[galaxy-dev] New Remote Job Runner

2011-01-16 Thread John Chilton
can be found at: https://bitbucket.org/jmchilton/lwr/src Thanks for your time, John John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chil...@msi.umn.edu

[galaxy-dev] Enabling iterative test-driven development of tools

2011-03-09 Thread John Chilton
can make to get this work included in galaxy-central. Thanks for your time and consideration, -John John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chil...@msi.umn.edu

[galaxy-dev] Apache Configuration for Exporting Histories and Workflows

2011-07-22 Thread John Chilton
/for_direct_import? I assume this wouldn't also open a hole that would allow unpublished workflows or histories to be accessed by others (at my institution or else wise), is this correct? Thanks for your time, -John John Chilton Software Developer

[galaxy-dev] Defining Job Runners Dynamically

2011-10-15 Thread John Chilton
. -John John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chil...@msi.umn.edu ___ Please keep all replies

[galaxy-dev] Data Retention Policies

2011-10-23 Thread John Chilton
Hello All, This is more of a general policy question. The head of our Research Informatics Support Systems group here at the University of Minnesota wants to know how other institutions are handling the large amount of data generated by next generation sequencing facilities and processed

Re: [galaxy-dev] Possible Galaxy memory leak?

2012-02-29 Thread John Chilton
We had intermittent issues like this for an embarrassingly long time at MSI, but since we applied this patch https://bitbucket.org/galaxy/galaxy-central/pull-request/36/fix-for-dynamic_optionspy Galaxy has been running smoothly for weeks. Seems unlikely this is the problem in your case (unless you

Re: [galaxy-dev] Is there a way to dynamically assign Queues in Galaxy

2012-06-01 Thread John Chilton
I posted a message about this half a year ago and issued a pull request (which is now conflicted). I developed some code which was not a turn key solution but I thought it was a good first step and it was very expressive. It would allow you to do stuff like inspect input sizes or parameter values

Re: [galaxy-dev] populating history with input files automatically from remote site?

2012-06-07 Thread John Chilton
://bitbucket.org/jmchilton/galaxy-vm-launcher/src/8ac4834dc08c/lib/galaxy.py https://bitbucket.org/jmchilton/cloud-galaxy-dist/src/af9199b15195/scripts/api/handle_uploads.py Hope this is helpful, -John John Chilton Senior Software Developer University

[galaxy-dev] Tool Shed Workflow

2012-06-07 Thread John Chilton
institution. Thanks for your time, -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 ___ Please keep all

Re: [galaxy-dev] Tool Shed Workflow

2012-06-08 Thread John Chilton
7, 2012, at 11:55 PM, John Chilton wrote: I have read through the documentation a couple times, but I still have a few questions about the recent tool shed enhancements. At MSI we have a testing environment and a production environment and I want to make sure the tool versions

Re: [galaxy-dev] Tool Shed Workflow

2012-06-08 Thread John Chilton
On Fri, Jun 8, 2012 at 3:27 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi John, On Jun 8, 2012, at 1:22 PM, John Chilton wrote: Hello Greg, Thanks for the prompt and detailed response (though it did make me sad). I think deploying tested, static components and configurations to production

[galaxy-dev] Dynamic job runner configuration followup

2012-06-10 Thread John Chilton
it is possible. -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 ___ Please keep all replies on the list

Re: [galaxy-dev] Tool Shed Workflow

2012-06-12 Thread John Chilton
, 2012, at 12:36 AM, John Chilton wrote: We don't pull down from bitbucket directly to our production environment, we pull galaxy-dist changes into our testing repository, merge (that can be quite complicated, sometimes a multihour process), auto-deploy to a testing server, and then finally we

Re: [galaxy-dev] Tool migration errors

2012-07-11 Thread John Chilton
On Wed, Jul 11, 2012 at 3:25 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Thon, On Jul 11, 2012, at 3:38 PM, Anthonius deBoer wrote: My Galaxy version is the most recent, but I had cloned this from an earlier version and have made lots of changes over the months... This could pose

Re: [galaxy-dev] Unable to queue job, resubmitting might help

2012-07-12 Thread John Chilton
We have been experiencing this issue lately too since downgrading the galaxy web processes from a machine with 128G of RAM to a VM with 4G. There is a memory leak in the pbs stuff somewhere, it has been mentioned on the list before, no one seems to have found the cause or how to prevent it. It

Re: [galaxy-dev] Local instance is running way too slow!!!

2012-07-24 Thread John Chilton
-request/20/fastq_groomer-optimizations -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 On Tue, Jul 24, 2012 at 6:32 PM, Kenny Sabir traks...@gmail.com wrote

Re: [galaxy-dev] patch contribution (was Re: So I think I fixed a bug.)

2012-08-23 Thread John Chilton
John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 On Thu, Aug 23, 2012 at 8:29 AM, Langhorst, Brad langho...@neb.com wrote: Maybe I'm just doing it wrong… but I find

Re: [galaxy-dev] Possible bug in dynamic options

2012-08-24 Thread John Chilton
I cannot speak to the code running twi, but are using a unique_value filter? The dynamic_options code use to completely lock up our galaxy server for minutes at a time before I applied this optimization:

Re: [galaxy-dev] patch contribution (was Re: So I think I fixed a bug.)

2012-08-29 Thread John Chilton
the repository to galaxy-central-new-feature - what does this achieve? I'm pretty new to mercurial and more familiar with git, so that could be why I'm confused. Thanks, Clare On 24 August 2012 00:07, John Chilton chil...@msi.umn.edu wrote: I don't know that difficult is the right word, I would

Re: [galaxy-dev] dynamically send jobs to second cluster on high load

2012-09-24 Thread John Chilton
to determine if the dedicated Galaxy resource is busy (or maybe just what queue manager you are using if any). Let me know if you go ahead and get this working, I am eager to hear success stories. -John John Chilton Senior Software Developer University

[galaxy-dev] Workflow Batching Enhancements

2012-10-05 Thread John Chilton
assume I am fairly off base on this link idea. Thanks, -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https

Re: [galaxy-dev] pass more information on a dataset merge

2012-10-08 Thread John Chilton
requests to improve batching workflows and multi-input tool parameters instead, but I hope to eventually get around to it. -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612

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

2012-10-10 Thread John Chilton
to the issues? Thanks 10e+06 --Mark Johnson NCBI On 10/10/12 2:45 PM, John Chilton wrote: Hey Mark, A few things, instead of printing stuff out you could use the global variable log in the binary.py file. Maybe something like log.warn(SNIFFING csra). I think your logging statements

Re: [galaxy-dev] pass more information on a dataset merge

2012-10-15 Thread John Chilton
the idea is valuable outside of proteomics. Galaxy team, would you be okay with including this and if so is there anything you would like to see either at a high level or at the level of the actual implementation. -John John Chilton Senior

Re: [galaxy-dev] Number of outputs = number of inputs

2012-10-16 Thread John Chilton
hacking on it though :) -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https://github.com/jmchilton Web: http

Re: [galaxy-dev] Number of outputs = number of inputs

2012-10-17 Thread John Chilton
Sorry about that. -John On Tue, Oct 16, 2012 at 8:48 AM, John Chilton chil0...@umn.edu wrote: I don't believe this is possible in Galaxy right now. Are the outputs independent or is information from all inputs used to produce all outputs? If they are independent, you can create a workflow

Re: [galaxy-dev] windows nodes on cloudman/ec2

2012-10-19 Thread John Chilton
: https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https

[galaxy-dev] Galaxy Tool Loading

2012-10-22 Thread John Chilton
John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https://github.com/jmchilton Web: http://jmchilton.net order.patch Description

Re: [galaxy-dev] Enhancement: selecting input

2012-10-24 Thread John Chilton
on input data parameters. Then a multi-selection widget is rendered instead of a drop down list. We have addressed rerunning tools, interaction with the workflow editor, workflow imports and exports, etc -John John Chilton Senior Software Developer

Re: [galaxy-dev] Multiple inputs in a workflow (variable number of inputs) ?

2012-11-12 Thread John Chilton
The general case is hard and it was brought up repeatedly at the Galaxy community conference. One path might be this work (https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes) on defining datasets that represent homongenous collections of files, but there are no easy

Re: [galaxy-dev] Tags API

2012-11-12 Thread John Chilton
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 api/histories/history_id/contents/dataset_id/tags/tag_name or POST to

Re: [galaxy-dev] workflow input param issue

2012-12-03 Thread John Chilton
I am really very sorry about that. It seems this must be related to my pull request fixing multiple input tool parameters. I have spent some time this morning trying to reproduce your error, but I cannot. That said I think I can fix it, this patch should work: diff --git

Re: [galaxy-dev] pass more information on a dataset merge

2012-12-03 Thread John Chilton
which should set it to NULL if it's missing? -Alex -Original Message- From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton Sent: Wednesday, 17 October 2012 3:21 AM To: Khassapov, Alex (CSIRO IMT, Clayton) Subject: Re: [galaxy-dev] pass more information

Re: [galaxy-dev] Permission denied error for velveth

2012-12-04 Thread John Chilton
I don't have a velvet or a submit-jobs-as-user environment setup so I cannot test this, but it seems like this should have a an easy fix. Can someone who is experiencing the problem try the attached patch or has something like this been tried and there is some other problem? -John (09:43:01 AM)

Re: [galaxy-dev] Permission denied error for velveth

2012-12-06 Thread John Chilton
me to run more test, just email me. regards, Andreas On 04.12.2012 18:27, John Chilton wrote: I don't have a velvet or a submit-jobs-as-user environment setup so I cannot test this, but it seems like this should have a an easy fix. Can someone who is experiencing the problem try the attached

Re: [galaxy-dev] binary data types get corrupted on upload

2012-12-07 Thread John Chilton
Hi Ido, Is .sqlite a common compressed file type (i.e. zip, gzip, or bz2) just with a different extension? If it is, I think upload.py is always going to try to decompress it. That that has long been a behavior I would like to be able to disable on a per file type basis. If this is the problem

Re: [galaxy-dev] user creation using API

2013-01-07 Thread John Chilton
I am pretty confident there is no way to do this via the API currently, though I imagine it wouldn't be terribly complicated to add and the community would appreciate the contribution. If API-based access isn't a strong requirement and you have direct access to the Galaxy server here is a

Re: [galaxy-dev] backtrace when attempting to view a shared workflow

2013-01-08 Thread John Chilton
I am a little paranoid that I am the one that broke something (I guess that is pattern matching more than paranoia), but I have looked through that code and it is not immediately obvious to me what the problem is. If you have some time, can you try cloning the workflow and ripping various parts

Re: [galaxy-dev] Uploading files to history via API

2013-01-14 Thread John Chilton
Hey Neil, Just last week pull request 94 was accepted into galaxy-central that direct upload of files to history (without needing a URL). The python bioblend (https://github.com/afgane/bioblend) API client does not yet have it but it would be relatively easy to add, you will want to look at

Re: [galaxy-dev] lwr job runner error.

2013-01-27 Thread John Chilton
There were some problems with backing out of recent LWR changes. They have been re-added correctly in galaxy-central. If you require the use of the LWR, I would suggest pulling in changes from galaxy-central through be7625f376d16cefa2fb4984fa6483f37b4b71d4. If you do not require the LWR I believe

Re: [galaxy-dev] How to use the API when using a proxy server

2013-01-31 Thread John Chilton
I don't know how to speak intelligently about this, so excuse my imprecise language. The idea is that you need to still pass session information (REMOTE_USER) along so JavaScript can access the API, but for /api you need to make that optional. I have an Apache server using TKTAuth. For that

Re: [galaxy-dev] permissions on library contents

2013-02-05 Thread John Chilton
Only setting library permissions has been implemented. A new methods would need to be added to this controller if you would like to read library permission. If you want to change the library permissions using the API, you can post against that URL and include the following options in your

Re: [galaxy-dev] Preffered way of running a tool on multiple input files

2013-02-12 Thread John Chilton
Hagai, Jorrit Boekel and I have implemented essentially literally what you described. https://bitbucket.org/galaxy/galaxy-central/pull-request/116/multiple-file-datasets-implementation Merge this in to your Galaxy tree https://bitbucket.org/jmchilton/galaxy-central-multifiles-feb2013. Switch

Re: [galaxy-dev] Tool wrapper XSD

2013-02-19 Thread John Chilton
Hey Pierre, If you are going to write one and want a starting point, here is the schema I used for incorporating Galaxy tools into a Java web service workflow framework called TINT: https://github.com/jmchilton/TINT/blob/master/projects/TropixGalaxy/schema/galaxy.xsd It is mostly a subset of

Re: [galaxy-dev] Downloading datasets without username/password when login is required

2013-02-25 Thread John Chilton
I have also encountered the need for this and believe it is important. I have issued a pull request implementing this. https://bitbucket.org/galaxy/galaxy-central/pull-request/131/implement-equivalent-of-dataset-display/diff Thanks, -John On Thu, Dec 13, 2012 at 2:20 PM, Sytchev, Ilya

Re: [galaxy-dev] Composite datatype output for Cuffdiff

2013-02-27 Thread John Chilton
Hey Jeremy, I am trying to think about a path forward with this composite multiple file dataset implementation. It seems there is consensus among the galaxy team that it shouldn't be included because grouping actual datasets would be superior. In that light, I am revisiting this e-mail, because

Re: [galaxy-dev] blend4j

2013-02-28 Thread John Chilton
This is not a blend4j issue, it is more of a Galaxy API issue. I think it is essentially a known problem that you cannot specify runtime parameters for workflow, only data inputs. Here the relevant piece of Galaxy code: inputs = {} for step in latest_workflow.steps: if

Re: [galaxy-dev] blend4j

2013-03-03 Thread John Chilton
Can you reproduce this on the main or test galaxy server @ Penn and make the workflow public? -John On Fri, Mar 1, 2013 at 11:21 AM, Marc Logghe marc.log...@ablynx.com wrote: From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Marc Logghe

Re: [galaxy-dev] Composite datatype output for Cuffdiff

2013-03-03 Thread John Chilton
Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John Chilton Sent: Thursday, 28 February 2013 2:06 AM To: Jeremy Goecks Cc: Jim Johnson; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff Hey

Re: [galaxy-dev] Implementing dataset collections

2013-03-04 Thread John Chilton
into main Galaxy implementation. As we are using Galaxy for CT reconstruction tools, where input and output can consist of a couple thousand files, other options are not feasible, i.e. grouping datasets. -Alex On Mon, Mar 4, 2013 at 5:42 AM, John Chilton chil...@msi.umn.edu wrote: Hi Alex

Re: [galaxy-dev] Validating dynamic inputs stream of consciousness

2013-03-06 Thread John Chilton
team I would be happy to implement any of this with any desired changes. Thanks all, -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 https://twitter.com

Re: [galaxy-dev] Validating dynamic inputs stream of consciousness

2013-03-06 Thread John Chilton
On Wed, Mar 6, 2013 at 12:39 PM, James Taylor ja...@jamestaylor.org wrote: On Wed, Mar 6, 2013 at 12:22 PM, John Chilton chil...@msi.umn.edu wrote: This whole concept puts a lot of onus on the tool developer. A biologist who has taken a two week course on perl could probably write a Galaxy

Re: [galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset

2013-03-08 Thread John Chilton
Does rewriting this: def errors( self, trans, id ): try: hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) except: hda = None if not hda: hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get(

Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username

2013-03-14 Thread John Chilton
Greg, I think you can do this with dynamic job runners. http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html Step 1) Set: default_cluster_job_runner = dynamic:///python/default_runner Step 2) Create the file `lib/galaxy/jobs/rules/200_runners.py`, with contents something like

Re: [galaxy-dev] Conditional tool options based on input file format?

2013-03-15 Thread John Chilton
Hey Peter, I wonder if it is better to ask the user what type they would like to select and then have the input param inside the conditional. My concern about you approach is who it would interplay with workflows. Say you build a workflow that processes XML files with one input, say an XML file.

Re: [galaxy-dev] Is parallelism not working with galaxy-central?

2013-03-17 Thread John Chilton
I believe the following changeset fixes this problem. https://bitbucket.org/jmchilton/galaxy-central-lwr/commits/3b6c209d2d078bad2fa9957fe989345d3d2533ae I have incorporated the fix into pull request 138 that has other job runner fixes and enhancements. -John P.S. Peter's point about the

Re: [galaxy-dev] Conditional tool options based on input file format?

2013-03-18 Thread John Chilton
On Fri, Mar 15, 2013 at 9:58 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Mar 15, 2013 at 2:51 PM, John Chilton chil...@msi.umn.edu wrote: Hey Peter, I wonder if it is better to ask the user what type they would like to select and then have the input param inside the conditional

Re: [galaxy-dev] REST API: upload of dataset to history possible ?

2013-04-04 Thread John Chilton
On Tue, Apr 2, 2013 at 5:23 AM, Marc Logghe marc.log...@ablynx.com wrote: Hi, Is it currently possible to upload an input dataset to a history via the REST API ? This has been possible since pull request 94:

Re: [galaxy-dev] What is up with the multiple dataset selection for workflows

2013-04-04 Thread John Chilton
I don't know, these are the same reservations I initially had as well. It seems that select2 could simply be disabled for multiple select boxes or for these multiple select boxes. My thought was with the fixes from pull request 136 that select2 was at worst a side-grade for multiple selection, but

Re: [galaxy-dev] REST API: upload of dataset to history possible ?

2013-04-08 Thread John Chilton
...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton Sent: Monday, April 08, 2013 2:50 PM To: Marc Logghe Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? Can you retry that with ? as the db key, admittedly that could use some more documentation

Re: [galaxy-dev] Galaxy hg repository problem abort: path ... traverses symbolic link

2013-04-11 Thread John Chilton
Hey Peter, Hopefully Nate will have some wisdom, all I have is a workaround (I have fought with this on multiple forks and this is the best I have come up with). Check out a clean version of the tools branch somehow (it seems like the working contents can get stuck in an invalid state that

Re: [galaxy-dev] tool_dependencies inside tool_dependencies

2013-04-16 Thread John Chilton
Stepping back a little, is the right way to address Python dependencies? I was a big advocate for inter-repository dependencies, but I think taking it to the level of individual python packages might be going too far - my thought was they were needed for big 100Mb programs and stuff like that. At

[galaxy-dev] External Display Applications

2013-04-18 Thread John Chilton
This message is a continuation of a conversation from IRC, but it is too long for that medium. This is probably only directly meant for 3 or 4 people, but I sending this out wide and attaching the IRC conversation from yesterday because setting up and maintaining third party display applications

Re: [galaxy-dev] user names with authentication

2013-04-18 Thread John Chilton
Crazy coincidence, I had the same problem and hadn't even seen the original e-mail from Jillian. My pull request implementing this was merged by Nate earlier this week. https://bitbucket.org/galaxy/galaxy-central/pull-request/157/increased-flexibility-for-ftp-directory/diff You can just grab the

Re: [galaxy-dev] Knowing who is currently logged into your system

2013-04-22 Thread John Chilton
Hello Akshay, I have just issued a pull request to Galaxy to allow different toolbox views. https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters/diff If this gets incorporated, you would need to write some python to build these views (or filters) and

Re: [galaxy-dev] GalaxyAdmins Group: Future Directions?

2013-04-25 Thread John Chilton
I agree that we shouldn't be hasty, but my two cents is that the galaxy-dev list should be split in two. Ironically, I think most of the traffic on this list right now is related to deployment issues - in that respect I would see it almost as Galaxy admins stay here and developer chatter move to a

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

2013-04-27 Thread John Chilton
I put together a script to do this. It is described in the galaxy-dev thread titled: [galaxy-dev] user creation using API. It doesn't actually use the API, it uses the db_shell.py script. Hope this helps. -John On Thu, Apr 25, 2013 at 7:11 PM, Adam Brenner aebre...@uci.edu wrote: Howdy All,

[galaxy-dev] Galaxy, CloudMan nginx 1.4.0

2013-04-28 Thread John Chilton
I wanted to update CloudMan to use nginx 1.4.0 for web socket proxy support, but I hit a problem. nginx-upload-module does not work with nginx 1.4.0 and the author has no intention of continuing work on the module. https://github.com/vkholodkov/nginx-upload-module/issues/41 There is a patch that

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

2013-04-29 Thread John Chilton
Hey, it is not just me! Your commits are definitely in galaxy-dist, they just might not be part of the most recent stable tag. https://bitbucket.org/galaxy/galaxy-dist/commits/80291f7ad4576c95f70eaed2f36cc5a95cf303fb The hg new workflow is easy to mess up, it use to be that you could just trust

Re: [galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread John Chilton
Hello Dr. Krampis, At the present, the LWR is most valuable when there is not a shared file system between the server executing the jobs and the server hosting Galaxy. In this case you seem to have a shared filesystem so I would think setting up something like sun grid engine to manage the jobs

Re: [galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread John Chilton
...@gmail.com] On Behalf Of John Chilton [chil...@msi.umn.edu] Sent: Monday, May 06, 2013 9:50 AM To: Krampis, Konstantinos Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] LWR runner configuration for shared folder in cluster Hello Dr. Krampis, At the present, the LWR is most

Re: [galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread John Chilton
and just call client.setup() directly. You will want to submit the original command-line, not a rewritten one. Also in finish job, I think you will just want to skip the for loops with the downloads. Thanks, -John On Mon, May 6, 2013 at 11:55 AM, John Chilton chil...@msi.umn.edu wrote: On Mon, May

Re: [galaxy-dev] Multiple values in when tags for conditiona parameters

2013-05-09 Thread John Chilton
Yup, off list by mistake. -John On Thu, May 9, 2013 at 8:40 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Off list by mistake? On Thu, May 9, 2013 at 1:25 PM, John Chilton chil0...@umn.edu wrote: This is one of the use cases I was trying to address with tool macros. This has the added

Re: [galaxy-dev] tool_dependencies inside tool_dependencies

2013-05-15 Thread John Chilton
, 2013 at 2:46 PM, John Chilton chil...@msi.umn.edu wrote: Stepping back a little, is the right way to address Python dependencies? Looks like I missed this thread, hence: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014169.html I was a big advocate for inter-repository dependencies

Re: [galaxy-dev] tool_dependencies inside tool_dependencies

2013-05-17 Thread John Chilton
/posts/TkCFwA2jkDN -John On Tue, May 14, 2013 at 3:59 PM, Nate Coraor n...@bx.psu.edu wrote: Greg created the following card, and I'm working on a few changes to your commit: https://trello.com/card/toolshed-consider-enhancing-tool-dependency-definition-framework-per-john-chilton-s-pull

Re: [galaxy-dev] tool_dependencies inside tool_dependencies

2013-05-20 Thread John Chilton
and then commit my additions and changes. Today is the freeze so I'd like to get this in to the next release. Thanks, ---nate On May 17, 2013, at 11:21 AM, John Chilton wrote: Hey All, There was a long conversation about this topic in IRC yesterday (among people who don't actually use the tool shed

Re: [galaxy-dev] Multi File upload api

2013-05-30 Thread John Chilton
Alex, if I am not mistaken you guys are using a fairly old version of the multiple file dataset code. I think on the server side you would need to apply the following three changesets to update the library backend to support the creation of multifile datasets (I guess if you are doing path pasting

Re: [galaxy-dev] Status of Galaxy Cloud Instance dev

2013-05-31 Thread John Chilton
Hey Dannon, Thanks for the link, I saw that you had moved some cards to a CloudMan board but I was never able to find it. Could you enable comments for non-board members like the Galaxy Development Trello allows? You know I have a compulsion to comment on everything Galaxy related anywhere on

Re: [galaxy-dev] Multi File upload api

2013-05-31 Thread John Chilton
Of John Chilton Sent: Friday, 31 May 2013 5:50 AM To: Khassapov, Alex (CSIRO IMT, Clayton) Cc: Burdett, Neil (ICT Centre, Herston - RBWH); galaxy-...@bx.psu.edu Subject: Re: Multi File upload api Alex, if I am not mistaken you guys are using a fairly old version of the multiple file dataset

Re: [galaxy-dev] Creating workflow which includes Multifile upload

2013-06-05 Thread John Chilton
If you don't have pull request 122 in your code base, you will want to add it: https://bitbucket.org/galaxy/galaxy-central/pull-request/122/add-optional-upload-attribute-to-tool/diff Then, all you need to do is add the attribute ' workflow_compatible=false ' to your top level tool XML element in

Re: [galaxy-dev] Error / import rpy module

2013-06-05 Thread John Chilton
?msg_id=30999482 Although we haven't started to us it, I recommend using rpy2: http://rpy.sourceforge.net/rpy2.html Indeed - rpy v1 is still being maintained in SVN, but hasn't had an official release with these fixed for over two years. Most tools have been refactored by John Chilton see

Re: [galaxy-dev] Tool Visibility

2013-06-05 Thread John Chilton
Add workflow_ compatible =false to the tool XML element to hide it in the workflow editor. Check the tools/data_source/upload.xml for an example of this. If you would like to hide it both in the workflow editor and the side bar but still allow for other direct links to it you can setup dynamic

Re: [galaxy-dev] Tool Visibility

2013-06-05 Thread John Chilton
...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote: Add workflow_ compatible =false to the tool XML element to hide it in the workflow editor. Check the tools

Re: [galaxy-dev] Tool Visibility

2013-06-05 Thread John Chilton
(mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote: Add workflow_ compatible =false to the tool XML element to hide it in the workflow editor. Check the tools/data_source/upload.xml for an example of this. If you would like

Re: [galaxy-dev] Tophat2 output issue on LWR runner

2013-06-18 Thread John Chilton
Hey Nikos, Thanks for the interest in the LWR and frankly I am excited to hear that bowtie worked properly. Some of these core NGS tools that require implicit indices spanning multiple files are not really addressed by the LWR currently, it only knows how to stage files that actually appear in

Re: [galaxy-dev] Tophat2 output issue on LWR runner

2013-06-28 Thread John Chilton
was logged in lwr/paster.log Bests, Nikos 2013/6/18 John Chilton chil...@msi.umn.edu Hey Nikos, Thanks for the interest in the LWR and frankly I am excited to hear that bowtie worked properly. Some of these core NGS tools that require implicit indices spanning multiple files are not really

Re: [galaxy-dev] Exit_code not working anymore

2013-07-12 Thread John Chilton
I noticed this was a problem with the transition to setting metadata externally by default. Return code is completely ignored now (always has been when external metadata setting was enabled). Didn't have time to test the patch, but did post link to one in trello some time ago. On a train without

Re: [galaxy-dev] Implementing blend4j

2013-07-13 Thread John Chilton
So you have packaged blend4j and all of its dependencies into one jar file? I don't have any experience doing that. I could imagine potentially some files conflicting and only one version being written and so jersey-json breaks? Is this a possibility, some of the jar metadata sort of files? I

Re: [galaxy-dev] Implementing blend4j

2013-07-15 Thread John Chilton
the package in the central maven repositories. I think for now all the functionality I need is in your version of blend4j. But if I think of something new I'll try to participate. Thanks On 13 July 2013 08:58, John Chilton chil...@msi.umn.edu wrote: So you have packaged blend4j and all of its

[galaxy-dev] Galaxy-less Tool Installing

2013-07-15 Thread John Chilton
One of my goals for the GCC was to sell the idea that tool shed repositories need to be installable without a database present. I talked with James Taylor and Enis Afgan about this idea briefly and they seemed to believe this was a good idea - I kept meaning to discuss it with Greg but I never

Re: [galaxy-dev] Galaxy-less Tool Installing

2013-07-16 Thread John Chilton
process so that it would function in an environment without a Galaxy database, I'm not sure how much effort would need to go into doing so, or where to start. I'll have to think about this for a while. Greg Von Kuster On Jul 15, 2013, at 7:27 PM, John Chilton chil...@msi.umn.edu wrote

Re: [galaxy-dev] Galaxy-less Tool Installing

2013-07-16 Thread John Chilton
On Tue, Jul 16, 2013 at 1:16 PM, James Taylor ja...@jamestaylor.org wrote: On Mon, Jul 15, 2013 at 7:27 PM, John Chilton chil...@msi.umn.edu wrote: One of my goals for the GCC was to sell the idea that tool shed repositories need to be installable without a database present. I John, as I've

[galaxy-dev] RFC: Implement 'cloudbiolinux_install' tool shed package install action.

2013-08-06 Thread John Chilton
I have implemented a cool idea Brad Chapman had the recent BOSC Codefest. It would save me tons of effort related to maintaining separate proteomics module definitions for the tool shed and CloudBioLinux for Galaxy-P. I thought I would throw this out there and see if anyone has any comments:

Re: [galaxy-dev] Appending _task_%d suffix to multi files

2013-08-07 Thread John Chilton
I have added an feature request issue on galaxy-extras to support this. Earlier this year, Hagai Cohen was exploring the existing Galaxy tools and it seems like some of them expect dataset files to end with .dat. So I reworked the multiple file dataset stuff so each of the individual parts ended

Re: [galaxy-dev] Tool params passed to python dynamic job runner

2013-08-07 Thread John Chilton
I am not sure why the quotations marks are there in the first place, but I do see the problem. replace and strip return new strings, they don't modify the existing variable. This is demonstrated below: % python x = ' Moo Cow ' x ' Moo Cow ' x.replace(\, ).strip() 'Moo Cow' x ' Moo Cow '

Re: [galaxy-dev] Tool params passed to python dynamic job runner

2013-08-07 Thread John Chilton
python script. Hopefully that makes more sense... Thanks so much for the help! -Carrie From: jmchil...@gmail.com [jmchil...@gmail.com] on behalf of John Chilton [chil...@msi.umn.edu] Sent: Wednesday, August 07, 2013 3:52 PM To: Ganote, Carrie L Cc

Re: [galaxy-dev] Licensing Galaxy workflows; are they software or documents?

2013-08-20 Thread John Chilton
I don't have time to argue about this especially because I agree that cc is likely better than OSS licenses, but I am just too passionate about this point not too. Workflows are 100% software!!! A python script is just a protocol or a cookbook that tells a Python interpreter (runtime) how to

Re: [galaxy-dev] Implementing blend4j

2013-08-20 Thread John Chilton
-1/version /dependency -John On Mon, Jul 15, 2013 at 6:17 PM, John Chilton chil...@msi.umn.edu wrote: Fantastic. blend4j definitely should be in a public repository, just don't know how and have not had the time. Any help in that process would be most welcome. -John On Jul 15, 2013 10

Re: [galaxy-dev] tool_dependencies.xml format

2013-08-26 Thread John Chilton
James, et. al. I think it is interesting that there was push back on providing infrastructure (tool actions) for obtaining CBL from github and performing installs based on it because it was not in the tool shed and therefore less reproducible, but the team believes infrastructure should be put in

Re: [galaxy-dev] tool_dependencies.xml format

2013-08-27 Thread John Chilton
, Nate Coraor n...@bx.psu.edu wrote: On Aug 26, 2013, at 11:59 AM, James Taylor wrote: On Mon, Aug 26, 2013 at 11:48 AM, John Chilton chil...@msi.umn.edu wrote: I think it is interesting that there was push back on providing infrastructure (tool actions) for obtaining CBL from github

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