Re: [galaxy-dev] Recommendation for Grid/Cluster management ?

2011-01-10 Thread Ross
suggestions ?  -gordon ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev -- Ross Lazarus MBBS MPH Associate Professor, HMS; Director of Bioinformatics, Channing Laboratory; 181 Longwood Ave

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Ross
/ -- Ross Lazarus MBBS MPH Associate Professor, HMS; Director of Bioinformatics, Channing Laboratory; 181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850 Head, Medical Bioinformatics, BakerIDI; PO Box 6492, St Kilda Rd Central; Melbourne, VIC 8008, Australia; Tel: +61 385321444

Re: [galaxy-dev] unable to login user to local instance

2011-02-17 Thread Ross
:) ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH Associate Professor, HMS; Director of Bioinformatics, Channing Laboratory; 181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850 Head, Medical

Re: [galaxy-dev] Link address to specific section of tools in Galaxy

2011-04-29 Thread Ross
___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor

Re: [galaxy-dev] Galaxy tools written in java

2011-05-07 Thread Ross
in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical

Re: [galaxy-dev] [galaxy-user] Composite Datatypes Q.

2011-05-07 Thread Ross
, 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director

Re: [galaxy-dev] Auto file convert

2011-05-16 Thread Ross
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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical

Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from vadimveren...@gmail.com

2011-05-16 Thread Ross
message). -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies

Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from vadimveren...@gmail.com

2011-05-17 Thread Ross
better... On Mon, May 16, 2011 at 11:13 PM, Ross ross.laza...@gmail.com wrote: Hi, thanks for reporting this error. Ploteig is a perl script that is part of the eigensoft package and it seems to be inaccessible while eigensoft is executing judging from the error message. We'll fix this as soon

Re: [galaxy-dev] Is dynamic associated information per dataset possible?

2011-05-30 Thread Ross
Duddy, John wrote: The sample tracking system looks interesting. It looks like this is designed to have the sequencers modeled in Galaxy, have Galaxy pull the data from the sequencers, and might assume 1-1 pairing between sequencing run and samples. I'd like to be able to support pushing

Re: [galaxy-dev] Script which creates users

2011-06-01 Thread Ross
the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444

Re: [galaxy-dev] Multiple galaxy instances

2011-06-01 Thread Ross
On Wed, Jun 1, 2011 at 3:34 PM, Nate Coraor n...@bx.psu.edu wrote: Jean-Baptiste Denis wrote: My goal is to delagate the management of library/datasets to a galaxy admin of each team from the beginning : i do NOT want a SINGLE independant super admin to manage the access for multiple team, it

Re: [galaxy-dev] change dataset label in exec_after_process()

2011-06-24 Thread Ross
(), exec_before_process(), exec_after_process() it doesn't change the dataset name even after refreshing my history. Has anyone had success setting dataset label/name and other attributes using one of the custom code hook functions?? -- Ross Lazarus MBBS MPH; Associate Professor, Harvard

Re: [galaxy-dev] Can't find Samtools binary

2011-06-24 Thread Ross
://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies

Re: [galaxy-dev] rgWebLogo3 with Probabilities instead of Entropy

2011-06-30 Thread Ross
Thanks - code to accompany good suggestions is always appreciated :) I'll write a test and get a patched version on test as soon as I get some time - travelling all day today - will let you know when it's done On Fri, Jul 1, 2011 at 7:20 AM, Assaf Gordon gor...@cshl.edu wrote: Hello Ross

Re: [galaxy-dev] rgWebLogo3 with Probabilities instead of Entropy

2011-07-06 Thread Ross
FYI: I patched the wrapper to offer all the weblogo Y axis scale options and an additional test to central #5766 and some additional dependency error reporting in #5772 - latest wrapper version is 0.4 On Fri, Jul 1, 2011 at 8:28 AM, Ross ross.laza...@gmail.com wrote: Thanks - code

Re: [galaxy-dev] [galaxy-bugs] Error message when trying to dowload Manhattan plot using the web version

2011-07-19 Thread Ross
to upload the file again, but change the filename? I just wonder if that original file didn't get cleared out. Alison -Original Message- From: Ross [mailto:ross.laza...@gmail.com] Sent: Monday, July 18, 2011 8:51 AM To: Alison Harrill Subject: Re: [galaxy-bugs] Error message when trying

Re: [galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc

2011-07-28 Thread Ross
___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director

Re: [galaxy-dev] Quota

2011-08-12 Thread Ross
the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444

Re: [galaxy-dev] Picard installation problem

2011-08-14 Thread Ross
Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Ross
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote: I meant to say label=${input} or label=${input.value}. Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell. This is a common idiom -

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Ross
to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :) On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi Ross, Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked

Re: [galaxy-dev] Error in FastQC

2011-09-01 Thread Ross
Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444

Re: [galaxy-dev] accessing files_path directory in subsequent analysis steps

2011-09-01 Thread Ross
Nikhil, You've found an old wart - try using extra_files_path I don't remember exactly why but it's write to files_path but read from extra_files_path :0 On Fri, Sep 2, 2011 at 9:21 AM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, So I am writing XML files for an analysis pipeline.  The

Re: [galaxy-dev] Command line option

2011-09-10 Thread Ross
client.  To manage your subscriptions to this and other Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics

Re: [galaxy-dev] outputting different numbers of files based on variables?

2011-09-15 Thread Ross
If you need every output as an item in your history, does the example in http://lists.bx.psu.edu/pipermail/galaxy-user/2009-September/000743.html help? Naming might be a wart. Otherwise the html datatype is really handy for throwing variegated output into a single history item page. It can look

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-09-15 Thread Ross
 wrote: Hi Ross, Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked).  So my idea below did work, but it seems like a hack

Re: [galaxy-dev] Installation troubles with numpy dependency

2011-09-20 Thread Ross
use the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444

Re: [galaxy-dev] Error in FastQC

2011-09-25 Thread Ross
. On Sun, Sep 25, 2011 at 9:33 PM, Antonio Ribeiro acbello...@gmail.com wrote: Hi Ross and Matthew, I'm a newbie to Galaxy and got the same error while trying to process some Illumina data... Thanks for your posting and tips! So, just to confirm the understanding: when installing a local instance

Re: [galaxy-dev] picard error.

2011-09-26 Thread Ross
:04 AM, Ross ross.laza...@gmail.com wrote: Michael, Thanks for pointing these warning errors out. I think they're harmless and can be ignored but I'll definitely take a look later today and check in a fix. As I recall, we had some discussion some months ago about whether to allow the user

Re: [galaxy-dev] moving the galaxy-dist folder structure

2011-10-13 Thread Ross
___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School

Re: [galaxy-dev] Importing Historys in other Galaxy instances

2011-10-25 Thread Ross
Hi, Stefanie. I think you might want a URL pointing to an archived history if you want to move your history to a different Galaxy? I imported your test history into my account on main, then I used the 'export to file' option (it might not be optimally named since it really creates an importable

Re: [galaxy-dev] Importing Historys in other Galaxy instances

2011-10-25 Thread Ross
an import job that never finishes? On Tue, Oct 25, 2011 at 9:02 PM, Stefanie Ververs stefanie.verv...@fh-stralsund.de wrote: Hi Ross, that is exactly what I tried - Export to file and then enter the link into Import from File. But the History never appears in the account on our Galaxy

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-10-31 Thread Ross
to this and other Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Ross
, metadata may need tweaking after the upload - which is why artifacts likely needed downstream are best written as separate history items with metadata correctly set. On Tue, Nov 1, 2011 at 11:03 AM, Jesse Erdmann jerdm...@umn.edu wrote: On Tue, Nov 1, 2011 at 9:07 AM, Ross ross.laza...@gmail.com

Re: [galaxy-dev] making data libraries from database tables

2011-11-08 Thread Ross
Hi James, Existing tools mostly take file paths. This has arguably useful side effects in isolating cluster node execution from the galaxy server process and persisting the computation input on a file-system - arguably more stable long term than queries on dynamic database tables - and maybe not

Re: [galaxy-dev] microarray NGS

2011-11-09 Thread Ross
Hi Ivan, In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because Unfortunately, rexpression is not supported at present- the source is readily available from bitbucket but the original author

[galaxy-dev] FastQC 0.10.0

2011-11-16 Thread Ross
Please ignore this message unless you maintain a local Galaxy instance and use FastQC. The most recent FastQC release 0.10.0 fixes some bugs but also completely changes the HTML layout of the report in ways that break the old wrapper. I've updated the wrapper script and tests to cope with this,

Re: [galaxy-dev] Name your own tool's output?

2011-11-17 Thread Ross
? Timothy ___ 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/ -- Ross Lazarus MBBS MPH

Re: [galaxy-dev] Name your own tool's output?

2011-11-18 Thread Ross
... On Fri, Nov 18, 2011 at 10:50 AM, Paniagua, Eric epani...@cshl.edu wrote: Hi Ross, That's excellent, thanks for jumping in! I've been charged with constructing a Galaxy tool kit for basic microarray data analysis for my group's Galaxy instance, and I looked at your Rgenetics

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

2011-11-30 Thread Ross
-A __**_ 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/ -- Ross Lazarus MBBS MPH

Re: [galaxy-dev] possibly weird config requests...

2011-12-04 Thread Ross
use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all

Re: [galaxy-dev] Excel upload problems

2011-12-08 Thread Ross
/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions

Re: [galaxy-dev] SAM/BAM Hybrid Selection Metrics

2012-01-09 Thread Ross
. ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head

Re: [galaxy-dev] Error download composite dataset from history

2012-01-18 Thread Ross
at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client

Re: [galaxy-dev] Error download composite dataset from history

2012-01-19 Thread Ross
Hi, L-A, 2012/1/19 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hi Ross Thanks a million, I hg-pull'ed it solved the problem!! Please push it to galaxy-dist? ;) Glad to hear it works - thanks for reporting back. I ran in another little bug though, but nothing serious, you might

Re: [galaxy-dev] software installs: PATH vs env.sh

2012-01-24 Thread Ross
to this and other Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all

Re: [galaxy-dev] tool shed offline?

2012-01-31 Thread Ross
://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client. To manage

[galaxy-dev] cool tool for the week

2012-02-18 Thread Ross
http://www.biodalliance.org/index.html embeddable - DAS native, but local server bigBed/bigWig files http://www.biodalliance.org/bin.html can be served. ___ Please keep all replies on the list by using reply all in your mail client. To

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

2012-02-20 Thread Ross
in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

2012-02-20 Thread Ross
, including the outputs in workflows when their number is not known at execution may be tricky, but at least this is a generic approach and won't require any changes to any of the tools that generate Html outputs? On Tue, Feb 21, 2012 at 8:45 AM, Anthonius deBoer thondeb...@me.com wrote: Hi Ross

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

2012-02-21 Thread Ross
/Datatypes/Composite%20Datatypes There is a wiki on creating Composite Datatypes but not the equivalent reading of composite datatypes, is there? Thon On Feb 20, 2012, at 07:11 PM, Ross ross.laza...@gmail.com wrote: Thon, I just had an idea - write a new tool that takes an Html dataset from

Re: [galaxy-dev] strange error having to do with stderr redirection?

2012-02-21 Thread Ross
use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all

Re: [galaxy-dev] incorrect tmp dir handling in picard AddOrReplaceReadGroups

2012-04-03 Thread Ross
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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

2012-04-17 Thread Ross
___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

2012-04-17 Thread Ross
/app/lib path to the galaxy user's path so the nodes running jobs inherit those paths because of the -V switch. I hope this works! On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai caizhq2...@yahoo.com.cn wrote: Hi Ross, Thank you for your reply. I tried it, and it was still not working. Only

Re: [galaxy-dev] Workflow import error

2012-04-17 Thread Ross
to this and other Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

2012-04-18 Thread Ross
with more experience can help out. On Wed, Apr 18, 2012 at 10:50 AM, zhengqiu cai caizhq2...@yahoo.com.cn wrote: Hi Ross, Thank you for your reply. It still did not work. I think SGE knows the path of samtools. Here is a test case I added to Galaxy, and it creates the index for fasta file. I

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

2012-04-18 Thread Ross
can. On Wed, Apr 18, 2012 at 11:39 AM, zhengqiu cai caizhq2...@yahoo.com.cn wrote: Hi Ross, I did not compile samtools using the --prefix. The samtools I used comes with Galaxy AMI image, and I copied it to the same path on my EC2. How to compile samtools using --prefix? I just typed 'make

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-29 Thread Ross
that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now).  Would this be a good opportunity to set up the first (to my knowledge) regional user group?  If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann

Re: [galaxy-dev] About Galaxy Configuration

2012-05-23 Thread Ross
Hi, Ciara, AFAIK new tools always require a server restart at present, but an already loaded tool can have updates to the tool XML re-read using the 'Reload a tool's configuration' option from the administrative menu if your login is listed as an administrator in the config file. Restarting

Re: [galaxy-dev] Re : Error executing tool: cannot find 'database'

2012-05-30 Thread Ross
://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] wrapping qvalue in Galaxy

2012-06-06 Thread Ross
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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI

Re: [galaxy-dev] I can't see or access pictures in FastQC

2012-06-06 Thread Ross
://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] I can't see or access pictures in FastQC

2012-06-07 Thread Ross
haven't made any code changes, I'm going to guess that you might have a local web server configuration issue - but maybe Nate or Dan can help? On Thu, Jun 7, 2012 at 11:54 PM, Dorset, Daniel C daniel.dor...@vanderbilt.edu wrote: Hi Ross, thanks for the reply! I ran FastQC from the command line

Re: [galaxy-dev] I can't see or access pictures in FastQC

2012-06-07 Thread Ross
Thanks again for your help! Dan -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail

Re: [galaxy-dev] Tool Shed Workflow

2012-06-09 Thread Ross
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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI

Re: [galaxy-dev] Re : Composite output with self-declarated datatypes

2012-06-15 Thread Ross
. So is there any specified thing to do to recover the component files of a composite file ? Best regards, Marine -- *De :* Ross ross.laza...@gmail.com *À :* Marine Rohmer marine.roh...@yahoo.fr *Envoyé le :* Mercredi 13 juin 2012 10h50 *Objet :* Re

Re: [galaxy-dev] Re : Composite output with self-declarated datatypes

2012-06-15 Thread Ross
how to fix it either... Any ideas ? Thank you for your attention, Marine -- *De :* Ross ross.laza...@gmail.com *À :* Marine Rohmer marine.roh...@yahoo.fr *Cc :* galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu *Envoyé le :* Vendredi 15 juin 2012 12h40

Re: [galaxy-dev] FastQC Tool Errors

2012-06-22 Thread Ross
___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor

Re: [galaxy-dev] Configuring FastQC to run

2012-07-13 Thread Ross
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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444

Re: [galaxy-dev] Multiple .CEL file import for microarray analysis

2012-07-23 Thread Ross
Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep all replies on the list by using reply all in your mail client

[galaxy-dev] Fwd: none availability genome.fa files through mapping modules on local server

2012-09-18 Thread Ross
at 5:54 PM Subject: Re: [galaxy-dev] none availability genome.fa files through mapping modules on local server To: Ross ross.laza...@gmail.com We have checked again the tab delimiters and it works.. Many thanks. / Sandrine Le 9/14/2012 10:18 AM, Ross a écrit : make absolutely sure there are only

Re: [galaxy-dev] Display of HTML type broken in new Galaxy ?

2012-11-15 Thread Ross
to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J

Re: [galaxy-dev] Tool runners don't listen to settings in [galaxy:tool_runners]

2012-12-05 Thread Ross
Hi, Thon I'm guessing here: but now that bwa is kept in the toolshed, the tool name appears to be toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 according to your job runner entry - so I wonder if that whole ugly string now needs to be in the tool_runners section to over-ride

Re: [galaxy-dev] Integrating generated graphics from cli tool?

2012-12-20 Thread Ross
Alex, xvfb http://www.xfree86.org/4.0.1/Xvfb.1.html works for our headless node R graphics and possibly other packages. I seem to remember writing a wiki entry but a search didn't find it... I see someone on the dev list found the toolfactory code which does a lot of sensible things automatically

Re: [galaxy-dev] Tool error occurred when adding my tool to galaxy

2012-12-29 Thread Ross
I'm sure you checked carefully before posting, but your traceback ends with KeyError: 'thype' suggesting maybe a simple syntax/spelling problem to me. On Sat, Dec 29, 2012 at 7:36 PM, Tan Jun tanjun2...@gmail.com wrote: ** Hi, all I'm new here. These days I'm trying to add a tool in Galaxy,

Re: [galaxy-dev] filtering a param of type 'data' so only one type is available

2013-01-23 Thread Ross
the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ Please keep all replies on the list by using reply

Re: [galaxy-dev] filtering a param of type 'data' so only one type is available

2013-01-23 Thread Ross
, 2013 at 10:58 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Wed, Jan 23, 2013 at 3:51 PM, Ross ross.laza...@gmail.com wrote: Hi, Dan. Using format=rda will restrict the list to history items of the 'rda' datatype - but ONLY if the rda datatype has been defined! The easiest way to do

Re: [galaxy-dev] Best way to work with one directory and many files as 1 input

2013-01-30 Thread Ross
I'd suggest: 1) Make your new datatype a subclass of Html - it's a subclass of composite that contains an HTML document as the object's native display - so it can inform users what's there. 2) When constructing these new things, pass the file_path of the Html (composite) dataset subclass to your

Re: [galaxy-dev] What image formats can be displayed in the Galaxy view panel?

2013-02-07 Thread Ross
Luobin - one additional minor observation: In reality, Galaxy does not do the displaying - it just sends stuff to the users' web browser for display. So even when Galaxy knows what mimetype to attach to a specific image file, the users' web browser response to that mimetype will always remain the

Re: [galaxy-dev] Multiple Instances ...

2013-02-07 Thread Ross
Neil, If by 'multiple' you mean 'independent' galaxy instances, they must each talk to independent backend databases, so if you're thinking of running eg 2 or more independent instances at CSIRO, each for specific tool sets and sending each of your users to one or other of them based on some

[galaxy-dev] Fwd: Multiple Instances ...

2013-02-07 Thread Ross
separated or very bad things will happen. On Fri, Feb 8, 2013 at 2:20 PM, neil.burd...@csiro.au wrote: Thanks Ross. ** ** I did mean separate Galaxy instances like test and main with their own independent backend databases. ** ** How could I run say a test and a main from

[galaxy-dev] Fwd: Custom Cheetah filters?

2013-02-12 Thread Ross
Hi Russell, There may be a better way, but this works for me in the Toolfactory to create space and special character free names? param name=foo type=text value= label=Foo sanitizer invalid_char= valid initial=string.letters,string.digits/ /sanitizer /param On Wed, Feb 13, 2013 at 11:22 AM,

Re: [galaxy-dev] tool integration SOAPdenovo

2013-02-12 Thread Ross
I don't think there's one in a toolshed but someone's clearly done some work on it at http://galaxy.cbiit.cuhk.edu.hk/ Perhaps you may be able to convince them of the many benefits of contributing back to the community by sharing some of their tool code? On Wed, Feb 13, 2013 at 12:32 PM, Jorge

Re: [galaxy-dev] FastQC Question

2013-02-20 Thread Ross
Hello, Min This tool has been stable for a while now and that variable cl is defined as a list in line 52 just above line 63, so this error seems very strange unless you made changes to the source code? It's hard to know where to start helping because there are lots of useful pieces of

Re: [galaxy-dev] History not updating for multiple instances of Galaxy

2013-02-21 Thread Ross
/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] How to test DRMAA configuration?

2013-02-25 Thread Ross
See if adding the default queue name to the job runner path - eg: default_cluster_job_runner = drmaa:///default works any better? Galaxy will default to the local runner if it can't find the nominated drmaa path AFAIK and I don't think 'default' is the default :) On Tue, Feb 26, 2013 at 4:51

Re: [galaxy-dev] all the data files in .loc files needed to download ?

2013-02-27 Thread Ross
Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote: ** **Hello Carl, Thank you very much for your help.I have some

Re: [galaxy-dev] Built-in reference genome

2013-03-05 Thread Ross
Hi, Charles, builds.txt is what tells the Galaxy framework about available genomes. Various binary index files created from those genomes are separately managed for specific tools since some folks won't need some application specific sets of indexes for any given genome - so you need to edit a

Re: [galaxy-dev] Built-in reference genome

2013-03-05 Thread Ross
/Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa.sa I tried that and it does not work. Your response is appreciated. Charlie On Tue, Mar 5, 2013 at 7:11 PM, Ross ross.laza...@gmail.com wrote: Hi, Charles, builds.txt is what tells the Galaxy framework about available

Re: [galaxy-dev] Include some XML in configfiles tag

2013-03-07 Thread Ross
Hi, David. does enclosing your XML in a CDATA section help? It should just get written out without being interpreted, and it works for me in the toolfactory - the contents still get written out but without the CDATA section. configfiles configfile name=loadTestxml ![CDATA[ *!DOCTYPE crystal

Re: [galaxy-dev] Command Line Tool for Creating New Users

2013-04-29 Thread Ross
Neil, AFAIK, python will not load a module unless the relevant script file is marked as executable by the current user? Try something like: chmod ugo+x scripts/db_shell.py and see if that fixes your problem? On Tue, Apr 30, 2013 at 11:50 AM, neil.burd...@csiro.au wrote: Hi, I'm trying to

Re: [galaxy-dev] Command Line Tool for Creating New Users

2013-04-29 Thread Ross
Funny, it works for me. One last thought: You do still have the distributed __init__.py readable by your userid in /scripts so the module loader knows it's a python package directory? On Tue, Apr 30, 2013 at 12:05 PM, neil.burd...@csiro.au wrote: Thanks for the info Ross ** ** But I

Re: [galaxy-dev] Tool Shed test framework breaking where run_functional_tests.sh works

2013-05-10 Thread Ross
Buildbot can be triggered here http://buildbot.g2.bx.psu.edu/builders/central-py2.7-linux-x86_64-postgres manually I think. On Fri, May 10, 2013 at 10:56 PM, Greg Von Kuster g...@bx.psu.edu wrote: Is there a more optimal time to initiate this testing process to better accommodate those in

Re: [galaxy-dev] installing galaxy

2013-05-29 Thread Ross
at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J

[galaxy-dev] Fwd: installing galaxy

2013-05-29 Thread Ross
-- Forwarded message -- From: מירב . mer...@gmail.com Date: Wed, May 29, 2013 at 8:40 PM Subject: Re: [galaxy-dev] installing galaxy To: Ross ross.laza...@gmail.com It worked!! Thank you very mach [?] Merav 2013/5/29 Ross ross.laza...@gmail.com Hi, Merav. A fully functional

Re: [galaxy-dev] [GSoC 2013] Introduction

2013-05-31 Thread Ross
Hi, Saket. Welcome aboard - help is always available here or irc if you're in the right timezone. https://chgr.mc.vanderbilt.edu/plato/https://chgr.mc.vanderbilt.edu/plato/steps/3 is a brand new eQTL option from Marylyn Ritchie's group I stumbled across at

Re: [galaxy-dev] BWA installation

2013-06-03 Thread Ross
, 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser

Re: [galaxy-dev] Adding a Tool for PANAMA

2013-06-03 Thread Ross
Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: gt; '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '' character or you'll confuse the xml parser. It's often possible to hack a

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