Re: [galaxy-dev] [galaxy-user] parallel processing of multiple files on a multi-processor box?

2011-01-06 Thread James Taylor
Two parts to this probably. 1) It should definitely be possible to have parameters in tool configs that are set in a global configuration file, I actually thought tool_conf.xml might be a good place (inside the tool element). 2) For the particular case of processor cores, ideally we would

Re: [galaxy-dev] RPM repository for NGS tools in Galaxy

2011-03-02 Thread James Taylor
Mobile: +31 6 41709231 ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- jt James Taylor, Assistant Professor, Biology / Computer Science, Emory University

Re: [galaxy-dev] [Nbicgalaxy-admin] RPM repository for NGS tools in Galaxy

2011-03-04 Thread James Taylor
This would be great. The 'tool dependency injection' part of Galaxy is designed so any directory having this structure will work, and you can have as many as you want and they will be searched in order. On Mar 4, 2011, at 3:21 AM, David van Enckevort wrote: The repository with the latest

Re: [galaxy-dev] about bx-python and bigwig

2011-03-07 Thread James Taylor
Davide, see bx.bbi.bigwig_file.BigWigFile Implemented in Cython, there is also some BigBed support with a common class (bbi_file) for the indexing and aggregation pieces. This is currently read only. Also, not tested exhaustively on different types of bigwig, but I believe we have most

Re: [galaxy-dev] Restricted user builds

2011-03-28 Thread James Taylor
-dev -- jt James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ 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

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread James Taylor
I would humbly guess that most of those truncated files are due to problematic HTTP uploads - so it saves the day from another problem, which should be avoided all together. Maybe most, but definitely not all. We see all kinds of strange corruption. However, I have been thinking about

Re: [galaxy-dev] improved view details button

2011-04-11 Thread James Taylor
Assaf, it should be the last modification to the dataset's metadata, info, etc. Any change that would be made through the edit attributes page. I agree this is confusing and should probably not be shown to the user at all. On Apr 11, 2011, at 7:13 PM, Assaf Gordon wrote: It doesn't give

Re: [galaxy-dev] Getting binary programs into Galaxy distribution?

2011-05-25 Thread James Taylor
John, I'll take a look at the program. There isn't a great way to do this until the dependency installation system is working. A thin python wrapper (using Cython) would be the usual trick we would use. However: have you considered just using cat? This should be completely valid for gzip

Re: [galaxy-dev] Color blindness and Galaxy UI

2011-06-06 Thread James Taylor
Peter, most of the current UI theme was designed by someone who is red- green colorblind (me), and we avoid using color alone for encoding information. The change has been reverted, thanks for brining it to our attention. On Jun 5, 2011, at 7:40 AM, Peter Cock wrote: Do you have any color

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-27 Thread James Taylor
On Jul 27, 2011, at 10:26 AM, Jelle Scholtalbers wrote: Wouldn't it be better to at least validate e-mail addresses of new users on the main instance? This would probably resolve most issues related to unwanted content on the server? Not in our experience, valid email addresses are trivial

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-27 Thread James Taylor
No, data does not require a login to view if the dataset permissions are set permissively. This allows users to share direct links to datasets (which is meant to be a good feature ;). On Jul 27, 2011, at 11:45 AM, Paul Gordon wrote: On the other hand, isn't user data supposed to require a

Re: [galaxy-dev] using Galaxy for map/reduce

2011-08-02 Thread James Taylor
is that the history would not be completely populated by the time the page had returned. -- jt James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ Please keep all replies on the list by using reply all in your

Re: [galaxy-dev] Storing a dict as metadata

2011-08-26 Thread James Taylor
Not currently, but since a converted dataset is just a dataset, you could reuse all of the existing upload mechanism, and just add the converted dataset connection between the two after the fact. On Aug 26, 2011, at 11:54 AM, Duddy, John wrote: Is there a way to upload that converted

Re: [galaxy-dev] Storing a dict as metadata

2011-08-26 Thread James Taylor
On Aug 26, 2011, at 7:23 PM, Duddy, John wrote: I'm looking into these, and it seems that the spirit is to store a version of the data that is converted, like a FASTQ - BAM or some such use case, where one file can be extracted from the other. It was originally built for that (hence the

Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper?

2011-10-15 Thread James Taylor
they are being invoked by a web application). What are you trying to achieve with this? Is this for a tool generating an HTML report? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ Please keep all replies

Re: [galaxy-dev] (i18n) How to make Galaxy display in Japanese?

2011-10-16 Thread James Taylor
it should be decoupled from the actual tool config since the translators are usually not the tool authors. Best case would probably be to have many translation files which a given Galaxy instance compiles together. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University

Re: [galaxy-dev] Upload File Button

2011-10-19 Thread James Taylor
? There is currently no support for upload tool parameters in workflows. What behavior are you looking for in this case? The upload tool is very special, and the parameters are quite interdependent. Are you trying to create a new dataset from the uploaded file or something else? -- James Taylor, Assistant

Re: [galaxy-dev] Upload File Button

2011-10-19 Thread James Taylor
data used by tools is captured within immutable datasets to ensure reproducibility. You could implement this, but unless you still create a dataset for the uploaded file, I think it would break other things (like re-running tools). -- James Taylor, Assistant Professor, Biology / Computer Science

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-20 Thread James Taylor
error you get from url_for? There is no single variable that stores the app url, it is constructed from the routing system which url_for is connected to. If you look in form_builder.py for example you can see the use of url_for from non template code. -- James Taylor, Assistant Professor, Biology

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-21 Thread James Taylor
this would be a big mistake. Instead you probably want to capture the URL somehow when the job is created. I need to think about it some more. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ Please keep

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-21 Thread James Taylor
that scope. For tools/__init__.py there are some methods that have access and some that don't, it depends on how they are called (all the user interface generation related code has access to trans for example). -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University

Re: [galaxy-dev] Tool shed and datatypes

2011-10-21 Thread James Taylor
that type. Is there other information that should go in the requirement tag? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ Please keep all replies on the list by using reply all in your mail client

Re: [galaxy-dev] Fill field with user email, if logged in

2011-10-23 Thread James Taylor
/ config files. This could be implemented however. You would need to update the context used by Tool.update_state to be able to lookup these special variables, and perform substitution on values -- probably only the first time you get_initial_value for a ToolParameter. -- James Taylor, Assistant

Re: [galaxy-dev] Error in using Palmapper

2011-10-25 Thread James Taylor
anyone help me in this? I believe this question is for the Rätsch labs Galaxy instance and should be directed to gal...@tuebingen.mpg.de, which I have copied here. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University

Re: [galaxy-dev] Some questions about cloudman

2011-10-28 Thread James Taylor
*/ -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ 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

Re: [galaxy-dev] using nginx instead of paste as Galaxy web server

2011-11-02 Thread James Taylor
Dean, nginx integration works by proxying to the Paste server, but offloading some data intensive parts. So you still need that configuration as it is. Thanks! -- jt (composed on my phone) On Nov 2, 2011, at 12:35 PM, Dean Snyder dean.sny...@jhu.edu wrote: I switched from using the default

Re: [galaxy-dev] [galaxy-user] Cannot get rid of custom build error

2011-11-02 Thread James Taylor
James, do you have an entry for the fasta_to_len convertor in your datatypes_conf.xml? If not, you might want to update your config to include those entries from the sample. Thanks! -- jt (composed on my phone) On Nov 2, 2011, at 11:58 AM, James Vincent j...@uvm.edu wrote: Hello Devs, I

Re: [galaxy-dev] installing multiple versions of a tool / path configuration

2011-11-15 Thread James Taylor
On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote: If this is the case, what is the best way to install and maintain two versions of the same tool? I can write code into the wrapper to find the correct version of the tool in a given case, but I was wondering if there is a more standard

Re: [galaxy-dev] Bootstrapping the Galaxy installation process: populating the database

2011-11-15 Thread James Taylor
On Nov 15, 2011, at 7:40 PM, Duddy, John wrote: Currently, the schema is created the first time Galaxy is run. I did not see a way to cause that to happen via the manage_db.sh script. Have I missed something? If not, any pointers on how I might go about adding that (i.e. what stuff to call

Re: [galaxy-dev] Missing requirements in xml wrappers in galaxy-dist?

2011-11-16 Thread James Taylor
...@unimelb.edu.au wrote: Great! Thanks James, this is exactly what I need. On Wed, Nov 16, 2011 at 2:20 PM, James Taylor ja...@jamestaylor.org wrote: On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote: If this is the case, what is the best way to install and maintain two versions of the same tool? I

Re: [galaxy-dev] New Galaxy look from usegalaxy.org

2012-03-27 Thread James Taylor
-dist. regards, Leandro ___ 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/ -- jt James

[galaxy-dev] (no subject)

2012-07-13 Thread James Taylor
To: From: James Taylor ja...@jamestaylor.org Subject: Re: [galaxy-dev] List of browsers which supports galaxy Quoting Nate Coraor (2012-07-13 17:22:22) We don't maintain an official list except with Internet Explorer, for which support was dropped recently, as Peter noted above. We do

Re: [galaxy-dev] Help to run a C program

2012-07-26 Thread James Taylor
Quoting Rodrigo Faccioli (2012-07-26 00:08:23) I'd like to create a web-interface to run a C program. It is necessary a config file which is used as input to this program. Therefore, the values You probably want to look at the configfiles element for the tool configs:

Re: [galaxy-dev] help

2012-07-26 Thread James Taylor
Quoting romain desprat (2012-07-26 13:49:02) galaxy ( on the linux partition). Unfortunately, galaxy doesn t have enough memory to work with this file. Exactly what error is Galaxy reporting? ___ Please keep all replies on the list

Re: [galaxy-dev] annoying bug when deleting datasets

2012-07-26 Thread James Taylor
Quoting Peter Cock (2012-07-25 20:40:42) On Wed, Jul 25, 2012 at 9:35 PM, David Hoover hoove...@helix.nih.gov wrote: dataset from a history, all the delete icons disappear from the datasets. They come back if I refresh the page. Has anyone else My fault, should be fixed in 6d23049609a9.

[galaxy-dev] Workshop on Extending High-Performance Computing Beyond its Traditional User Communities

2012-07-31 Thread James Taylor
Galaxy developers, There is an upcoming workshop on accessible HPC that might be of interest to many of you. It would be great to see the Galaxy community perspective included in these discussions. Details follow. Thanks, James -- http://www.psc.edu/index.php/escience-2012-workshop

Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

2012-08-07 Thread James Taylor
Quoting Kenneth Auerbach (2012-08-07 01:19:56) Modification to universe_wsgi.ini file: #database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE database_connection =

Re: [galaxy-dev] GATK v2.x

2012-09-11 Thread James Taylor
David, because of the restrictive licensing terms of GATK2 the main Galaxy Team will not continue to develop any GATK tools except for those which remain under the open source license (basically, GATK 1.6). We will be very happy to have wrappers for these and other non-open-source tools

Re: [galaxy-dev] Redirect log files?

2012-09-16 Thread James Taylor
On Sunday, September 16, 2012, Fields, Christopher J wrote: This seems to correspond with what I have tried; I attempter setting log_destination in the config file (as James suggested) and the server wouldn't start What was the error? This should work. , but changing run.sh to point to

Re: [galaxy-dev] python egg cache exists error

2012-09-18 Thread James Taylor
Interesting. If I'm reading this correctly the problem is happening inside pkg_resources? (galaxy.eggs unzips eggs, but I think it does so on install [fetch_eggs] time not run time which would avoid this). If so this would seem to be a locking bug in pkg_resources. Dannon, we could put a guard

Re: [galaxy-dev] creating a galaxy dataset within a galaxy tool

2012-09-18 Thread James Taylor
Dan, I may not be following, but why not make the serialized R object a dataset (of its own datatype). Then the user can just pass it to the downstream tools just by specifying one parameter. -- jt On Tue, Sep 18, 2012 at 3:00 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: I want the user to

Re: [galaxy-dev] concatenate datasets: how to fixate first dataset

2012-09-19 Thread James Taylor
No, but this is a good idea that can be implemented as a new type of workflow module (fixed data set, like input dataset but specified at workflow build time). Can you file an issue in bitbucket describing how you would like this feature to work? Thanks! On Wednesday, September 19, 2012, Marc

Re: [galaxy-dev] Using an unique database for tow differents versions of Galaxy

2012-09-21 Thread James Taylor
If the two different Galaxy instances are different *versions* of Galaxy, this is unlikely to work out well. -- jt On Fri, Sep 21, 2012 at 11:59 AM, Chebbi Mohamed Amine chebbimam...@gmail.com wrote: Hello Galaxy-team! I installed recently two differents versions of Galaxy and I would like

Re: [galaxy-dev] Using an unique database for tow differents versions of Galaxy

2012-09-21 Thread James Taylor
Definitely not. And please keep replies on the list. -- jt On Fri, Sep 21, 2012 at 1:50 PM, Chebbi Mohamed Amine chebbimam...@gmail.com wrote: Yes the two instances are of two different versions. So if I understand well there is no mean to do it like this ? Thanks 2012/9/21 James Taylor

Re: [galaxy-dev] How to rotate Galaxy log file

2012-09-25 Thread James Taylor
Galaxy should probably be shutdown with --stop-daemon (depending on how you are running it). In the future we can look at making the logging handle the HUP signal. -- jt On Tue, Sep 25, 2012 at 11:40 AM, Scott McManus scottmcma...@gatech.edu wrote: Lukasz- How are you stopping the process?

Re: [galaxy-dev] Jeremy's DataProvider changes

2012-10-01 Thread James Taylor
It is definitely intended to be general (I believe there is a column data provider intended for scatterplot visualizations that should land soon). We definitely want this to be general enough to use for any visualization, so please consider this API and help us to make it as general as

Re: [galaxy-dev] Mail galaxy team

2012-10-09 Thread James Taylor
The Galaxy Web API is documented here: http://wiki.g2.bx.psu.edu/Learn/API -- jt On Tue, Oct 9, 2012 at 6:30 AM, harry humphries harry...@gmail.com wrote: We are trying to develop a plugin for drupal CMS that interacts with the galaxy api, basically we want to create a control panel for the

Re: [galaxy-dev] Adding binary datatype: upload problem

2012-10-11 Thread James Taylor
Mark, how are you running your Galaxy instance, and have you changed the value of log_level in your universe_wsgi.ini? By default Galaxy should be provide quite verbose logging on stdout. -- jt On Wed, Oct 10, 2012 at 2:21 PM, Mark Johnson mjohn...@ncbi.nlm.nih.gov wrote: I'm trying to add

Re: [galaxy-dev] Group parameters

2012-10-15 Thread James Taylor
Be aware that this may not work in future versions of Galaxy, and probably won't work in some places already (e.g. trackster). If this is a common need, one option would be to create a new type of grouping construct that would simply be a labeled group. In the config this would be: group

Re: [galaxy-dev] Jobs crash only in workflow context

2012-10-17 Thread James Taylor
Todd, this is definitely unusual. Can you post (or send directly) relevant sections from the Galaxy log? -- jt On Tue, Oct 16, 2012 at 8:15 PM, Todd Oakley todd.oak...@lifesci.ucsb.edu wrote: Hello, We just did a few tweaks to improve Galaxy performance, and a new issue popped up that I

Re: [galaxy-dev] Jobs are slow to start on my galaxy instance. Used to be much faster

2012-10-23 Thread James Taylor
On Tue, Oct 23, 2012 at 12:55 PM, Anthonius deBoer thondeb...@me.com wrote: I had sent James Taylor the schema as he requested, but I never heard anything so I guess he must not have found anything weird Yes, it appears to have all the right indexes to me

Re: [galaxy-dev] Galaxy, Apache, WSGI and mod_wsgi

2012-10-24 Thread James Taylor
The Galaxy application does store quite a bit in memory (not as globals though). This doesn't preclude running under mod_wsgi, but it will work best in a configuration that uses a small number of long running processes with multiple threads. Basically, we run nginx proxying paste on the main

Re: [galaxy-dev] Trackster error

2012-10-24 Thread James Taylor
FYI, trackster supports BigWig directly (no conversion or additional indexing) and quite efficiently, so you will likely have the most luck with that. -- jt On Wed, Oct 24, 2012 at 3:09 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: bigwig file.

Re: [galaxy-dev] Output file naming

2012-10-26 Thread James Taylor
On Fri, Oct 26, 2012 at 3:47 PM, Peter Cock p.j.a.c...@googlemail.com wrote: i.e. This isn't something each tool author should be doing, but something general that should be in Galaxy itself. Yes, we would very much like a visual/graphical indicator of dataset ancestry, and possibly an

Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?

2012-10-29 Thread James Taylor
Ann, I think you may be able to do this by generating another nexus file using configfiles in the Galaxy tool config which just contains a command block, similar to the example here: http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F -- jt On Mon, Oct

Re: [galaxy-dev] Error while uploading data from local directory

2012-10-29 Thread James Taylor
This is a bug that is fixed in revision ecd131b. Sorry for the inconvenience. -- jt On Sat, Oct 27, 2012 at 6:12 PM, Luciano Cosme cosme.sim...@gmail.com wrote: Howdy, I installed galaxy in a new server that I build and I am getting the following error when I try to upload the files from

Re: [galaxy-dev] Opinions on organizing tools into repos

2012-10-30 Thread James Taylor
On Mon, Oct 29, 2012 at 9:23 PM, Todd Oakley todd.oak...@lifesci.ucsb.edu wrote: We've developed a large number of tools to allow my lab to conduct phylogenetic analyses in Galaxy. Inspired by the mothur package in Galaxy, which is all in one repo, I made the decision to add all our related

Re: [galaxy-dev] phylotastic hackathon (Jan 28 - Feb 1, Tucson, AZ) of possible interest to galaxy developers

2012-11-05 Thread James Taylor
Arlin, this sounds great. There have been a few discussions on the list over the last two weeks about Phylogenetic tools, it would be great if the groups responsible could send representatives to the hackathon to coordinate. My group would definitely like to send at least one Galaxy core team

Re: [galaxy-dev] Where should I put a tool's required binaries?

2012-11-05 Thread James Taylor
If you want to keep your tools separated by name and version (recommended) see the section Managed Tool Dependencies at http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Nov 5, 2012 at 12:44 PM, Peter Cock

Re: [galaxy-dev] Uploading files onto local server

2012-11-09 Thread James Taylor
You can determine what revision you have by running hg tip in the galaxy checkout. Are you checking out from galaxy-dist or galaxy-central? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Nov 8, 2012 at 10:41 AM, John Clayton j.clay...@ibmc-cnrs.unistra.fr wrote: How

Re: [galaxy-dev] Tags API

2012-11-12 Thread James Taylor
On Mon, Nov 12, 2012 at 9:43 AM, John Chilton chil...@msi.umn.edu wrote: From IRC (weeks ago): (03:15:01 PM) jmchilton: Ideally, what would the API uri for assigning a tag to a histories dataset be? POST to api/tags/tag_name/item_class(e.g. HistoryDatasetAssociation)/encoded_id or POST to

Re: [galaxy-dev] piping two scripts in the same xml tool wrapper

2012-11-19 Thread James Taylor
On Sun, Nov 18, 2012 at 1:13 PM, Christophe Antoniewski droso...@gmail.com wrote: but the second script output is empty. I suspect that the second script is launched when the output of the first script is not available yet. I'm pretty sure we do not currently support multiple command tags.

Re: [galaxy-dev] Galaxy and ENCODE

2012-11-19 Thread James Taylor
/integrativeAnalysis/VM/ -- James Taylor, Assistant Professor, Biology/CS, Emory University On Sun, Nov 18, 2012 at 10:29 AM, Scooter Willis hwil...@scripps.edu wrote: I found out about Galaxy based on the ENCODE project making a big deal about packaging the software they used on a CD

Re: [galaxy-dev] First questions from a new developer

2012-11-19 Thread James Taylor
On Fri, Nov 16, 2012 at 2:35 PM, Joshua Orvis jor...@gmail.com wrote: If I removed that line how is it still part of the call? Is Galaxy caching the xml tool files? Did you restart Galaxy? Tool configuration files are read at startup. You can also force a tool to be reloaded in the admin

Re: [galaxy-dev] XGRID and Galaxy

2012-11-24 Thread James Taylor
if there is a way for xgrid to support the DRMAA API, in which case you can use the DRMAA runner. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Nov 22, 2012 at 9:47 PM, James Boocock smilefreak2...@gmail.com wrote: Hi Galaxy Dev Team. We are looking to put xgrid

Re: [galaxy-dev] Changing interface design

2012-11-30 Thread James Taylor
this. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Nov 30, 2012 at 6:30 AM, Bossers, Alex alex.boss...@wur.nl wrote: Philippe, As far as I know most of the styling is in galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present in that location

Re: [galaxy-dev] Auto delete dataset after workflow run?

2012-12-03 Thread James Taylor
On Wed, Apr 4, 2012 at 7:38 AM, Peter Cock p.j.a.c...@googlemail.com wrote: It would be quite a popular feature I think - perhaps replacing the current auto hide feature in workflows with auto delete or is that too drastic? I think a workflow level option to set whether non-output datasets are

Re: [galaxy-dev] RPy testsuite some tests passing - enough for Galaxy?

2012-12-05 Thread James Taylor
Rpy is only used by a handful of tools (should be listed on the tool dependencies page). Everything else in Galaxy should work fine without it. ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] Very confused about workflow_step_connection table?

2013-01-02 Thread James Taylor
associated with the workflow_step. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 1, 2013 at 6:21 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: Dear all, This is the content of my workflow_step_connection table

Re: [galaxy-dev] What is the difference between the table stored_workflow and workflow in Galaxy?

2013-01-02 Thread James Taylor
This pattern is used to implement versioning. Every time a workflow is saved a new entry in the workflow table is created. The stored_workflow table keeps a pointer (latest_workflow_id) to the most recent. ___ Please keep all replies on the

Re: [galaxy-dev] MGTAXA taxonomic prediction does not work...

2013-01-02 Thread James Taylor
I assume you are using the mgtaxa Galaxy instance at JCVI. I've copied the mgtaxa maintainer on this message. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Dec 28, 2012 at 11:56 AM, Edlund, Anna aedl...@jcvi.org wrote: Hello. My name is Anna Edlund and I have

Re: [galaxy-dev] Very confused about workflow_step_connection table?

2013-01-02 Thread James Taylor
To the workflow_step table. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 2, 2013 at 10:48 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: Ok. So they are the foreign key from which table? Or the same table workflow_step_connection? On Wed, Jan 2

Re: [galaxy-dev] Viewing Galaxy in Ipad

2013-01-04 Thread James Taylor
Carrie, Thank you so much for bringing this new webkit CSS attribute to our attention! This iOS bug has plagued us for years. I think what you want to do however is add this to the div containing the iframe. Specifically in templates/root/index.mako there is a unified-panel-body div that contains

Re: [galaxy-dev] Viewing Galaxy in Ipad

2013-01-04 Thread James Taylor
The fix is in this changeset, applied conditionally on iOS devices: https://bitbucket.org/galaxy/galaxy-central/commits/312ba8a948a1c678bea807f4a0d3320a On Fri, Jan 4, 2013 at 2:08 PM, James Taylor ja...@jamestaylor.org wrote: Carrie, Thank you so much for bringing this new webkit CSS

Re: [galaxy-dev] Viewing Galaxy in Ipad

2013-01-04 Thread James Taylor
It is working for me on a real ipad (3rd gen). It isn't perfect, sometimes it scrolls the whole page and other times the frame, but it does seem to mostly work. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Jan 4, 2013 at 3:55 PM, Ganote, Carrie L cgan...@iu.edu

Re: [galaxy-dev] Stumped by GridOperation

2013-01-07 Thread James Taylor
Ted, have you considered if you can do what you need with the 'allowed' method of GridOperation? It let's you define a callable condition that determines if that operation is allowed on a given item. It does not have access to trans but it would be reasonable to add that. -- James Taylor

Re: [galaxy-dev] Enhancing tool id=subtract_query1

2013-01-15 Thread James Taylor
Even for a small change a pull request is preferred since they allow the origin of the change to be tracked. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other

Re: [galaxy-dev] Can't see history settings, reload etc. after recent update

2013-01-15 Thread James Taylor
Do you see the same problem if you access main.g2.bx.psu.edu? What browser are you using? You may need to clear your browser cache. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Jan 14, 2013 at 11:03 PM, Anthonius deBoer thondeb...@me.comwrote: Hi, I just

Re: [galaxy-dev] macs error for chipseq data

2013-01-16 Thread James Taylor
This is great. For the Galaxy tools, will you be able to submit wrappers to the toolshed? This should make it easier for users to install into their local Galaxy instances. Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh

Re: [galaxy-dev] Workflows

2013-01-16 Thread James Taylor
are looking for. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 15, 2013 at 8:52 PM, neil.burd...@csiro.au wrote: Hi Sorry if these questions are obvious but I just don’t know how to find the answers. I’m trying to get one of the API examples to work

Re: [galaxy-dev] Error trying to remove trackster visualization in latest galaxy-dist

2013-01-17 Thread James Taylor
On Thu, Jan 17, 2013 at 1:16 PM, Anthonius deBoer thondeb...@me.com wrote: Not to be ungrateful for the hard work you guys are all doing and please don't get this the wrong way, but is there any QA that is being done on the galaxy-dist when it is being released? No worries Thon, we appreciate

Re: [galaxy-dev] BED files not recognized correctly

2013-01-24 Thread James Taylor
Are you seeing this with any BED file, or just those where the chrom column is 1 rather than chr1? Column auto-detection for interval files looks for a name like chr, contig, scaffold, ... -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 22, 2013 at 4:35 PM

Re: [galaxy-dev] Selecting Intermediary Files in a Workflow

2013-01-28 Thread James Taylor
You can work around this using the from_work_dir attribute when specifying the output file in your tool config. -- jt (composed on my phone) On Jan 27, 2013, at 6:13 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Jan 27, 2013 at 10:26 PM, Kolby Chien kc...@nau.edu wrote: Hello,

Re: [galaxy-dev] workflow Editor

2013-01-28 Thread James Taylor
now (particularly how tool states -- the values of the various input parameters -- are encoded). -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Jan 28, 2013 at 5:17 AM, ssha...@cdac.in wrote: Hi, I want to know about workflow editor and how it works internally

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread James Taylor
Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H mwald...@email.unc.edu wrote: To be honest, I barely understand this enough to just follow the wiki

Re: [galaxy-dev] Error trying to add tools from tool shed respository

2013-01-29 Thread James Taylor
Wasn't sure of the order, those are definitely after running the update. Dannon's advice makes a good point, upgrading to the latest mercurial should help. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 11:10 AM, Waldron, Michael H mwald

Re: [galaxy-dev] Different behavior of select tag in the tool configuration file when the number of options is different.

2013-01-30 Thread James Taylor
/b70fa48058f60c88dff0f29a084ee8b0876d033a/select2-for-big-selects -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 30, 2013 at 4:45 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Jan 30, 2013 at 3:01 AM, Luobin Yang yangl...@isu.edu wrote: Hi, I have a 'select' tag

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

2013-01-30 Thread James Taylor
people ar actively working on that code it might be best to wait, merging lots of code on top of renames can get messy. -- James Taylor, Assistant Professor, Biology/CS, Emory University ___ Please keep all replies on the list by using reply

Re: [galaxy-dev] show urls in csv (in eye mode)

2013-01-30 Thread James Taylor
You may want to be careful with this solution because it allows script injection, any HTML including javascript in the uploaded tabular file will be executed by the .html call, with complete access to everything in the Galaxy browser window (like your session cookies). -- James Taylor, Assistant

Re: [galaxy-dev] How to call a cgi web page in a galaxy folder from a script?

2013-01-30 Thread James Taylor
your script a Galaxy tool, but it depends on what you mean by how will I call it inside a script in galaxy?. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Sun, Jan 27, 2013 at 2:23 PM, Zinonas Antoniou z.anton...@gmail.com wrote: Hello, Now I have a web page (cgi

Re: [galaxy-dev] rerun tool in a workflow

2013-01-30 Thread James Taylor
Not currently, however we are planning to implement this in the future. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Sun, Jan 27, 2013 at 10:20 AM, Hagai Cohen hag...@cs.huji.ac.il wrote: Hi, is it possible that when I rerun a tool it will also rerun the tools

Re: [galaxy-dev] maximum recursion depth exceeded while calling a Python object

2013-01-30 Thread James Taylor
Can you send some additional lines of the error? The important part is to see what part of the stack is repeating. Based on what you have it suggests recursion in trying to do a datatype conversion. Have you modified datatypes_conf.xml and is it possible there is a problem there? Thanks! -- James

Re: [galaxy-dev] Error loading a BAM file -- dataset needs grooming

2013-01-30 Thread James Taylor
I believe Galaxy requires samtools to be installed to work with bam data. If you install samtools in a location Galaxy can see it then this error should no longer occur. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Jan 25, 2013 at 11:11 AM, Maureen J. Donlin donli

Re: [galaxy-dev] How do I allow a large group of users to RUN my workflow without them having to make a local copy

2013-02-01 Thread James Taylor
It seems strange not to be able to share workflows with groups if you can share them with individual users.. The group/role system for data libraries and the sharing system for other assets were developed concurrently. It would be reasonable (and probably not that difficult) to add groups to

Re: [galaxy-dev] galaxy assumed linux shell

2013-02-03 Thread James Taylor
Command lines inside tool configs are assumed to be 'sh' (posix bourne shell). If you are extending one of the runners, definitely stick to pure 'sh'. However, once your command is run, there is no reason you can't use any shell of your choice. -- James Taylor, Assistant Professor, Biology/CS

Re: [galaxy-dev] Can Galaxy run on Hadoop system?

2013-02-06 Thread James Taylor
a Galaxy frontend. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Feb 6, 2013 at 9:51 AM, lukeyoyo lukey...@gmail.com wrote: Hi, I am a computer engineer and have to deploy a cloud computing system, like Hadoop. I want to deploy a local Galaxy system on the Hadoop

Re: [galaxy-dev] Upload file : auto-detect based on file extension ?

2013-02-12 Thread James Taylor
I don't believe you can, although it should be possible to extend upload to provide that information. However, is there no header you can use in your filetype to detect it? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Feb 11, 2013 at 10:51 PM, David Angot dav

Re: [galaxy-dev] Reloading a tools configuration does not seem to actually work

2013-02-14 Thread James Taylor
together on this. -- James Taylor, Assistant Professor, Biology/CS, Emory University ___ 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

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 James Taylor
On Fri, Feb 15, 2013 at 9:30 AM, James Taylor ja...@jamestaylor.org wrote: 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

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