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
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
/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that would allow unpublished workflows or histories to be accessed by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
.
-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
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
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
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
://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
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
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
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
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
, 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
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
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
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
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:
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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(
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
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.
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
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
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:
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
...@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
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
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
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
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
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
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
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,
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
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
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
...@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
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
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
, 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
/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
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
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
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
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
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
?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
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
...@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
(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
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
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
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
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
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
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
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
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 '
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
-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
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
, 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
On Thu, Aug 29, 2013 at 4:17 PM, Guest, Simon simon.gu...@agresearch.co.nz
wrote:
There is a similar but probably larger set of Debian packages
available via Debian-Med and Bio-Linux too. The catch here is can you
install arbitrary versions of a tool in parallel? And I think the
answer
Glad to hear blend4j is working well, annoyed to here it is not
streaming files out by default.
Based on your ideas I started some work here, but it is not right. I
spent the last half an hour looking around Galaxy trying to figure out
why history creation via the API was broken, not realizing it
It looks like there was never a response, but I was looking at a
distantly related issue and came across this thread. If you eliminate
the email hidden parameter and just use:
dynamic_options=getExperiments(__trans__.user.email)
Would that work for your use case?
-John
On Tue, Sep 25, 2012 at
On Tue, Sep 17, 2013 at 7:43 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi,
oh I see. Great! I would vote to include them in the main samtools
package and extend the help text a little bit, so that the search will
find it.
Seconded, this would be helpful for some stuff I have been
On Tue, Sep 17, 2013 at 3:03 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi all,
that is now implemented in:
https://bitbucket.org/galaxy/galaxy-central/pull-request/219/implementation-of-the-a-r_environment-to/diff
Any comments are much appreciated.
Fantastic work, I like this a
You have to compile nginx with the auth-ldap module. Have you done
this? I am doing using CloudBioLinux and here is how it is being done
in that context, but it would probably be easier just doing it by
hand:
https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/galaxy/__init__.py
I
-dist/lib/galaxy/web/framework/__init__.py which I would
like to avoid for ease of maintainability purposes.
Thank you.
-Original Message-
From: John Chilton chil...@msi.umn.edu
Date: Wednesday, September 18, 2013 7:49 AM
To: Iry Witham iry.wit...@jax.org
Cc: galaxy-dev
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