Re: [galaxy-dev] [galaxy-user] Problem with new tool shed

On 11/10/11 06:25, Greg Von Kuster wrote: Hello Florent, On Oct 4, 2011, at 11:42 PM, Florent Angly wrote: Hi Greg, Thank you for your help. Your suggestion worked like a charm! I was expecting to see an error because I did not create the ../shed_tool/ folder that contains the tools install

Re: [galaxy-dev] Some changes to tophat and cufflinks wrappers for indexing loc files

1.)Please see attached. 2.)So I did this for tophat and cufflinks. This would be useful for cuffcompare. Cuffdiff uses the gtf files output from cufflinks and not reference gtf files. Following a conversation we had with James, I plan on editing the xml scripts to pull the genome attri

Re: [galaxy-dev] Some changes to tophat and cufflinks wrappers for indexing loc files

> I made some changes to the cufflinks and tophat wrapper to pull gtf files > from an indexed loc file as opposed to from history. The diff’s are > attached. I made it an optional feature. Please let me know if this makes its > way into galaxy-central. Ilya, This looks like a good start. A co

Re: [galaxy-dev] samtools mpileup update

Glen: Please, contribute it to Tool Shed once you are done with testing. This will be much appreciated. Thanks! anton Anton Nekrutenko http://galaxyproject.org On Oct 12, 2011, at 4:00 PM, Glen Beane wrote: > I have an mpileup tool for Galaxy I've developed. After a little more > testi

Re: [galaxy-dev] samtools mpileup update

I have an mpileup tool for Galaxy I've developed. After a little more testing I may be able to share it. the tool also converts the bcl output of mpileup to vcf On Oct 12, 2011, at 2:41 PM, Jennifer Jackson wrote: > Hello David, > > An update is planned, but we can't provide an exact time-li

Re: [galaxy-dev] [galaxy-user] Problem starting galaxy on Cygwin

Oren,I've moved this thread over to the galaxy-dev mailing list since it deals with a local installation.  Users on this list are more likely to have an answer for this type of question.That said, we don't officially support running Galaxy under Cygwin (or Windows at all), and I don't know of anyon

Re: [galaxy-dev] Trasfering Galaxy workflows to other instances

Hello Ilya, I've recently enhanced the workflow import features to allow for uploading an exported Galaxy workflow file. This will replace the current TextArea that forces you to paste the workflow text in order to import it. I'm not quite able to commit this change yet as I am in the process

Re: [galaxy-dev] Specifying data types for workflow inputs

Hi  -DannonI am attaching a sample workflow so you can hopefully reproduce locally: Galaxy-Workflow-Test_Workflow.ga Description: Binary data I have a history that contains datasets of various different types.  I would expect when I run this workflow, however, that only the datasets in my history

Re: [galaxy-dev] samtools mpileup update

Hello David, An update is planned, but we can't provide an exact time-line yet. To track the issue, this bitbucket ticket can be followed: https://bitbucket.org/galaxy/galaxy-central/issue/524/ Apologies for the delay in reply, Best, Jen Galaxy team On 8/23/11 9:10 AM, David Hoover wrote:

Re: [galaxy-dev] Specifying data types for workflow inputs

Thanks for the response. I am not seeing this behavior in my workflows. When I go to run the workflow, a gatk dbsnp file is the default selected for all my input dataset steps, even though some of them must be fastqillumina or bed/interval files, etc (depending on the step they are wired into)

Re: [galaxy-dev] hardware for local galaxy install

HI Jeremy, Many thanks for the feedback (I thought I'd cc'd the dev list but apparently not!) any advice is most useful especially as they are keen to hear what we want (they already have a list of demands from the aerospace guys!). Best Wishes, David. __ Dr Da

Re: [galaxy-dev] Specifying data types for workflow inputs

Ann,Unless I misunderstand what you're asking for, this should already be the case.  For instance, if a workflow step takes in a file of 'tabular' type, only tabular files (and subtypes, including interval, etc.) should be presented as dropdowns in the list.  Types such as plain text, binary files,

[galaxy-dev] Specifying data types for workflow inputs

I am developing a custom workflow in galaxy. I have 4 input files that need to be fed into various steps of the workflow. I would like to be able to specify a data type for the inputs such that the pre-populated drop downs are filtered to datasets of the appropriate type as well as being able

[galaxy-dev] Trasfering Galaxy workflows to other instances

Is there a way of uploading workflows by saving the workflow to a file and copying the workflow files to a directory or editing a database file to point to them. When external authentication is invoked linking to workflows does not seem to work and copy and pasting from a file is very tedious.

Re: [galaxy-dev] strange history error

Thanks, we actually had the wrong cookie_path set and that seemed to be causing the problem. Ilya -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Wednesday, October 12, 2011 1:09 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] strange h

Re: [galaxy-dev] scatterplot broken

Again, solved my own problem. diff -r 949e4f5fa03a tools/plotting/scatterplot.py --- a/tools/plotting/scatterplot.py Mon Aug 29 14:42:04 2011 -0400 +++ b/tools/plotting/scatterplot.py Wed Oct 12 10:35:58 2011 -0400 @@ -20,7 +20,8 @@ xlab = sys.argv[6] ylab = sys.argv[7] -ma

[galaxy-dev] hardware for local galaxy install

David, Please direct questions about local installations to the galaxy-dev mailing list (cc'd); there are a large number of experienced people of this list that can likely help with this and similar questions. > Just a quick question about the compute infrastructure of the setup running > the

Re: [galaxy-dev] trinity on galaxy

HI, Thanks for the feedback we'll incorporate it into our setup. In the meantime, our fix inside the perl script (which increases the heap from 1GB to 2GB) appears to have worked a treat and we have lots of lovely looking transcripts! So for anyone following this that seems to be a good place t

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

On Wed, Oct 12, 2011 at 5:23 PM, Hans-Rudolf Hotz wrote: > Hi Timothy > > Are you talking about the name as it will appear in the history? > > Then have a look at the following wiki page: > > http://wiki.g2.bx.psu.edu/**Admin/Tools/Tool%20Config%** > 20Syntax#A.3Coutputs.3E_tag_**set

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

Hi, I a similar vein to http://gmod.827538.n3.nabble.com/Dynamic-default-values-tt3010740.html I am trying to populate a default value based on settings elsewhere, in this case the user email if they are logged in. So far I have: Yes No

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

Hi Timothy I don't really see the connection to you first question, but maybe I misunderstood the first one Anyway, you probably need to define those output files which are required by "B" as 'Static Multiple Outputs' and the rest as 'Variable Static Outputs determined by parameter valu

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

Hi Timothy Are you talking about the name as it will appear in the history? Then have a look at the following wiki page: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set Regards, Hans On 10/12/2011 10:50 AM, Timothy Wu wrote: Hi, I thought I had already

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

On Wed, Oct 12, 2011 at 4:50 PM, Timothy Wu <2hug...@gmail.com> wrote: > Hi, > > I thought I had already asked this question a while ago, but I can't find > it so I guess I haven't. > > When porting my own tool, is there anyway to customize the name of the > output? > > Timothy > I have another p

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

Hi, I thought I had already asked this question a while ago, but I can't find it so I guess I haven't. When porting my own tool, is there anyway to customize the name of the output? Timothy ___ Please keep all replies on the list by using "

Re: [galaxy-dev] strange history error

Hi just asking the obvious questions to double check: - are you sure, this second instance is not accessing the same PostgreSQL/MySQL database as the first one? - are you sure, the user you are logged-in does exist in the PostgreSQL/MySQL database? I kind of remember getting a similar