Re: [galaxy-dev] bug: unsorted bam files and import into data library

[Jennifer Jackson]

Hi Florian,

I am fairly certain that this exact issue is still open, and so have 
opened a bitbucket ticket to track progress:

http://bitbucket.org/galaxy/galaxy-central/issue/718/unsorted-bam-files-and-import-into-data

If this has been corrected already, one of us will send an update tomorrow.

Thanks!

Jen
Galaxy team


On 9/3/11 4:41 PM, Florian Wagner wrote:

Hi,

when a tool outputs an unsorted bam file, the indexing fails (quietly)
and its metadata variable "bam_index" points to an inexistent file. This
causes a nasty bug when trying to import the dataset into a data library
and actually makes the library unusable unless you delete the broken
entry from the - in my case Postgresql - database by hand. Are you
working on it?

Thanks, Florian
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Re: [galaxy-dev] No Display at UCSC Main link.

[Jennifer Jackson]

Hello again,

The link is not a Galaxy Main public instance share link, which would 
start with: http://main.g2.bx.psu.edu


Having the datatype as BED and the database as hg19 would (for all of 
the cases I can think of) bring up the "View at UCSC" link, if the 
instance is set up to have "display at UCSC" configured.


So, the root cause of the problem is probably with how this other 
instance is set up. If this is not your instance, you will want to 
contact the folks running it to see if they have plans to configure UCSC 
display. If this is yours, follow the instructions on this wiki to get 
set up:


http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
See the section: Display at UCSC

Hopefully this helps,

Best,

Jen
Galaxy team


On 2/14/12 9:26 PM, Luobin Yang wrote:

Hi, Jen,

The dataset is BED datatype and the database is hg19. Actually this
history contains the same steps as those in Galaxy101 tutorial.

I created the link for the history and here it is:




So basically I do not see an option called "Display at UCSC Main", but
it has two other options, "View in GeneTrack" and "Display at Ensemble
Current"

Thanks,
Luobin

On Tue, Feb 14, 2012 at 9:35 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:

Hi Luobin,

To display at UCSC, the datatype has to be a UCSC display type and
the database has to be a UCSC genome browser. Often, small changes
can be made to tune a dataset to help it fit into these
requirements. Other times, a dataset will need to be transformed
into another type or it can't be viewed at all because the genome is
not available at UCSC.

You should try to modify these attributes yourself first. Common
UCSC datatypes from Galaxy are: BED, bigBED, BAM. For the list of
UCSC known datatypes, see:
http://genome.ucsc.edu/FAQ/__FAQformat.html
.

Known databases would be any that you also can find at:
http://genome.ucsc.edu as full genome assemblies. The short label
used at UCSC should match the database assignment at Galaxy. For
example, the most recent human would be "hg19" at both.

If you are still stuck and would like to send me a shared history
link, I can provide feedback about how to modify (if possible) to
view at UCSC. Use "Options -> Share or Publish", generate the link,
and email this link directly back to me. Be sure to include the
dataset #, so that I know which in your history you want to view at
UCSC.

Best,

Jen
Galaxy team


On 2/14/12 11:50 AM, Luobin Yang wrote:

Hi,

I have a local instance of Galaxy, but I found there is no
"Display at
UCSC Main" link for some datasets that can be viewed in GeneTrack or
displayed by Ensemble, what has been wrong?

Thanks,
Luobin


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[galaxy-dev] Support for PolyPhen2

[Praveen Raj Somarajan]

Hi Dev Team,

Do you have any plan to integrate PolyPhen2 to Galaxy? I feel, it would be good 
if you can, as this extends the functionality of NGS analysis and (definetly) 
it would be value addition to Galaxy as well.

Let me know your comments.

Best,

Raj



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Re: [galaxy-dev] No Display at UCSC Main link.

[Jennifer Jackson]

Hi Luobin,

To display at UCSC, the datatype has to be a UCSC display type and the 
database has to be a UCSC genome browser. Often, small changes can be 
made to tune a dataset to help it fit into these requirements. Other 
times, a dataset will need to be transformed into another type or it 
can't be viewed at all because the genome is not available at UCSC.


You should try to modify these attributes yourself first. Common UCSC 
datatypes from Galaxy are: BED, bigBED, BAM. For the list of UCSC known 
datatypes, see: http://genome.ucsc.edu/FAQ/FAQformat.html.


Known databases would be any that you also can find at:
http://genome.ucsc.edu as full genome assemblies. The short label used 
at UCSC should match the database assignment at Galaxy. For example, the 
most recent human would be "hg19" at both.


If you are still stuck and would like to send me a shared history link, 
I can provide feedback about how to modify (if possible) to view at 
UCSC. Use "Options -> Share or Publish", generate the link, and email 
this link directly back to me. Be sure to include the dataset #, so that 
I know which in your history you want to view at UCSC.


Best,

Jen
Galaxy team

On 2/14/12 11:50 AM, Luobin Yang wrote:

Hi,

I have a local instance of Galaxy, but I found there is no "Display at
UCSC Main" link for some datasets that can be viewed in GeneTrack or
displayed by Ensemble, what has been wrong?

Thanks,
Luobin


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[galaxy-dev] Problem with python ./scripts/make_egg_packager.py

[Jose William Valero Velasquez]

Hi,

I'm writing you because i'm trying to install galaxy in a server running
suse  behind a proxy, so i have to build the eggs like if the server were
offline, in the guide says that i should execute the
command ./scripts/make_egg_packager.py but i get the following error, and i
don't really understand whats happening:

File "scripts/make_egg_packager.py", line 21, in 

c = Crate()

TypeError: __init__() takes at least 2 arguments (1 given)


I'd really apreciate your help to figure out how to solve this issue.


William Valero

Universidad Nacional de Colombia.
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[galaxy-dev] Condor in bioinformatics pipeline

[Jennifer Jackson]

Hi Nathan,

I am going to move your question over to the galaxy-...@bx.psu.edu 
mailing list to see if anyone in the development community has feedback.


Galaxy-user is mostly a Q & A list for scientists working with tools on 
the main Galaxy public server.

http://wiki.g2.bx.psu.edu/Mailing%20Lists#The_lists

Thanks!

Jen
Galaxy team


On 2/3/12 7:21 AM, Nathan Panike wrote:

Has anyone had success using the Condor scheduling system with the
following software?

RSEM
ChimeraScan
GATK
BreakDancer
VariationHunter

Thanks,

Nathan Panike, n...@cs.wisc.edu
UW-Madison Center for High Throughput Computing
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Re: [galaxy-dev] Galaxy Cloudman - How to analyse > 1TB data ?

[Brad Chapman]

Yves;

> I am currently investigating if Galaxy Cloudman can help us in analyzing
> large NGS datasets.
> 
> I was first impressed by the simple setup, the autoscaling and
> useability of Galaxy Cloudman but soon ran into the EBS limit of 1 TB L
> 
> I thought to be clever and umounted the /mnt/galaxyData EBS volume,
> created a logical volume of 2 TB and remounted this volume to
> /mnt/galaxyData.

How did you create this volume? I know there are some tricks to get
around the 1Tb limit:

http://alestic.com/2009/06/ec2-ebs-raid

In the screenshot you sent it looks like Cloudman is a bit confused
about the disk size. The Disk Status lists 1.2Tb out of 668Gb, which
might be the source of your problems.

> All is green as you can see from the picture below but running a tool is
> not possible since Galaxy is not configured to work with logical volume
> I assume.

Can you describe what errors you are seeing?

> It is truly a waste having this fine setup (autoscaling) but this is not
> useable if there is not enough storage ?
> 
> Does anybody has experience with this ? Tips, tricks ...

The more general answer is that folks do not normally use EBS this way
since having large permanent EBS filesystems is expensive. S3 stores larger
data, up to 50Tb, at a more reasonable price. S3 files are then copied to a
transient EBS store, processed, and uploaded back to S3. This isn't as
automated since it will be highly dependent on your workflow and what
files you want to save, but might be worth exploring in general when
using EC2.

Hope this helps,
Brad
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Re: [galaxy-dev] Uploading large file in browser

[Nic Barker]

Hi Nate,
That's good to hear. Just letting you know that testing on my local install of 
galaxy, if the following stars align:
-Google Chrome 17 / Firefox 10 (Mac os x)
-Nginx as galaxy's front end web server 
-Nginx's optional upload module installed

HTML uploading of large files to galaxy (tested up to 20gb) just "works". I 
believe this is due to chrome and FF's support of the encoding type 
"multipart/form-data".
Cheers,
-Nic

On 14/02/2012, at 4:00 AM, Nate Coraor wrote:

> On Feb 9, 2012, at 7:05 PM, Nic Barker wrote:
> 
>> Hi All,
>> Apologies for resurrecting an old thread, but an HTML5 chunk uploader as 
>> Hyunsoo previously suggested would actually be very useful for my 
>> organisation, in terms of streamlining our workflow for less technically 
>> able users. I was wondering if there was any intention to include 
>> functionality like this at some point, although I'm perfectly happy to use 
>> other methods if there isn't.
>> Cheers,
>> -Nic
> 
> Hi Nic,
> 
> I started working on HTML5 uploading a while back but didn't get too far with 
> it.  We'll definitely get back to rewriting uploading at some point.
> 
> --nate
> 
>> 
>> On 31/01/2012, at 7:12 AM, Nate Coraor wrote:
>> 
>>> On Jan 26, 2012, at 4:29 AM, Hans-Rudolf Hotz wrote:
>>> 
 
 
 On 01/25/2012 08:20 PM, Kim, Hyunsoo wrote:
> Hi again,
> 
> I'm kind of lost here. Does "Data Library" allow regular users to upload 
> files directly to Galaxy from their remote work station, or does it allow 
> users to use files that are already exist in Galaxy?
 
 just to clarify: regular user can copy (ie: using scp) their data to the 
 galaxy server, and then use the advantages of Data Libraries, see the 
 "user_library_import_dir" option in the 'universe_wsgi.ini' file.
 
 Regards, Hans
>>> 
>>> It's also possible to use the "FTP Upload" functionality with a protocol 
>>> other than standard FTP (i.e. with scp) so that users can upload scp'd 
>>> files directly to a history.
>>> 
>>> --nate
>>> 
 
 
> My intention was to using HTML5 file uploader which chunks large file(>  
> 2GB) into smaller pieces so that regular users can upload large files 
> through Galaxy's GUI without external FTP tool.
> 
> Thanks,
> Hyunsoo
> 
> -Original Message-
> From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
> Sent: Wednesday, January 25, 2012 4:02 AM
> To: Kim, Hyunsoo
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Uploading large file in browser
> 
> 
> 
> On 01/24/2012 10:27 PM, Kim, Hyunsoo wrote:
>> Hello,
>> 
>> I have local instance of galaxy and wanted to modify "upload file" so
>> that I will be able to upload large files (>  2GB).
>> 
>> The reason I am trying to do this in browser is that extra tools for
>> FTP do not really work in my environment because of all the
>> constraints and firewalls.
>> 
>> I came up with jQuery file upload tool
>> (http://blueimp.github.com/jQuery-File-Upload/), and the tool seems
>> fine if it is possible me to integrate into my galaxy instance.
>> 
>> My questions are:
>> 
>> -Is it too cumbersome to achieve this goal with external tools?
>> 
>> -how deep should I hit the galaxy (at the code level) to integrate
>> this jquery tool?
>> 
>> -Are there any alternatives to upload large files in browser without FTP?
> 
> as an alternative: have you looked into using "Data Libraries", see:
> 
> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
> 
> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
> 
> 
> Regards, Hans
> 
> 
>> Thanks,
>> 
>> Daniel
>> 
>> 
>> 
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>>> 
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>> 
>> 
> 


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Re: [galaxy-dev] Batch limit on Wokflows

[Petit III, Robert A.]

Thats it!  Consider this resolved, and total operator error.  I tried using the 
'Input Dataset' step, and am no longer having issues.  

Thanks for the help Dannon.


From: Petit III, Robert A.
Sent: Tuesday, February 14, 2012 3:49 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Batch limit on Wokflows

Workflow is beginning directly with a tool.

An example test workflow I've been trying is, I have 20 fasta files, and the 
workflow has only the FASTA-to-Tabular tool.

Thanks,
Robert

From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, February 14, 2012 3:33 PM
To: Petit III, Robert A.
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Batch limit on Wokflows

I hadn't had a chance to follow up again yet, but in your workflow, are you 
using an Input Dataset step, or do you have the workflow beginning directly 
with a tool?

-Dannon

On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote:

> Here's the latest.  I have tested this on Chrome, Firefox, and IE.
>
> I've tried the latest revisions of galaxy-central (71031bf3105c) and 
> galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go 
> to localhost:8080).  I am still running into same issue.  All is well with 19 
> or less datasets in the history, but as soon as I add a 20th I can no longer 
> run a workflow on multiple datasets.
>
> Are there any known issues running galaxy on Ubuntu 10.04?
>
> 
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
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Re: [galaxy-dev] Batch limit on Wokflows

[Petit III, Robert A.]

Workflow is beginning directly with a tool.

An example test workflow I've been trying is, I have 20 fasta files, and the 
workflow has only the FASTA-to-Tabular tool.

Thanks,
Robert

From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, February 14, 2012 3:33 PM
To: Petit III, Robert A.
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Batch limit on Wokflows

I hadn't had a chance to follow up again yet, but in your workflow, are you 
using an Input Dataset step, or do you have the workflow beginning directly 
with a tool?

-Dannon

On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote:

> Here's the latest.  I have tested this on Chrome, Firefox, and IE.
>
> I've tried the latest revisions of galaxy-central (71031bf3105c) and 
> galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go 
> to localhost:8080).  I am still running into same issue.  All is well with 19 
> or less datasets in the history, but as soon as I add a 20th I can no longer 
> run a workflow on multiple datasets.
>
> Are there any known issues running galaxy on Ubuntu 10.04?
>
> 
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
>
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Re: [galaxy-dev] Batch limit on Wokflows

[Dannon Baker]

I hadn't had a chance to follow up again yet, but in your workflow, are you 
using an Input Dataset step, or do you have the workflow beginning directly 
with a tool?

-Dannon

On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote:

> Here's the latest.  I have tested this on Chrome, Firefox, and IE.
> 
> I've tried the latest revisions of galaxy-central (71031bf3105c) and 
> galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go 
> to localhost:8080).  I am still running into same issue.  All is well with 19 
> or less datasets in the history, but as soon as I add a 20th I can no longer 
> run a workflow on multiple datasets.
> 
> Are there any known issues running galaxy on Ubuntu 10.04?
> 
> 
> 
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
> 
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
> 
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Re: [galaxy-dev] Batch limit on Wokflows

[Petit III, Robert A.]

Here's the latest.  I have tested this on Chrome, Firefox, and IE.

I've tried the latest revisions of galaxy-central (71031bf3105c) and 
galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to 
localhost:8080).  I am still running into same issue.  All is well with 19 or 
less datasets in the history, but as soon as I add a 20th I can no longer run a 
workflow on multiple datasets.

Are there any known issues running galaxy on Ubuntu 10.04?



This e-mail message (including any attachments) is for the sole use of
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Re: [galaxy-dev] Problem previewing a tool in the Toolshed

[Greg Von Kuster]

Hi Carlos,

Not every tool form parameter will properly display when previewing the tool in 
the tool shed because the tool shed doesn't have access to some Galaxy 
components (e.g., a Galaxy history ) that are required for some tool parameter 
types.  When I get a chance, I'll take a closer look, but if your tool is 
functional when installed from the tool shed to a local Galaxy instance, all 
should be ok.

Thanks for your contribution!

Greg Von Kuster

On Feb 14, 2012, at 1:49 PM, Carlos Borroto wrote:

> Hi,
> 
> I'm currently developing my first Galaxy tool. I'm working on a
> wrapper for R's library cummeRbund[1]. I got to the point where the
> tool although incomplete on functionality, I think is ready to be
> uploaded to the Toolshed. I was able to do so. I also made sure I
> could then install it on my local instance using the toolshed
> repository.
> 
> Everything is working as expected, except, the tool preview is not
> working correctly. There is no error, but the inputs, most of them
> conditional inputs, aren't being displayed correctly. This is the
> direct link to the tool in the test toolshed:
> http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?operation=view_or_manage_repository&id=575665a9f01c6d41
> 
> [1]http://compbio.mit.edu/cummeRbund/
> 
> Kind regards,
> Carlos
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Re: [galaxy-dev] galaxy cloud help

[brennac2]

Perfect-- it works now.  I will email to Galaxy-Dev next time

Thank you,
-CB

On 2/14/12 11:50 AM, "Dannon Baker"  wrote:

>Sure, I'm happy to help, though in the future it's probably best to mail
>galaxy-dev (cc'd for ticket tracking) directly as there are several of us
>that may be able to answer and get a response out sooner.
>
>That said, your problem is likely due to a permissions issue with the new
>tool snapshot(snap-b28be9d5) created yesterday that I've fixed, it should
>work next time you start an instance.  Let me know if this doesn't
>resolve things for you.
>
>Thanks!
>
>-Dannon
>
>On Feb 14, 2012, at 10:57 AM, brenn...@mskcc.org wrote:
>
>> I got your email from a [galaxy-dev] entry.  Could I ask you for help
>>with a cloud installation problem or could you point me to the best
>>place to submit the question?  I will describe the problem below but
>>understand if you are not able to provide support.
>>  
>> Thank you in advance,
>>  
>> Cameron Brennan, MD
>> Human Oncology and Pathogenesis Program
>> Memorial Sloan-Kettering Cancer Center
>> New York
>>  
>> Problem:
>> I have gotten Cloudman running on EC2 but the ³Service Status² shows
>>yellow for Applications (green for Data). The Galaxy Daemon won¹t start.
>> The log points to a problem mounting galaxyTools and indeed when I SSH
>>in, /mnt/galaxyTools is absent.  The log errors are:
>>  
>> ³Cannot retrieve reference to volume ŒNone¹; setting volume id to None.
>>Error: EC2ResponseError: Š¹.0fb <Š lots of characters> Š c3aa9
>>  
>> And
>>  
>> Error mounting file system Œ/mnt/galaxyTools¹ from Œ/dev/sdg3¹, running
>>command Œ/bin/mount /dev/sdg3 /mnt/galaxyTools¹ returned code Œ32¹ and
>>following stderr² Œmount: you must specify the filesystem type Œ
>>  
>> 
>>  
>>  
>>=
>>  
>>  Please note that this e-mail and any files transmitted from
>>  Memorial Sloan-Kettering Cancer Center may be privileged,
>>confidential,
>>  and protected from disclosure under applicable law. If the reader
>>of
>>  this message is not the intended recipient, or an employee or agent
>>  responsible for delivering this message to the intended recipient,
>>  you are hereby notified that any reading, dissemination,
>>distribution, 
>>  copying, or other use of this communication or any of its
>>attachments
>>  is strictly prohibited.  If you have received this communication
>>in 
>>  error, please notify the sender immediately by replying to this
>>message
>>  and deleting this message, any attachments, and all copies and
>>backups
>>  from your computer.
>> 
>
>



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[galaxy-dev] No Display at UCSC Main link.

[Luobin Yang]

Hi,

I have a local instance of Galaxy, but I found there is no "Display at UCSC
Main" link for some datasets that can be viewed in GeneTrack or displayed
by Ensemble, what has been wrong?

Thanks,
Luobin
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[galaxy-dev] Problem previewing a tool in the Toolshed

[Carlos Borroto]

Hi,

I'm currently developing my first Galaxy tool. I'm working on a
wrapper for R's library cummeRbund[1]. I got to the point where the
tool although incomplete on functionality, I think is ready to be
uploaded to the Toolshed. I was able to do so. I also made sure I
could then install it on my local instance using the toolshed
repository.

Everything is working as expected, except, the tool preview is not
working correctly. There is no error, but the inputs, most of them
conditional inputs, aren't being displayed correctly. This is the
direct link to the tool in the test toolshed:
http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?operation=view_or_manage_repository&id=575665a9f01c6d41

[1]http://compbio.mit.edu/cummeRbund/

Kind regards,
Carlos
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Re: [galaxy-dev] [galaxy-user] Result of annotation hg18 and hg19 on one file

[Dannon Baker]

Hi,

Based on your previous questions, I'm going to guess that you're trying to add 
multiple tools, run both on an input dataset in series, and see the results in 
the History.  Is this the case?  If you're referring to how to combine these 
into one process, take a look at the Galaxy workflow capabilities.  In any 
event, if you could clarify what you're trying to accomplish I'm sure I can 
help out.

Also, I've moved this question over to the galaxy-dev mailing list which should 
be used for anything development related, tools included.

Thanks!

-Dannon

On Feb 13, 2012, at 1:25 PM, La Chi wrote:

> Hi everyone,
> how can i write the result of both functions in one single file then history 
> panel will show its result..
> thanks
> ___
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Re: [galaxy-dev] galaxy cloud help

[Dannon Baker]

Sure, I'm happy to help, though in the future it's probably best to mail 
galaxy-dev (cc'd for ticket tracking) directly as there are several of us that 
may be able to answer and get a response out sooner.

That said, your problem is likely due to a permissions issue with the new tool 
snapshot(snap-b28be9d5) created yesterday that I've fixed, it should work next 
time you start an instance.  Let me know if this doesn't resolve things for you.

Thanks!

-Dannon

On Feb 14, 2012, at 10:57 AM, brenn...@mskcc.org wrote:

> I got your email from a [galaxy-dev] entry.  Could I ask you for help with a 
> cloud installation problem or could you point me to the best place to submit 
> the question?  I will describe the problem below but understand if you are 
> not able to provide support.
>  
> Thank you in advance,
>  
> Cameron Brennan, MD
> Human Oncology and Pathogenesis Program
> Memorial Sloan-Kettering Cancer Center
> New York
>  
> Problem:
> I have gotten Cloudman running on EC2 but the “Service Status” shows yellow 
> for Applications (green for Data). The Galaxy Daemon won’t start.  The log 
> points to a problem mounting galaxyTools and indeed when I SSH in, 
> /mnt/galaxyTools is absent.  The log errors are:
>  
> “Cannot retrieve reference to volume ‘None’; setting volume id to None. 
> Error: EC2ResponseError: …’.0fb <… lots of characters> … c3aa9
>  
> And
>  
> Error mounting file system ‘/mnt/galaxyTools’ from ‘/dev/sdg3’, running 
> command ‘/bin/mount /dev/sdg3 /mnt/galaxyTools’ returned code ‘32’ and 
> following stderr” ‘mount: you must specify the filesystem type ‘
>  
> 
>  
>  =
>  
>  Please note that this e-mail and any files transmitted from
>  Memorial Sloan-Kettering Cancer Center may be privileged, confidential,
>  and protected from disclosure under applicable law. If the reader of
>  this message is not the intended recipient, or an employee or agent
>  responsible for delivering this message to the intended recipient,
>  you are hereby notified that any reading, dissemination, distribution, 
>  copying, or other use of this communication or any of its attachments
>  is strictly prohibited.  If you have received this communication in 
>  error, please notify the sender immediately by replying to this message
>  and deleting this message, any attachments, and all copies and backups
>  from your computer.
> 


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Re: [galaxy-dev] cloudman/galaxy on EC2 - snapshot not found

[Dannon Baker]

Hi Jorrit,

There was a permissions issue with the new tool snapshot(snap-b28be9d5) created 
yesterday that I've fixed, it should work next time you start an instance.

Thanks!

-Dannon


On Feb 14, 2012, at 10:37 AM, Jorrit Boekel wrote:

> Dear list,
> 
> I am trying to deploy Galaxy as an environment for proteomics tools in 
> amazon's EC2 cloud, probably/preferably via Cloudman. I have used both the 
> biocloudcentral portal and a manual approach to set up cloudman/galaxy, but 
> run into the same error message which seems to start with a problem with a 
> snapshot that does not exist:
> 
>   • 15:16:05 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data' 
> does not exist (yet?)
>   • 15:16:26 - Error creating volume: EC2ResponseError: 400 Bad Request 
> InvalidSnapshot.NotFoundThe snapshot 'snap-b28be9d5' does not exist.---some 
> long identifier---
>   • 15:16:26 - Error adding filesystem service 'Filesystem-galaxyTools': 
> 'NoneType' object has no attribute 'id'
>   • 15:16:26 - STATUS CHECK: File system named 'galaxyTools' is not 
> mounted. Error code 0
>   • 15:16:37 - Error mounting file system '/mnt/galaxyData' from 
> '/dev/xvdg2', running command '/bin/mount /dev/xvdg2 /mnt/galaxyData' 
> returned code '32' and following stderr: 'mount: you must specify the 
> filesystem type '
> 
> My instance type is t1.micro (testing on AWS free tier), but I've tried 
> m1.large, and that didn't help. I noted that the snapshot ID is always the 
> same. Since the AMI is from March 2011 (at least the one I select manually), 
> I assume that I have something wrong in my settings or that Amazon has 
> changed something somewhere.
> 
> cheers,
> Jorrit Boekel
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Re: [galaxy-dev] Galaxy workflow data

[Langhorst, Brad]

Paul:

I was about to suggest the same - great idea!
++

brad
On Feb 14, 2012, at 11:08 AM, Dannon Baker wrote:

> Hi Paul,
> 
> Thanks for this suggestion, it would definitely make sense to create a 
> reference to the actual workflow inputs in the new history.  I'll see what I 
> can do!
> 
> -Dannon
> 
> On Feb 14, 2012, at 11:05 AM, Paul Gordon wrote:
> 
>> Hi all,
>> 
>> I have noticed that when I run a workflow with output to a new history, the 
>> data sets used as input to the workflow do not become part of the new 
>> history.  Unfortunately, if a job fails in the workflow, the "rerun" 
>> interface for the job can't access the original data…it needs to be manually 
>> imported.  While this is a minor annoyance, it becomes quite the pain if you 
>> ran the workflow for a bunch of input files.  Can I put in a request that 
>> input data be imported automatically into workflow run histories, or have I 
>> missed something in the workflow run options?
>> 
>> Cheers,
>> 
>> Paul
>> 
>> 
>> ___
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> 
> 
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Brad Langhorst
langho...@neb.com
978-380-7564




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Re: [galaxy-dev] Galaxy workflow data

[Dannon Baker]

Hi Paul,

Thanks for this suggestion, it would definitely make sense to create a 
reference to the actual workflow inputs in the new history.  I'll see what I 
can do!

-Dannon

On Feb 14, 2012, at 11:05 AM, Paul Gordon wrote:

> Hi all,
> 
> I have noticed that when I run a workflow with output to a new history, the 
> data sets used as input to the workflow do not become part of the new 
> history.  Unfortunately, if a job fails in the workflow, the "rerun" 
> interface for the job can't access the original data…it needs to be manually 
> imported.  While this is a minor annoyance, it becomes quite the pain if you 
> ran the workflow for a bunch of input files.  Can I put in a request that 
> input data be imported automatically into workflow run histories, or have I 
> missed something in the workflow run options?
> 
> Cheers,
> 
> Paul
> 
> 
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[galaxy-dev] Galaxy workflow data

[Paul Gordon]

Hi all,

I have noticed that when I run a workflow with output to a new history, the
data sets used as input to the workflow do not become part of the new
history.  Unfortunately, if a job fails in the workflow, the "rerun"
interface for the job can't access the original dataŠit needs to be manually
imported.  While this is a minor annoyance, it becomes quite the pain if you
ran the workflow for a bunch of input files.  Can I put in a request that
input data be imported automatically into workflow run histories, or have I
missed something in the workflow run options?

Cheers,

Paul




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[galaxy-dev] cloudman/galaxy on EC2 - snapshot not found

[Jorrit Boekel]

Dear list,

I am trying to deploy Galaxy as an environment for proteomics tools in 
amazon's EC2 cloud, probably/preferably via Cloudman. I have used both 
the biocloudcentral portal and a manual approach to set up 
cloudman/galaxy, but run into the same error message which seems to 
start with a problem with a snapshot that does not exist:


 * 15:16:05 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
   does not exist (yet?)
 * 15:16:26 - Error creating volume: EC2ResponseError: 400 Bad Request
   |InvalidSnapshot.NotFound|The snapshot 'snap-b28be9d5' does not
   exist.---some long identifier---
 * 15:16:26 - Error adding filesystem service 'Filesystem-galaxyTools':
   'NoneType' object has no attribute 'id'
 * 15:16:26 - STATUS CHECK: File system named 'galaxyTools' is not
   mounted. Error code 0
 * 15:16:37 - Error mounting file system '/mnt/galaxyData' from
   '/dev/xvdg2', running command '/bin/mount /dev/xvdg2
   /mnt/galaxyData' returned code '32' and following stderr: 'mount:
   you must specify the filesystem type '


My instance type is t1.micro (testing on AWS free tier), but I've tried 
m1.large, and that didn't help. I noted that the snapshot ID is always 
the same. Since the AMI is from March 2011 (at least the one I select 
manually), I assume that I have something wrong in my settings or that 
Amazon has changed something somewhere.


cheers,
Jorrit Boekel
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Re: [galaxy-dev] Galaxy server configuration question

[huayan gao]

Good point, Nate! I will move galaxy out of my documentroot then.

Best,

Huayan

On Tue, Feb 14, 2012 at 1:21 AM, Nate Coraor  wrote:
> On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
>
>> Hi Nate.
>>
>> I am ok now.
>>
>> The code I copied from wiki was using galaxy_dist, while my folder name is 
>> galaxy-dist.
>> After I changed the path in the code, the problem solved.
>
> Hi Huayan,
>
> I've updated the wiki to refer to galaxy-dist rather than galaxy_dist.  Sorry 
> for the confusion.
>
> I would suggest moving galaxy out of /var/www/html.  From the documentation:
>
>    Please note that Galaxy should never be located on disk inside Apache's 
> DocumentRoot. By default, this would expose all of Galaxy (including 
> datasets) to anyone on the web.
>
> Galaxy is a proxied application and as such, only the static content like 
> javascript and images are served directly by Apache (and this is set up with 
> the RewriteRules), everything else is passed through to the Galaxy 
> application via a proxied http connection.  Right now I could presumably use 
> the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to 
> view a dataset directly.
>
> --nate
>
>>
>>
>>
>> Best,
>> Huayan
>>
>>
>> On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote:
>>
>>> Hi Nate,
>>>
>>> I removed the proxy section in httpd file and got the following screenshot. 
>>> It seems working but not in the way we expected.
>>> I will keep looking for the solution but do you know how to fix it?
>>>
>>> It seems to say, "the file .../static/welcome.html is missing" or something 
>>> like that.
>>>
>>> Thanks,
>>> Huayan
>>>
>>>
>>>
>>>
>>> 
>>>
>>>
>>>
>>> On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote:
>>>
 Hi Nate,


 Yes, I did follow the instructions. But I came to the question in 
 httpd.conf file.
 I put galaxy-dist under my document root which is /var/www/html/.
 When my server is up, I can access my UCSC genome browser mirror site 
 through my ip address, for example, http://61.244. xxx.xxx.
 Then how should I set up in httpd.conf file so I can access galaxy using 
 my ip address, for example, http://61.244. xxx.xxx/galaxy?




 Thanks,
 Best,
 Huayan




 On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:

> On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
>
>> Dear Sir or Madam,
>>
>> I am installing a galaxy server on CentOS with UCSC Genome Browser 
>> mirror site. The mirror site works well. I installed the galaxy in the 
>> same server.
>> Now my question is: how to set up httpd.conf file so I can access both 
>> websites(UCSC Genome Browser, and Galaxy) remotely?
>
> Hi Huayan,
>
> Have you consulted the production server documentation?
>
>   http://usegalaxy.org/production
>
> --nate
>
>>
>>
>>
>> Best,
>> Huayan
>> ___
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>

>>>
>>
>

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Re: [galaxy-dev] Error executing tool: 'hg19'

[Jeremy Goecks]

Can you confirm that the following lines are in your datatypes_conf.xml file?

--







--

If so, the other issue is that you'll need to restart Galaxy in order for the 
changes to take hold. Apologies for not mentioning this step previously.

J.

On Feb 14, 2012, at 3:18 AM, Joachim Jacob wrote:

> First, thanks. I just created a new user, and I am ready to go with that user.
> FYI, the reset of the datatypes_conf.xml did not do the trick: following 
> error appears on the custom builds page: NoConverterException: "Conversion 
> from 'fasta' to 'len' not possible"
> 
> 
> Thanks,
> Joachim
> 
> On 02/13/2012 06:02 PM, Jeremy Goecks wrote:
>> 
>> This bug has been fixed in galaxy-central but, as per one of the threads you 
>> found, has not made it to galaxy-dist yet.
>> 
>> Try this:
>> 1. assuming you haven't made any changes to datatypes_conf.xml, copy 
>> datatypes_conf.xml.sample to datatypes_conf.xml
>> 2. visit the custom builds page (User tab --> Custom Builds) and see if the 
>> Page loads properly; if it does, your custom build should work and 
>> everything should be fine.
>> 3. this is a user-specific problem, so you can always create a new user and 
>> you should be good to go. If you want to continue to use the problematic 
>> account and the above doesn't work, you'll need to manually--via SQL--delete 
>> the user preferences for the problematic user.
>> 
>> Best,
>> J.
>> 
>> On Feb 13, 2012, at 10:30 AM, Joachim Jacob wrote:
>> 
>>> For completeness: this is a local galaxy instance running for few months 
>>> now, updated recently (27 Jan 'release').
 Hello Joachim,
> After a quick try with visualising track in Trackster (importing one 
> chromosome of hg19 - which did not succeed BTW), none of the tools in my 
> local galaxy appear to work.
 What are the steps you're taking to produce this issue?
 
>>> I had a BAM file that I wanted to test to view with Trackster. I clicked 
>>> that icon in the dataset . In the next screen: save in new visualation, 
>>> which I called test. And I selected there 'Add a custom build'. Next I 
>>> could select which fasta from my history containing the reference: selected 
>>> the correct one. I named it "hg19_chrom21". But then, clicking OK, gave an 
>>> error.
>>> 
>>> From then on, all tools give the error: Error executing tool: 'hg19'. The 
>>> point is, I cannot recreate that BAM file, since the required tools are not 
>>> working anymore... Basically, my Galaxy has become useless. Before I dig up 
>>> my backup, I hope somebody can help me?
> They all send this error message:
> 
> Error executing tool: 'hg19'
 Are you seeing this error in failed datasets? If not, where are you seeing 
 this error?
>>> This error appears in the middle pane, after clicking execute.
>>> 
>>> 
> This bug has been reported before, but I was wondering if somebody 
> suggest a fix for this?
 Can you provide a link to the thread/issue where this has been reported?
>>> http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html
>>> http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html
>>> 
 Thanks,
 J.
>>> Thank for looking into this.

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Re: [galaxy-dev] Running workflows on mulitple paired-end data sets

[Dannon Baker]

Thon,

Not currently, though the question comes up often enough that I'll try and bump 
it up my list.  

Instead of interlacing and deinterlacing a better workaround for now might be 
to use the API to execute over all these samples.

-Dannon

On Feb 13, 2012, at 8:46 PM, Anthonius deBoer wrote:

> 
> Hi,
> 
> Is there an intelligent way to run a workflow that starts with more than one 
> pair of paired-end data sets in a workflow?
> I can run multiple workflows when there is a SINGLE input file, but in the 
> case of many paired end workflows, you need to provide two paired samples and 
> just adding another input workflow step does not work, since you can only 
> select a single file in the second input workflow set.
> 
> I realize that there is an issue with the cycling through the datasets since 
> they need to be paired-up and it would be very easy to mess this up if you 
> allow two (or more) input data sets, but since paired end data is going to be 
> very common, I would assume a special paired end input workflow step that is 
> intelligent and can pair up the input datasets before handing them off to the 
> workflow would be very useful.
> 
> I can think of workarounds ofcourse, such as creating an interlaced file 
> containing both pairs and then just de-interlacing them in the workflow, but 
> that is kludgy and will result in a lot of data duplication for no reason...
> 
> I have to run 88 samples which will soon grow to over 200 samples, so running 
> each step manually is not really an option and I would hate to have to 
> program the workflow steps myself...
> 
> Any ideas?
> 
> Thanks
> 
> Thon
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Re: [galaxy-dev] Error executing tool: 'hg19'

[Joachim Jacob]

First, thanks. I just created a new user, and I am ready to go with that 
user.
FYI, the reset of the datatypes_conf.xml did not do the trick: following 
error appears on the custom builds page: NoConverterException: 
"Conversion from 'fasta' to 'len' not possible"



Thanks,
Joachim

On 02/13/2012 06:02 PM, Jeremy Goecks wrote:

This bug has been fixed in galaxy-central but, as per one of the threads you 
found, has not made it to galaxy-dist yet.

Try this:
1. assuming you haven't made any changes to datatypes_conf.xml, copy 
datatypes_conf.xml.sample to datatypes_conf.xml
2. visit the custom builds page (User tab -->  Custom Builds) and see if the 
Page loads properly; if it does, your custom build should work and everything 
should be fine.
3. this is a user-specific problem, so you can always create a new user and you 
should be good to go. If you want to continue to use the problematic account 
and the above doesn't work, you'll need to manually--via SQL--delete the user 
preferences for the problematic user.

Best,
J.

On Feb 13, 2012, at 10:30 AM, Joachim Jacob wrote:


For completeness: this is a local galaxy instance running for few months now, 
updated recently (27 Jan 'release').

Hello Joachim,

After a quick try with visualising track in Trackster (importing one chromosome 
of hg19 - which did not succeed BTW), none of the tools in my local galaxy 
appear to work.

What are the steps you're taking to produce this issue?


I had a BAM file that I wanted to test to view with Trackster. I clicked that icon in the 
dataset . In the next screen: save in new visualation, which I called test. And I 
selected there 'Add a custom build'. Next I could select which fasta from my history 
containing the reference: selected the correct one. I named it "hg19_chrom21". 
But then, clicking OK, gave an error.

 From then on, all tools give the error: Error executing tool: 'hg19'. The 
point is, I cannot recreate that BAM file, since the required tools are not 
working anymore... Basically, my Galaxy has become useless. Before I dig up my 
backup, I hope somebody can help me?

They all send this error message:

Error executing tool: 'hg19'

Are you seeing this error in failed datasets? If not, where are you seeing this 
error?

This error appears in the middle pane, after clicking execute.



This bug has been reported before, but I was wondering if somebody suggest a 
fix for this?

Can you provide a link to the thread/issue where this has been reported?

http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html


Thanks,
J.

Thank for looking into this.
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