Re: [galaxy-dev] Hiding a tool via tool_conf.xml
On Thu, Feb 10, 2011 at 5:58 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm aware that in an individual tool's XML wrapper you can add hidden=true to the tool element to hide the tool from the listing shown in Galaxy's left hand panel (but the tool is still loaded and can be called by old workflows etc). Can this be done via the tool_conf.xml file as well? This would seem useful from a system configuration point of view where it seems wrong to edit the tool wrappers themselves. In fact, it might also be nice to add hidden=true support to section as well as tool in tool_conf.xml - although I'm not so sure how useful that would be. Peter I've filed an enhancement request for this: https://bitbucket.org/galaxy/galaxy-central/issue/481/ Peter ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters
Hi all, I have a multi-step workflow where I've marked some parameters to be set at run time (in this case, a minimum read length, used in two different workflow steps). I want to use the same parameter value in multiple tools, rather than give the user one prompt for each tool. Is this possible? Related to this, it would be nice to specify a default in the workflow (overriding any default in the tool wrapper), and give some caption text to the workflow level parameter. I guess some of this functionality would be related to any enhancement to make a workflow act like a tool (e.g. to combine subworkflows into larger workflows). Thanks, Peter ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters
On Wed, Mar 2, 2011 at 3:42 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
P.S. I do like the color highlighting and live substitution of
the workflow parameters into each tool step that uses them.
Very slick!
That was the good news. Now the bad news - two bug reports.
Firstly if you clear the workflow parameter (leaving it empty), then
the caption is used for the highlighted placeholders BUT only the
first word is used, e.g.
${Minimum read length (after any clipping)}
Initially the the placeholders show Minimum read length (after any
clipping), and if you enter a value like 30 then 30 is shown. If
you then edit the field to become empty, the placeholder now
shows just Minimum.
Furthermore, if I leave my workflow parameters empty, and
press execute, I get a traceback ending with:
AttributeError: 'WorkflowStep' object has no attribute 'module'
Since an empty value is valid for some tools for some parameters
(e.g. optional text fields) I would have expected any error later -
from the tools themselves if they don't like the empty value.
Peter
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Re: [galaxy-dev] RPM repository for NGS tools in Galaxy
Hi Leon, Thanks for sharing this with the community! As far as similar activities, we are actively working on a solution for packaging and deploying tools. Enis can share more about that, it is what we use already to automatically build our cloud images with all tools and data installed. Importantly, we are not using an existing package manager like RPM for (mostly) two reasons. First, we're trying to avoid focusing specifically on redhat et al. But more importantly, we want to avoid installing anything at the system level. In particular because it is difficult to have multiple versions of the same tool installed and usable at the same time. Instead, we are installing everything in isolated directories like: $GALAXY_APPS/package/version/ And adding the appropriate information to the environment at runtime based on requirement tags in the tool config. On Mar 2, 2011, at 12:38 PM, Leon Mei wrote: Dear colleagues, In order to ease administration on our servers running at VIB and NBIC, we will set up an RPM Repository for bioinformatics tools, the primary focus being NGS tools. The purpose is to come to a stable repository of easily installable packages for the common bioinformatics tools that can be used in a local Galaxy server. A list of tools under consideration can be found at https://wiki.nbic.nl/index.php/NBIC_%26_VIB_Bioinformatics_RPM_Repository So are there already similar activities going on? If yes, we would really love to hear your experience and probably work together on this. If you would like to join this effort and contribute into this repository, you are more than welcome to contact us as well! Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_meiMobile: +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 ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Running a workflow programatically
Darren, While this is not currently possible, I'm currently finishing up a first pass on a workflow API that will allow this sort of interaction and hope to have an early version available by the end of this week. I can update you when that has been committed. -Dannon On Feb 24, 2011, at 9:29 PM, Darren Brown wrote: Hello folks, I am using a workflow that needs to be run many times on many different inputs. I have hacked around and figured out how to pull multiple inputs from a history, but I am a little baffled on how to run a galaxy workflow programatically. I have searched around fairly exhaustively and am wondering if this is something that anyone else has come across and accomplished. And links or pointers? Take care, Darren ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Running a workflow programatically
Hello Dannon, That is surprising and excellent! Can't wait to hear more. Take care, Darren On Wed, Mar 2, 2011 at 11:38 AM, Dannon Baker dannonba...@me.com wrote: Darren, While this is not currently possible, I'm currently finishing up a first pass on a workflow API that will allow this sort of interaction and hope to have an early version available by the end of this week. I can update you when that has been committed. -Dannon On Feb 24, 2011, at 9:29 PM, Darren Brown wrote: Hello folks, I am using a workflow that needs to be run many times on many different inputs. I have hacked around and figured out how to pull multiple inputs from a history, but I am a little baffled on how to run a galaxy workflow programatically. I have searched around fairly exhaustively and am wondering if this is something that anyone else has come across and accomplished. And links or pointers? Take care, Darren ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
