying some changes to the tool, I 'hg >

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

You must escape any ampersand in the XML as & and then it should work. Peter On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | wrote: > Hi all, > > > The download URL seems not to be accepted in tool_dependencies.xml. It is an > URL from sourceforge, the direct link to a package. > > The e

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

On Mon, Sep 30, 2013 at 12:23 PM, Bjoern Gruening wrote: > Hi, > > it does not mean anything, but for me its working locally on a Fedora > (stable) machine. > > If I can anything do to fix that, please let me know. > Bjoern Thanks Bjoern - I'm pretty sure this is a Tool Shed issue, rather than th

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

Hi Greg, Sorry to dig up this unsolved thread from a few months back. Recap of the bug: I have developed a small tool. I have put it in my local Toolshed, and installed it. After applying some changes to the tool, I 'hg push'ed the changes to my repository on my toolshed. I uninstalled the t

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

Hi Joachim, try to remove the last part '?r=&ts=1380535239&use_mirror=surfnet' Cheers, Bjoern > Hi all, > > > The download URL seems not to be accepted in tool_dependencies.xml. It > is an URL from sourceforge, the direct link to a package. > > The error upon uploading the tool to my toolshe

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

This problem is probably due to the 2 ampersands '&', which are not allowed in XML. Try substituting them with '&'. Nicola Il giorno lun, 30/09/2013 alle 13.51 +0200, Joachim Jacob | VIB | ha scritto: > Hi all, > > > The download URL seems not to be accepted in tool_dependencies.xml. It > is

[galaxy-dev] Download URL not accepted in tool_dependencies.xml

Hi all, The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package. The error upon uploading the tool to my toolshed: ** Metadata may have been defined for some items in revision '5665a799775d'. Correct the foll

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

Hi, it does not mean anything, but for me its working locally on a Fedora (stable) machine. If I can anything do to fix that, please let me know. Bjoern > On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote: > > I updated R, numpy, scipy, scikit and removed the atlas dependency. It > > seems to

Re: [galaxy-dev] puzzle: tool result always "set dataset state to ERROR"

On Mon, Sep 30, 2013 at 7:07 AM, ruiwang.sz wrote: > Hi Peter, > > Thanks! I got it working by putting a suppressMessages() around the function > call. Great, but what I meant was just add this to your XML file to tell Galaxy to ignore the stderr and only use the return code for deciding if there

[galaxy-dev] Test Toolshed Biopython package dependency & NumPy

On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote: > I updated R, numpy, scipy, scikit and removed the atlas dependency. It > seems to work fine for the ChemicalToolBox. I do not remove the lapack > dependency, because I did not get any complains until now. I'm seeing problems on the Test Tool