date:20170710

Re: [galaxy-dev] any introduce for how Mako and JavaScript work in galaxy?

2017-07-10 Thread Steven Shen

It is of great help to me.Thank you very much.

steven


2017-07-08 0:38 GMT+08:00 Björn Grüning :

> Hi Steven,
>
> we have collected a few tutorials and slides here:
>
> http://galaxyproject.github.io/training-material/topics/dev/
>
> especially this:
>
> https://galaxyproject.github.io/training-material//topics/
> dev/tutorials/webhooks/tutorial.html
>
> and this:
>
> https://galaxyproject.github.io/training-material//topics/
> admin/tutorials/advanced-galaxy-customisation/slides.html
>
> Might be interesting for you depending on the modification you need to
> make.
>
> Hope this helps,
> Bjoern
>
> Am 07.07.2017 um 04:11 schrieb Steven Shen:
> > Hi everyone,
> >
> > I want to make some change for my local galaxy web, actually I can edit
> > galaxy_path/static/scripts/bundled/*.js directly.
> >
> > It seems mako templates are used for galaxy, as well as many JavaScript
> > files, but I don't know how they work. So is there any introduce for how
> > mako and JavaScript files working in galaxy?
> >
> > Thank you very much.
> >
> > Steven
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
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> >   https://lists.galaxyproject.org/
> >
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> >
>
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Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

2017-07-10 Thread Peter van Heusden

Hi Matthias

My job_conf.xml still has the old config of running upload locally, so it
has a section





after the  section. Are you using a proxy such as nginx with
your Galaxy server?

Thanks,
Peter

On Mon, 10 Jul 2017 at 11:50 Matthias Bernt  wrote:

> Hi Peter,
>
> FYI: just found on the galaxy documentation a paragraph that even
> recommends running upload on the cluster:
>
> https://galaxyproject.org/admin/config/performance/cluster/
>
> """
> If your cluster nodes have Internet access (NAT is okay) and you want to
> run the data source tools (upload, ucsc, etc.) on the cluster (doing so
> is highly recommended), set new_file_path in galaxy.ini to a directory
> somewhere in your shared filesystem:
> """
>
> Cheers,
> Matthias
>
>
> On 10.07.2017 11:11, Matthias Bernt wrote:
> > Dear Peter,
> >
> > my job_conf.xml is attached.
> >
> >
> > Best,
> > Matthuas
> >
> > On 08.07.2017 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:
> >> Send galaxy-dev mailing list submissions to
> >> galaxy-dev@lists.galaxyproject.org
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> https://lists.galaxyproject.org/listinfo/galaxy-dev
> >> or, via email, send a message with subject or body 'help' to
> >> galaxy-dev-requ...@lists.galaxyproject.org
> >>
> >> You can reach the person managing the list at
> >> galaxy-dev-ow...@lists.galaxyproject.org
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of galaxy-dev digest..."
> >>
> >>
> >> HEY!  This is important!  If you reply to a thread in a digest, please
> >> 1. Change the subject of your response from "Galaxy-dev Digest Vol
> >> ..." to the original subject for the thread.
> >> 2. Strip out everything else in the digest that is not part of the
> >> thread you are responding to.
> >>
> >> Why?
> >> 1. This will keep the subject meaningful.  People will have some idea
> >> from the subject line if they should read it or not.
> >> 2. Not doing this greatly increases the number of emails that match
> >> search queries, but that aren't actually informative.
> >>
> >> Today's Topics:
> >>
> >> 1. Re: any introduce for how Mako and JavaScript work ingalaxy?
> >>(Daniel Blankenberg)
> >> 2. Re: ustacks - bad interpreter (Björn Grüning)
> >> 3. Re: Improved DRMAAJobRunner (Peter van Heusden) (Matthias Bernt)
> >> 4. Re: Improved DRMAAJobRunner (Peter van Heusden)
> >>(Peter van Heusden)
> >>
> >>
> >> --
> >>
> >> Message: 1
> >> Date: Thu, 6 Jul 2017 22:36:27 -0400
> >> From: Daniel Blankenberg 
> >> To: Steven Shen 
> >> Cc: galaxy-dev@lists.galaxyproject.org
> >> Subject: Re: [galaxy-dev] any introduce for how Mako and JavaScript
> >> work ingalaxy?
> >> Message-ID:
> >>  >
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Hi Steven,
> >>
> >> For a quick first pass, have you taken a look at https://github.com/
> >> galaxyproject/galaxy/blob/dev/client/README.md?
> >>
> >>
> >> Thanks for using Galaxy,
> >>
> >> Dan
> >>
> >> On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen 
> >> wrote:
> >>
> >>> Hi everyone,
> >>>
> >>> I want to make some change for my local galaxy web, actually I can edit
> >>> galaxy_path/static/scripts/bundled/*.js directly.
> >>>
> >>> It seems mako templates are used for galaxy, as well as many JavaScript
> >>> files, but I don't know how they work. So is there any introduce for
> how
> >>> mako and JavaScript files working in galaxy?
> >>>
> >>> Thank you very much.
> >>>
> >>> Steven
> >>>
> >>> ___
> >>> 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:
> >>>https://lists.galaxyproject.org/
> >>>
> >>> To search Galaxy mailing lists use the unified search at:
> >>>http://galaxyproject.org/search/
> >>>
> >> -- next part --
> >> An HTML attachment was scrubbed...
> >> URL:
> >> <
> https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20170706/8fbd5cbe/attachment-0001.html
> >
> >>
> >>
> >> --
> >>
> >> Message: 2
> >> Date: Sat, 8 Jul 2017 11:31:31 +0200
> >> From: Björn Grüning 
> >> To: David Meltzer , Nate Coraor
> >> 
> >> Cc: "galaxy-dev@lists.galaxyproject.org"
> >> 
> >> Subject: Re: [galaxy-dev] ustacks - bad interpreter
> >> Message-ID: 
> >> Content-Type: text/plain; charset=utf-8
> >>
> >> Hi,
> >>
> >> please also make sure you have a recent

Re: [galaxy-dev] Fwd: Mismatched Files

2017-07-10 Thread Dave Bouvier


Changsu,

It sounds very much like multiple distinct galaxy instances are running 
against the same database, is that the case here? What happens in those 
situations is that each galaxy instance associates a dataset ID with a 
specific file, and the contents of the file might be tool output from a 
different galaxy instance.


-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org

On 07/06/2017 04:25 PM, Changsu Dong wrote:

Hello,

I am a galaxy user at Hunter College in New York. Recently we have 
encountered mismatching files throughout various tools under the same 
history. We are running our RNAseq analysis on the Dockerized 
containers. I need the BAM files (accepted hits) which produced by 
Tophats for the MulticovBed to get the read count. Those BAM files 
should be the binary 'accepted hit' files but instead they are showing 
random output from other tools(see the image below). This not only 
happened to BAM files but for most of the tools and most of the 
datasets. For example, the output for Groomer is not actually from 
Groomer but rather from the Tophat 'deletion' or an output from Cufflinks.


We are not sure if you are familiar with this issue whether it's a 
container or a Galaxy known issue. It would be great if you could point 
me to a right direction on how to resolve this issue.


Inline image 1


Sincerely,
Changsu



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[galaxy-dev] How to use the input freebayes "input_bams" to rename output

2017-07-10 Thread Charles Girardot

Hi all, 

I am a big fan of dataset renaming in my workflows, it helps a lot when you 
process tons of samples in parallel. 

I have integrated FreeBayes in a workflow but renaming the output to “#{ 
input_bams }.vcf” fails.

I remember that when the input is a list, one needs to use some weird formulas, 
for example in the tool “Filter BAM datasets on a variety of attributes (Galaxy 
Tool Version 0.0.1)” that also defines a “input_bams", we could solve the issue 
with :

#{input_bams_0.input_bam}

So I mimicked this and tried #{input_bams_0.input_bam} , #{input_bams_0.input} 
and #{input_bams_0.bam} without success. 

Does anyone has an idea what the correct spelling is for Freebayes ? I am sorry 
Jelle (our galaxy admin) is away this week  so I can’t tell you our server 
version but it is ~2 years old. 

Thanks

Charles 

=
Charles Girardot
Head of Genome Biology Computational Support (GBCS)
and Senior Bioinformatician in the Furlong Lab
European Molecular Biology Laboratory
Tel: +49 6221 387 -8585
Fax: +49-(0)6221-387-8166 
Email: charles.girar...@embl.de
Web : http://gbcs.embl.de
Room V205
Meyerhofstraße 1, 
69117 Heidelberg, Germany
=


















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Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

2017-07-10 Thread Matthias Bernt


Hi Peter,

FYI: just found on the galaxy documentation a paragraph that even 
recommends running upload on the cluster:


https://galaxyproject.org/admin/config/performance/cluster/

"""
If your cluster nodes have Internet access (NAT is okay) and you want to 
run the data source tools (upload, ucsc, etc.) on the cluster (doing so 
is highly recommended), set new_file_path in galaxy.ini to a directory 
somewhere in your shared filesystem:

"""

Cheers,
Matthias


On 10.07.2017 11:11, Matthias Bernt wrote:

Dear Peter,

my job_conf.xml is attached.


Best,
Matthuas

On 08.07.2017 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:

Send galaxy-dev mailing list submissions to
galaxy-dev@lists.galaxyproject.org

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-dev digest..."


HEY!  This is important!  If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-dev Digest Vol 
..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the 
thread you are responding to.


Why?
1. This will keep the subject meaningful.  People will have some idea 
from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match 
search queries, but that aren't actually informative.


Today's Topics:

1. Re: any introduce for how Mako and JavaScript work ingalaxy?
   (Daniel Blankenberg)
2. Re: ustacks - bad interpreter (Björn Grüning)
3. Re: Improved DRMAAJobRunner (Peter van Heusden) (Matthias Bernt)
4. Re: Improved DRMAAJobRunner (Peter van Heusden)
   (Peter van Heusden)


--

Message: 1
Date: Thu, 6 Jul 2017 22:36:27 -0400
From: Daniel Blankenberg 
To: Steven Shen 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] any introduce for how Mako and JavaScript
work ingalaxy?
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi Steven,

For a quick first pass, have you taken a look at https://github.com/
galaxyproject/galaxy/blob/dev/client/README.md?


Thanks for using Galaxy,

Dan

On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen  
wrote:



Hi everyone,

I want to make some change for my local galaxy web, actually I can edit
galaxy_path/static/scripts/bundled/*.js directly.

It seems mako templates are used for galaxy, as well as many JavaScript
files, but I don't know how they work. So is there any introduce for how
mako and JavaScript files working in galaxy?

Thank you very much.

Steven

___
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--

Message: 2
Date: Sat, 8 Jul 2017 11:31:31 +0200
From: Björn Grüning 
To: David Meltzer , Nate Coraor

Cc: "galaxy-dev@lists.galaxyproject.org"

Subject: Re: [galaxy-dev] ustacks - bad interpreter
Message-ID: 
Content-Type: text/plain; charset=utf-8

Hi,

please also make sure you have a recent conda version. This 80 character
length smalls a lot like an old conda restriction.

Cheers,
Bjoern

Am 07.07.2017 um 18:09 schrieb David Meltzer:

Good afternoon,


Thank you for that! I will look in to it!


Best Regards,

David Jacob Meltzer


*From: *Nate Coraor 
*Date: *Friday, July 7, 2017 at 5:02 PM
*To: *David Meltzer 
*Cc: *Yvan Le Bras ,
"galaxy-dev@lists.galaxyproject.org" 


*Subject: *Re: [galaxy-dev] ustacks - bad interpreter


Hi David,


You may want to have a look at the first line of:


/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py 




The shell is claiming it is:

Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

2017-07-10 Thread Matthias Bernt


Dear Peter,

my job_conf.xml is attached.


Best,
Matthuas

On 08.07.2017 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:

Send galaxy-dev mailing list submissions to
galaxy-dev@lists.galaxyproject.org

To subscribe or unsubscribe via the World Wide Web, visit
https://lists.galaxyproject.org/listinfo/galaxy-dev
or, via email, send a message with subject or body 'help' to
galaxy-dev-requ...@lists.galaxyproject.org

You can reach the person managing the list at
galaxy-dev-ow...@lists.galaxyproject.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-dev digest..."


HEY!  This is important!  If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the 
original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you 
are responding to.

Why?
1. This will keep the subject meaningful.  People will have some idea from the 
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search 
queries, but that aren't actually informative.

Today's Topics:

1. Re: any introduce for how Mako and JavaScript work ingalaxy?
   (Daniel Blankenberg)
2. Re: ustacks - bad interpreter (Björn Grüning)
3. Re: Improved DRMAAJobRunner (Peter van Heusden) (Matthias Bernt)
4. Re: Improved DRMAAJobRunner (Peter van Heusden)
   (Peter van Heusden)


--

Message: 1
Date: Thu, 6 Jul 2017 22:36:27 -0400
From: Daniel Blankenberg 
To: Steven Shen 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] any introduce for how Mako and JavaScript
work in galaxy?
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi Steven,

For a quick first pass, have you taken a look at https://github.com/
galaxyproject/galaxy/blob/dev/client/README.md?


Thanks for using Galaxy,

Dan

On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen  wrote:


Hi everyone,

I want to make some change for my local galaxy web, actually I can edit
galaxy_path/static/scripts/bundled/*.js directly.

It seems mako templates are used for galaxy, as well as many JavaScript
files, but I don't know how they work. So is there any introduce for how
mako and JavaScript files working in galaxy?

Thank you very much.

Steven

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--

Message: 2
Date: Sat, 8 Jul 2017 11:31:31 +0200
From: Björn Grüning 
To: David Meltzer , Nate Coraor

Cc: "galaxy-dev@lists.galaxyproject.org"

Subject: Re: [galaxy-dev] ustacks - bad interpreter
Message-ID: 
Content-Type: text/plain; charset=utf-8

Hi,

please also make sure you have a recent conda version. This 80 character
length smalls a lot like an old conda restriction.

Cheers,
Bjoern

Am 07.07.2017 um 18:09 schrieb David Meltzer:

Good afternoon,

  


Thank you for that! I will look in to it!

  


Best Regards,

David Jacob Meltzer

  


*From: *Nate Coraor 
*Date: *Friday, July 7, 2017 at 5:02 PM
*To: *David Meltzer 
*Cc: *Yvan Le Bras ,
"galaxy-dev@lists.galaxyproject.org" 
*Subject: *Re: [galaxy-dev] ustacks - bad interpreter

  


Hi David,

  


You may want to have a look at the first line of:

  


/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py

  


The shell is claiming it is:

  


#!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a1

  


When it should be:

  


#!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/python

  


However, it could be that the line is correct and the output was
truncated, or the shell has a length limit for the shebang (although the
truncated string is only 79 characters, I'd be surprised if the limit
for your shell was that short).

  


--nate

  


On

Re: [galaxy-dev] any introduce for how Mako and JavaScript work in galaxy?

Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

Re: [galaxy-dev] Fwd: Mismatched Files

[galaxy-dev] How to use the input freebayes "input_bams" to rename output

Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

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