Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

[Hans-Rudolf Hotz]

Hi Nilaksha

Use the "!" icon (View details) to get the full path to the data set, 
and the use 'cp' or 'scp' (if not on the same host) on your terminal.



Hope this helps, Hans-Rudolf


On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:

Hello all,

I'm currently successfully running a pipeline for metagenomic analysis
on my locally installed galaxy instance and everything seemed to good by
far. But when I'm trying to download my processed blast xml output (I
used blast+ wrappers for this) , by clicking the small disk button
nothing happens. I tried several options.
1) clicked the 'disk' icon to initiate the downloading
2) right clicked the 'disk' icon and tried to use saved linked as, but a
dialog box doesnot appear for saving
3) tried copying the link and used curl on bash terminal, but progress
bar is stuck at 0%.

I think this is happening because my blast output dataset is much larger
(around ~10GB) , but if that's the case, how am I supposed to get the
data out of galaxy any way??

Thank a lot in advance.

Regards!
Nilaksha


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[galaxy-dev] Problem downloading large processed datasets : galaxy local instance

[Nilaksha Neththikumara]

Hello all,

I'm currently successfully running a pipeline for metagenomic analysis on
my locally installed galaxy instance and everything seemed to good by far.
But when I'm trying to download my processed blast xml output (I used
blast+ wrappers for this) , by clicking the small disk button nothing
happens. I tried several options.
1) clicked the 'disk' icon to initiate the downloading
2) right clicked the 'disk' icon and tried to use saved linked as, but a
dialog box doesnot appear for saving
3) tried copying the link and used curl on bash terminal, but progress bar
is stuck at 0%.

I think this is happening because my blast output dataset is much larger
(around ~10GB) , but if that's the case, how am I supposed to get the data
out of galaxy any way??

Thank a lot in advance.

Regards!
Nilaksha
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[galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Wang, Xiaofei]

Dear there,

When I used SnpEff in local galaxy instance, I got an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 
at java.lang.ClassLoader.defineClass1(Native Method) at 
java.lang.ClassLoader.defineClassCond(ClassLoader.j


Also, when I used the FASTQ Summary Statistics, I got an error like this:
Traceback (most recent call last): File 
"/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
 line 48, in if __name__ == "__main__": main() File "/Users/...

I tried to google and solve them by myself. But I really do not know how to do 
that. Could anybody give me some clue? Thanks a lot for your help!

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[galaxy-dev] Select Random Lines - Not Working

[Unmesh Jadhav]

Hello,

I am trying to Select Random Lines (10million out of 39 million in a bed
file) using the Galaxy tool and the tool is not responding for more than
almost 12 hrs now.

I have used this tool before for similar jobs and it has performed really
well and fast.

I would really appreciate if you could suggest how we handle this.

Thank you,

Unmesh
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[galaxy-dev] Package/Module RPY

[Hayes, Curt]

Hi there all,

I have searched previous posts, nothing since 2010. I have a local install 
(production config - postgres, etc - on CENTOS 6.5).
Does anyone have RPY working? I install via toolshed and the folder is empty, 
and shows missing dependencies.

>From Galaxy User:
Dataset generation errors
Dataset 81: Build base quality distribution on data 9

Tool execution generated the following error message:
Traceback (most recent call last):
  File 
"/apps/galaxy/galaxy-dist/tools/metag_tools/short_reads_figure_score.py", line 
12, in 
from rpy import *
ImportError: No module named rpy

I have attempted to download/install the scripts but they fail with multiple 
errors (most posts out there have a bad URL) - 
http://getgalaxyp.org/install.html says use: curl 
http://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar > rpy.tar.gz
if you view that it redirects you to another URL.

Via shell: R is installed: R version 2.13.0 (2011-04-13)

Can someone provide me some help please to get it working via Galaxy? I 
understand it works in Central.

>From Toolshed:
Name

Version

Type

Installation status

rpy

1.0.3

package

Error


Toolshed Error:
In file included from src/rpymodule2110.c:51: src/RPy.h:56:20: error: Python.h: 
No such file or directory In file included from 
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68, 
from 
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, 
from src/RPy.h:89, from src/rpymodule2110.c:51: 
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2: 
error: #error Must use Python with unicode enabled. 

Thanks,
Curt

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[root@seachlinux rpy]# python setup.py install
RHOMES= []
DEBUG= False
Setting RHOMES to  ['/usr/lib64/R']
### Using R verion 2.13.0 installed at /usr/lib64/R ###
RHOME= /usr/lib64/R
copying src/rpymodule.c -> src/rpymodule2130.c
copying src/R_eval.c -> src/R_eval2130.c
copying src/io.c -> src/io2130.c
running install
running build
running build_py
running build_ext
building '_rpy2130' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic 
-D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic 
-D_GNU_SOURCE -fPIC -fwrapv -fPIC -DWITH_NUMERIC=3 
-DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2130 -DINIT_RPY=init_rpy2130 
-UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include 
-I/usr/lib64/python2.6/site-packages/numpy/core/include 
-I/usr/include/python2.6 -c src/rpymodule2130.c -o 
build/temp.linux-x86_64-2.6/src/rpymodule2130.o -shared -llapack
In file included from src/rpymodule2130.c:51:
src/RPy.h:63:20: error: Python.h: No such file or directory
In file included from 
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68,
 from 
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
 from src/RPy.h:99,
 from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2: 
error: #error Must use Python with unicode enabled.
In file included from 
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
 from src/RPy.h:99,
 from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:227:
 error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘npy_intp’
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:228:
 error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘npy_uintp’
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:330:
 error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:331:
 error: expected ‘)’ before ‘*’ token
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:333:
 error: expected declaration specifiers or ‘...’ before ‘npy_intp’
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:333:
 error: expected declaration specifiers or ‘...’ before ‘npy_intp’
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:334:
 error: expected declaration specifiers or ‘...’ 

Re: [galaxy-dev] Galaxy unhandled exception checking jobs error

[John Chilton]

This change is very small and was not committed to the stable branch
of galaxy-central so I would just modify the your Galaxy's copy of the
pbs runner file directly until the next release:

% wget 
https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0/raw
-O /tmp/pbs.patch
% hg import --no-commit /tmp/pbs.patch

When you go to update Galaxy next it will probably warn you that this
file has been modified - at that time you can just run the following
command to cleanup your Galaxy instance:

% hg revert lib/galaxy/jobs/runners/pbs.py

Hope this helps. The Galaxy team is actively discussing alternative
ways to distribute fixes between large releases - hopefully I can stop
e-mailing out random mercurial commands at some point :).

Back to your broader question however, the Galaxy release and update
process is such that you really shouldn't lose your configuration as a
result of updating Galaxy. Galaxy distributes sample tool_conf.xml,
universe_wsgi.ini, etc... files but the actual configuration files
themselves are not tracked in the Galaxy central repositories so these
files should be unaffected by updates. Deviations from this ideal
should be rare and I believe will be spelled out the dev news for
releases as they occur. Hope this helps.

-John



On Wed, Apr 2, 2014 at 12:27 PM, Ravi Alla  wrote:
> John,
> Thanks for this. I am new to managing galaxy, but how do I go about updating 
> my galaxy to reflect these changes? I found directions on 
> https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date 
> about pulling changes from the bitbucket repository. Does this preserve my 
> previous galaxy settings?
> Do I have to back up before I do this? I spent considerable time to get 
> galaxy to work on the cluster and don't want to ruin it.
> Thank you
> Ravi
> On Apr 2, 2014, at 9:58 AM, John Chilton  wrote:
>
>> This looks very to similar to an issue discussed here:
>> http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html.
>>
>> The default branch of Galaxy contains changeset that should address
>> this issue - 
>> https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0.
>>
>> Hope this helps.
>>
>> -John
>>
>> On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla  wrote:
>>> Hi guys,
>>> I keep getting an error everytime I start up the galaxy server. I am
>>> guessing this has to do with a job that galaxy is trying to resume and
>>> cannot find.
>>>
>>> galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception
>>> checking active jobs
>>> Traceback (most recent call last):
>>>  File
>>> "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>>> line 366, in monitor
>>>self.check_watched_items()
>>>  File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
>>> line 363, in check_watched_items
>>>( failures, statuses ) = self.check_all_jobs()
>>>  File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
>>> line 452, in check_all_jobs
>>>c = pbs.pbs_connect( pbs_server_name )
>>> TypeError: in method 'pbs_connect', argument 1 of type 'char *'
>>>
>>> Because of this error I cannot get any other jobs to run either. They just
>>> sit queued on the cluster.
>>> Any ideas?
>>> Thanks
>>>
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>>>
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>>>  http://galaxyproject.org/search/mailinglists/
>

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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Wang, Xiaofei]

>After SnpEff Databases > Execute you still need to pick genome of
interest and run "SnpEff Download". SnpEff Databases just downloads a
list of available genomes.

You mean "SnpEff Download" under Data Manager? But, there is no response when I 
click on it. 

Unfortunately, I tried to uninstall the snpEff tool shed and re-install it 
again to see if I can get response. But, when I go to Admin > Data > Manage 
local data (beta) this time, there is no snpEff data manager and only the BWA 
and Fetching genome (I installed them by myself) are left there. Do you know 
why? 

When I search the tool sheds like BWA data manager, I did not find there is 
snpEff data manager. Do you know where could I find it? Why the snpEff data 
manager has been there last time?

Thank you so much!

Best,

Xiaofei


From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, April 02, 2014 4:17 PM
To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

> Dear Bjoern,
> As your suggestion, I tried to install the snpEff annotation. But, I think I 
> am still be stuck there. What I did is:
> Admin > Data > Manage local data (beta), then the message is shown as below. 
> (For the BWA and Fetching genome,
> I installed them from tool_sheds by myself. For the SnpEff staff, it has been 
> there when I checked the data manager.)
> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff 
> annotations in View managed data by Tool Data Table part, it is still empty.

After SnpEff Databases > Execute you still need to pick genome of
interest and run "SnpEff Download". SnpEff Databases just downloads a
list of available genomes.

Hope that will help!
Bjoern

>
> Could you give me more details about how to install the annotation with the 
> snpeff data manager under the Admin panel?
>
> I really appreciate for your help, and thank you so much for your patience!
>
> Best,
>
> Xiaofei
> Data Manager
>
> Choose your data managing option from below.
>
>*   Access data managers - get data, build indexes, etc
>
>   *   SnpEff 
> Databases
>  - Read the list of available snpEff databases
>
>   *   SnpEff 
> Download
>  - Download a new database
>
>   *   BWA 
> index
>  - builder
>
>   *   BWA Color 
> index
>  - builder
>
>   *   Reference 
> Genome
>  - fetching
>
>*   View managed data by manager
>
>   *   SnpEff 
> Databases
>  - Read the list of available snpEff databases
>
>   *   SnpEff 
> Download
>  - Download a new database
>
>   *   BWA 
> index
>  - builder
>
>   *   BWA Color 
> index
>  - builder
>
>   *   Reference 
> Genome
>  - fetching
>
>*   View managed data by Tool Data Table
>
>   *   
> snpeff_databases
>
>   *   
> snpeff_genomedb
>
>   *   
> snpeff_regulationdb
>
>   *   
> snpeff_annotations
>
>   *   
> bwa_indexes

Re: [galaxy-dev] ENA SRA data retrieval with Cloudman

[Mohammad Heydarian]

Hi Dannon,
Thanks so much, your protocol was extremely helpful!

Thanks for looking into ENA SRA. In our experience, the ENA SRA is the
easiest and most reliable way of importing public NGS data into Galaxy. The
ENA SRA has an actual button to click that will import your data set of
choice into Galaxy, while retaining the data set ID. It is much more
straight forward (and reliable) than using any of the NCBI databases.

Thanks for your help with all of this, Dannon! Have a great night.

Cheers,
Mo Heydarian

PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
402 Biophysics
Baltimore, MD 21205


On Wed, Apr 2, 2014 at 6:21 PM, Dannon Baker  wrote:

> On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian wrote:
>
>> Hi Dannon,
>> Thanks for this information. Will the ENA SRA button be enabled on the
>> next update of Cloudman?
>>
>
> I'll check to make sure there wasn't a good reason to remove it (couldn't
> find one in my first pass, and it's available on main, so it should be in
> the cloud), but yes.
>
> Is there a protocol (or help page) available for how to re-enable tools in
>> the 'tool_conf.xml'?
>>
>
> With everything headed to the toolshed, hopefully this is a thing of the
> past very soon.  The only documentation I found on the wiki is here:
> https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
>
> In short, you'll need to:
>
> 1) ssh to your cloud galaxy instance
> 2) navigate to /mnt/galaxy/galaxy-app
> 3) open tool_conf.xml in your favorite editor, and add the line below,
> exactly, in the Get Data section (the first one, begins on line 3):
>
>  
>
> 4) Close down ssh,
> 5) In a web browser, go to the cloud admin panel and click restart for the
> Galaxy service.
>
>
>
>> One of the great things about Galaxy Cloudman is that someone who doesn't
>> know programming (myself and many other biologists and clinicians) can
>> seamlessly use the platform. Unfortunately, when trivial issues arise where
>> the solution is to insert a line or two of code in the universe of Galaxy
>> Cloudman people like me are stymied and really don't even know where to
>> start.  I know it requires work at some level, but a tutorial on "how to
>> find your 'tool_conf.xml'" (or "dummies guide to quick Cloudman fixes")
>> would likely be helpful to many end users (including myself).
>>
>
> We definitely do try to make it as ready-to-go out of the box as possible,
> but that's a great idea.  I'll try to document this better.
>
>
>> Thanks again, Dannon!
>>
>
> Anytime, thanks for your patience and for using Galaxy/Cloudman!
>
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Re: [galaxy-dev] label element

[John Chilton]

This was kindly fixed by Nicola Soranzo
(https://bitbucket.org/galaxy/galaxy-central/pull-request/346/fix-for-https-trellocom-c-8npgym3u-1430/diff)
and merged into the latest stable branch of galaxy-central. There are
ongoing discussions internally about how to best get these between
release fixes out but for now there is are some tips in this e-mail
(http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-tp4663719p4663831.html)
about upgrading to the latest stable branch.

-John

On Wed, Apr 2, 2014 at 6:55 PM, Jun Fan  wrote:
> Hi all,
>
>
>
>   It seems that the recent release does not support label element
> anymore, i.e. no sub-section with the section title displayed in grey. Is
> there any alternative way to organize the tool under one big section?
>
>
>
> Best regards!
>
> Jun
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] label element

[Jun Fan]

Hi all,

  It seems that the recent release does not support label element anymore, 
i.e. no sub-section with the section title displayed in grey. Is there any 
alternative way to organize the tool under one big section?

Best regards!
Jun
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Re: [galaxy-dev] ENA SRA data retrieval with Cloudman

[Dannon Baker]

On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian wrote:

> Hi Dannon,
> Thanks for this information. Will the ENA SRA button be enabled on the
> next update of Cloudman?
>

I'll check to make sure there wasn't a good reason to remove it (couldn't
find one in my first pass, and it's available on main, so it should be in
the cloud), but yes.

Is there a protocol (or help page) available for how to re-enable tools in
> the 'tool_conf.xml'?
>

With everything headed to the toolshed, hopefully this is a thing of the
past very soon.  The only documentation I found on the wiki is here:
https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial

In short, you'll need to:

1) ssh to your cloud galaxy instance
2) navigate to /mnt/galaxy/galaxy-app
3) open tool_conf.xml in your favorite editor, and add the line below,
exactly, in the Get Data section (the first one, begins on line 3):

 

4) Close down ssh,
5) In a web browser, go to the cloud admin panel and click restart for the
Galaxy service.



> One of the great things about Galaxy Cloudman is that someone who doesn't
> know programming (myself and many other biologists and clinicians) can
> seamlessly use the platform. Unfortunately, when trivial issues arise where
> the solution is to insert a line or two of code in the universe of Galaxy
> Cloudman people like me are stymied and really don't even know where to
> start.  I know it requires work at some level, but a tutorial on "how to
> find your 'tool_conf.xml'" (or "dummies guide to quick Cloudman fixes")
> would likely be helpful to many end users (including myself).
>

We definitely do try to make it as ready-to-go out of the box as possible,
but that's a great idea.  I'll try to document this better.


> Thanks again, Dannon!
>

Anytime, thanks for your patience and for using Galaxy/Cloudman!
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Re: [galaxy-dev] ENA SRA data retrieval with Cloudman

[Mohammad Heydarian]

Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the next
update of Cloudman?

Is there a protocol (or help page) available for how to re-enable tools in
the 'tool_conf.xml'? One of the great things about Galaxy Cloudman is that
someone who doesn't know programming (myself and many other biologists and
clinicians) can seamlessly use the platform. Unfortunately, when trivial
issues arise where the solution is to insert a line or two of code in the
universe of Galaxy Cloudman people like me are stymied and really don't
even know where to start. I know it requires work at some level, but a
tutorial on "how to find your 'tool_conf.xml'" (or "dummies guide to quick
Cloudman fixes") would likely be helpful to many end users (including
myself).

Thanks again, Dannon!

Cheers,
Mo Heydarian

PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
402 Biophysics
Baltimore, MD 21205


On Wed, Apr 2, 2014 at 5:03 PM, Dannon Baker  wrote:

> Hey Mo,
> Sorry for the super delayed response here.  I can't find a decision to
> remove it documented anywhere, so my guess is that this tool was
> unintentionally removed when we last updated the volume.  It's actually
> still available on disk, though, and can be re-enabled in your
> tool_conf.xml by adding the following back to your Get Data section:
>
> 
>
> -Dannon
>
>
> On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian wrote:
>
>> Hi Cloudman Development Team,
>> I noticed on the most recent Cloudman release (revision
>> 11219:5c789ab4144a)
>> that there is no option to "Get Data" from the ENA SRA. We've found that
>> retrieving large (fastq) data sets from public databases into
>> Galaxy/Cloudman is the most convenient from the ENA SRA option in the "Get
>> Data" menu. Will this option be coming back, or is the ENA SRA option
>> permanently removed?
>>
>>
>> Cheers,
>> Mo Heydarian
>>
>>
>>
>> ___
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
___
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:
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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Björn Grüning]

Hi Xiaofei,


Dear Bjoern,
As your suggestion, I tried to install the snpEff annotation. But, I think I am 
still be stuck there. What I did is:
Admin > Data > Manage local data (beta), then the message is shown as below. 
(For the BWA and Fetching genome,
I installed them from tool_sheds by myself. For the SnpEff staff, it has been 
there when I checked the data manager.)
Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff 
annotations in View managed data by Tool Data Table part, it is still empty.


After SnpEff Databases > Execute you still need to pick genome of 
interest and run "SnpEff Download". SnpEff Databases just downloads a 
list of available genomes.


Hope that will help!
Bjoern



Could you give me more details about how to install the annotation with the 
snpeff data manager under the Admin panel?

I really appreciate for your help, and thank you so much for your patience!

Best,

Xiaofei
Data Manager

Choose your data managing option from below.

   *   Access data managers - get data, build indexes, etc

  *   SnpEff 
Databases
 - Read the list of available snpEff databases

  *   SnpEff 
Download
 - Download a new database

  *   BWA 
index
 - builder

  *   BWA Color 
index
 - builder

  *   Reference 
Genome
 - fetching

   *   View managed data by manager

  *   SnpEff 
Databases
 - Read the list of available snpEff databases

  *   SnpEff 
Download
 - Download a new database

  *   BWA 
index
 - builder

  *   BWA Color 
index
 - builder

  *   Reference 
Genome
 - fetching

   *   View managed data by Tool Data Table

  *   
snpeff_databases

  *   
snpeff_genomedb

  *   
snpeff_regulationdb

  *   
snpeff_annotations

  *   
bwa_indexes

  *   
bwa_indexes_color

  *   
all_fasta
   *
   *
   *
   *   
   *   From: Björn Grüning [bjoern.gruen...@gmail.com]
   *   Sent: Wednesday, April 02, 2014 12:55 PM
   *   To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
   *   Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
   *
   *   Hi,
   *
   *   that means that the snpeff annotation is missing. You can install it
   *   with the snpeff datamanager under your Admin panel. Have a look at the
   *   wiki page about data-manager and the snpeff wrapper documentation.
   *   You do not need to edit xml files. If so that is an bug in the wrapper
   *   and we should fix it :)
   *
   *   Cheers,
   *   Bjoern
   *
   *   Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
   *   >>> When I used SnpEff in local galaxy instance, I got an error:
   *   >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 

Re: [galaxy-dev] ENA SRA data retrieval with Cloudman

[Dannon Baker]

Hey Mo,
Sorry for the super delayed response here.  I can't find a decision to
remove it documented anywhere, so my guess is that this tool was
unintentionally removed when we last updated the volume.  It's actually
still available on disk, though, and can be re-enabled in your
tool_conf.xml by adding the following back to your Get Data section:



-Dannon


On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian wrote:

> Hi Cloudman Development Team,
> I noticed on the most recent Cloudman release (revision 
> 11219:5c789ab4144a)
> that there is no option to "Get Data" from the ENA SRA. We've found that
> retrieving large (fastq) data sets from public databases into
> Galaxy/Cloudman is the most convenient from the ENA SRA option in the "Get
> Data" menu. Will this option be coming back, or is the ENA SRA option
> permanently removed?
>
>
> Cheers,
> Mo Heydarian
>
>
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Wang, Xiaofei]

Dear Bjoern,
As your suggestion, I tried to install the snpEff annotation. But, I think I am 
still be stuck there. What I did is:
Admin > Data > Manage local data (beta), then the message is shown as below. 
(For the BWA and Fetching genome, I installed them from tool_sheds by myself. 
For the SnpEff staff, it has been there when I checked the data manager.) Next, 
I clicked on SnpEff Databases > Execute. But, when I checked the snpeff 
annotations in View managed data by Tool Data Table part, it is still empty.

Could you give me more details about how to install the annotation with the 
snpeff data manager under the Admin panel?

I really appreciate for your help, and thank you so much for your patience!

Best,

Xiaofei
Data Manager

Choose your data managing option from below.

  *   Access data managers - get data, build indexes, etc

 *   SnpEff 
Databases
 - Read the list of available snpEff databases

 *   SnpEff 
Download
 - Download a new database

 *   BWA 
index
 - builder

 *   BWA Color 
index
 - builder

 *   Reference 
Genome
 - fetching

  *   View managed data by manager

 *   SnpEff 
Databases
 - Read the list of available snpEff databases

 *   SnpEff 
Download
 - Download a new database

 *   BWA 
index
 - builder

 *   BWA Color 
index
 - builder

 *   Reference 
Genome
 - fetching

  *   View managed data by Tool Data Table

 *   
snpeff_databases

 *   
snpeff_genomedb

 *   
snpeff_regulationdb

 *   
snpeff_annotations

 *   
bwa_indexes

 *   
bwa_indexes_color

 *   
all_fasta
  *
  *
  *
  *   
  *   From: Björn Grüning [bjoern.gruen...@gmail.com]
  *   Sent: Wednesday, April 02, 2014 12:55 PM
  *   To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
  *   Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
  *
  *   Hi,
  *
  *   that means that the snpeff annotation is missing. You can install it
  *   with the snpeff datamanager under your Admin panel. Have a look at the
  *   wiki page about data-manager and the snpeff wrapper documentation.
  *   You do not need to edit xml files. If so that is an bug in the wrapper
  *   and we should fix it :)
  *
  *   Cheers,
  *   Bjoern
  *
  *   Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
  *   >>> When I used SnpEff in local galaxy instance, I got an error:
  *   >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 
at java.lang.ClassLoader.defineClass1(Native Method) at 
java.lang.ClassLoader.defineClassCond(ClassLoader.j
  *   >
  *   >
  *   >
  *   >
  *   >> Which Java version do you use. Please make sure you are running Java 
1.7.
  *   >
  *   >
  *   >
 

Re: [galaxy-dev] Problems submitting using PBS Pro 12.1

[Luca Toldo]

Thankyou Nate for your prompt and detailed support.
Unfortunately I am on a different time zone and I do not have access now to
the system.
Thankyou for the suggestion you provided me to do the debugging.
I will carry that out in about 12 hours from now and let you know.
Thankyou again
Luca
p.s. although I do agree that the problems I am facing are not as
"challenging" as the other aspects of galaxy, I am convinced that a
detailed explanation on the methodology to use for debugging this kind of
low level aspects will be extremely appreciated by many :-)


2014-04-02 21:05 GMT+02:00 Nate Coraor :

> Hi Luca,
>
> We generally have not provided detailed documentation on this portion
> since it's not really within the scope of Galaxy itself, and documentation
> would be likely to become out of date as these external libraries (like
> pbs-drmaa) are updated, and cluster configurations are very site-specific.
> We are happy to help, though.
>
> It might be useful to add some debugging about the generated jobTemplate
> in drmaa.py to see what params are being set.
>
> The value you've set as the path to the drmaa library
> ($DRMAA_LIBRARY_PATH) might provide some insight on the version, or the
> output of:
>
> strings $DRMAA_LIBRARY_PATH | grep 1\.0
>
> What are the problems you're experiencing compiling pbs-drmaa 1.0.17?
>
> --nate
>
>
>
> On Wed, Apr 2, 2014 at 2:52 PM, Luca Toldo  wrote:
>
>> Dear Nate, and Björn
>> thankyou for your help. As Björn said, indeed i get always the same error
>> message regardless if I use the id=nativeSpecification or not.  How can one
>> figure out the version of pbs-drmaa that the system is using ? It would be
>> really useful to have a step-by-step tutorial on how to configure this part
>> of the system. I've spent already several days trying to get it working and
>> it constantly fails.
>>
>> Unfortunately I also got serious problem trying to compile the
>> pbs-drmaa-1.0.17 as mentioned in my posting.
>>
>> What can I try next ? I was thinking to modify /jobs/runners/drmaa.py
>> adding more logging ...
>>
>> Thankyou for your advice !
>>
>>
>>
>> 2014-04-02 20:43 GMT+02:00 Nate Coraor :
>>
>> Thanks Björn. Luca, what version of pbs-drmaa are you using now?
>>>
>>>
>>>  On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning <
>>> bjoern.gruen...@gmail.com> wrote:
>>>
 Hi Nate,

 I tried to help Luca today, but I failed totally ...
 He is not using  at all. Or put it that
 way if he isn't using it, he gets the same error.

 Cheers,
 Bjoern

 Am 02.04.2014 20:34, schrieb Nate Coraor:

  Hi Luca,
>
> Are you passing any params to the runner for inclusion as PBS submit
> parameters ( in job_conf.xml)?
>
> --nate
>
>
> On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo 
> wrote:
>
>  Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
>>
>> galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
>> exception calling queue_job
>> Traceback (most recent call last):
>> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.
>> py",
>> line 62, in run_next
>>   method(arg)
>> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
>> line
>> 151, in queue_job
>>   external_job_id = self.ds.runJob(jt)
>> File
>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/
>> drmaa/__init__.py",
>> line 331, in runJob
>>   _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
>> File
>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py",
>> line
>> 213, in c
>>   return f(*(args + (error_buffer, sizeof(error_buffer
>> File
>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py",
>> line
>> 90, in error_check
>>   raise _ERRORS[code-1]("code %s: %s" % (code,
>> error_buffer.value))
>> InvalidAttributeValueException: code 14: Illegal attribute or
>> resource
>> value: Illegal attribute or resource value
>>
>>
>> If I do
>> qsub -q NGSq
>> /opt/ngs/bin/galaxy-dist/database/job_working_
>> directory/000/249/galaxy_249.sh
>>
>> however the qsub returns
>>
>> 12345.myserver
>>
>>
>> and the corresponding
>>
>> qstat | grep -i galaxy
>> 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq
>>
>> Is the above error message perhaps related with
>> a) PBS 12.1
>> b) drmaa-0.7-py2.6.egg
>>
>> I am trying to compile pbs-drmaa-1.0.17 but there are problems ...
>>
>> any advice ?
>>
>> any alternative ?
>>
>> Thanks
>> luca
>>
>>
>> ___
>> 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, p

Re: [galaxy-dev] Problems submitting using PBS Pro 12.1

[Nate Coraor]

Hi Luca,

We generally have not provided detailed documentation on this portion since
it's not really within the scope of Galaxy itself, and documentation would
be likely to become out of date as these external libraries (like
pbs-drmaa) are updated, and cluster configurations are very site-specific.
We are happy to help, though.

It might be useful to add some debugging about the generated jobTemplate in
drmaa.py to see what params are being set.

The value you've set as the path to the drmaa library ($DRMAA_LIBRARY_PATH)
might provide some insight on the version, or the output of:

strings $DRMAA_LIBRARY_PATH | grep 1\.0

What are the problems you're experiencing compiling pbs-drmaa 1.0.17?

--nate



On Wed, Apr 2, 2014 at 2:52 PM, Luca Toldo  wrote:

> Dear Nate, and Björn
> thankyou for your help. As Björn said, indeed i get always the same error
> message regardless if I use the id=nativeSpecification or not.  How can one
> figure out the version of pbs-drmaa that the system is using ? It would be
> really useful to have a step-by-step tutorial on how to configure this part
> of the system. I've spent already several days trying to get it working and
> it constantly fails.
>
> Unfortunately I also got serious problem trying to compile the
> pbs-drmaa-1.0.17 as mentioned in my posting.
>
> What can I try next ? I was thinking to modify /jobs/runners/drmaa.py
> adding more logging ...
>
> Thankyou for your advice !
>
>
>
> 2014-04-02 20:43 GMT+02:00 Nate Coraor :
>
> Thanks Björn. Luca, what version of pbs-drmaa are you using now?
>>
>>
>> On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning 
>> wrote:
>>
>>> Hi Nate,
>>>
>>> I tried to help Luca today, but I failed totally ...
>>> He is not using  at all. Or put it that
>>> way if he isn't using it, he gets the same error.
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> Am 02.04.2014 20:34, schrieb Nate Coraor:
>>>
>>>  Hi Luca,

 Are you passing any params to the runner for inclusion as PBS submit
 parameters ( in job_conf.xml)?

 --nate


 On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo 
 wrote:

  Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
>
> galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
> exception calling queue_job
> Traceback (most recent call last):
> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.
> py",
> line 62, in run_next
>   method(arg)
> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
> line
> 151, in queue_job
>   external_job_id = self.ds.runJob(jt)
> File
> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py",
> line 331, in runJob
>   _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
> File
> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py",
> line
> 213, in c
>   return f(*(args + (error_buffer, sizeof(error_buffer
> File
> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py",
> line
> 90, in error_check
>   raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
> InvalidAttributeValueException: code 14: Illegal attribute or resource
> value: Illegal attribute or resource value
>
>
> If I do
> qsub -q NGSq
> /opt/ngs/bin/galaxy-dist/database/job_working_
> directory/000/249/galaxy_249.sh
>
> however the qsub returns
>
> 12345.myserver
>
>
> and the corresponding
>
> qstat | grep -i galaxy
> 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq
>
> Is the above error message perhaps related with
> a) PBS 12.1
> b) drmaa-0.7-py2.6.egg
>
> I am trying to compile pbs-drmaa-1.0.17 but there are problems ...
>
> any advice ?
>
> any alternative ?
>
> Thanks
> luca
>
>
> ___
> 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:
>http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>http://galaxyproject.org/search/mailinglists/
>
>


 ___
 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:
http://lists.bx.psu.edu/

 To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


>>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and

Re: [galaxy-dev] Problems submitting using PBS Pro 12.1

[Luca Toldo]

Dear Nate, and Björn
thankyou for your help. As Björn said, indeed i get always the same error
message regardless if I use the id=nativeSpecification or not.  How can one
figure out the version of pbs-drmaa that the system is using ? It would be
really useful to have a step-by-step tutorial on how to configure this part
of the system. I've spent already several days trying to get it working and
it constantly fails.

Unfortunately I also got serious problem trying to compile the
pbs-drmaa-1.0.17 as mentioned in my posting.

What can I try next ? I was thinking to modify /jobs/runners/drmaa.py
adding more logging ...

Thankyou for your advice !



2014-04-02 20:43 GMT+02:00 Nate Coraor :

> Thanks Björn. Luca, what version of pbs-drmaa are you using now?
>
>
> On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning 
> wrote:
>
>> Hi Nate,
>>
>> I tried to help Luca today, but I failed totally ...
>> He is not using  at all. Or put it that
>> way if he isn't using it, he gets the same error.
>>
>> Cheers,
>> Bjoern
>>
>> Am 02.04.2014 20:34, schrieb Nate Coraor:
>>
>>  Hi Luca,
>>>
>>> Are you passing any params to the runner for inclusion as PBS submit
>>> parameters ( in job_conf.xml)?
>>>
>>> --nate
>>>
>>>
>>> On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo  wrote:
>>>
>>>  Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers

 galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
 exception calling queue_job
 Traceback (most recent call last):
 File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.
 py",
 line 62, in run_next
   method(arg)
 File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
 line
 151, in queue_job
   external_job_id = self.ds.runJob(jt)
 File
 "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py",
 line 331, in runJob
   _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
 File
 "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py",
 line
 213, in c
   return f(*(args + (error_buffer, sizeof(error_buffer
 File
 "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py",
 line
 90, in error_check
   raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
 InvalidAttributeValueException: code 14: Illegal attribute or resource
 value: Illegal attribute or resource value


 If I do
 qsub -q NGSq
 /opt/ngs/bin/galaxy-dist/database/job_working_
 directory/000/249/galaxy_249.sh

 however the qsub returns

 12345.myserver


 and the corresponding

 qstat | grep -i galaxy
 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq

 Is the above error message perhaps related with
 a) PBS 12.1
 b) drmaa-0.7-py2.6.egg

 I am trying to compile pbs-drmaa-1.0.17 but there are problems ...

 any advice ?

 any alternative ?

 Thanks
 luca


 ___
 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:
http://lists.bx.psu.edu/

 To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


>>>
>>>
>>> ___
>>> 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:
>>>http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>http://galaxyproject.org/search/mailinglists/
>>>
>>>
>
___
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Problems submitting using PBS Pro 12.1

[Björn Grüning]

Hi Nate,

I tried to help Luca today, but I failed totally ...
He is not using  at all. Or put it that 
way if he isn't using it, he gets the same error.


Cheers,
Bjoern

Am 02.04.2014 20:34, schrieb Nate Coraor:

Hi Luca,

Are you passing any params to the runner for inclusion as PBS submit
parameters ( in job_conf.xml)?

--nate


On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo  wrote:


Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers

galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
exception calling queue_job
Traceback (most recent call last):
File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 62, in run_next
  method(arg)
File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
151, in queue_job
  external_job_id = self.ds.runJob(jt)
File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py",
line 331, in runJob
  _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", line
213, in c
  return f(*(args + (error_buffer, sizeof(error_buffer
File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line
90, in error_check
  raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
InvalidAttributeValueException: code 14: Illegal attribute or resource
value: Illegal attribute or resource value


If I do
qsub -q NGSq
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh

however the qsub returns

12345.myserver


and the corresponding

qstat | grep -i galaxy
12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq

Is the above error message perhaps related with
a) PBS 12.1
b) drmaa-0.7-py2.6.egg

I am trying to compile pbs-drmaa-1.0.17 but there are problems ...

any advice ?

any alternative ?

Thanks
luca


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Re: [galaxy-dev] Problems submitting using PBS Pro 12.1

[Nate Coraor]

Thanks Björn. Luca, what version of pbs-drmaa are you using now?


On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning wrote:

> Hi Nate,
>
> I tried to help Luca today, but I failed totally ...
> He is not using  at all. Or put it that
> way if he isn't using it, he gets the same error.
>
> Cheers,
> Bjoern
>
> Am 02.04.2014 20:34, schrieb Nate Coraor:
>
>  Hi Luca,
>>
>> Are you passing any params to the runner for inclusion as PBS submit
>> parameters ( in job_conf.xml)?
>>
>> --nate
>>
>>
>> On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo  wrote:
>>
>>  Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
>>>
>>> galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
>>> exception calling queue_job
>>> Traceback (most recent call last):
>>> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>>> line 62, in run_next
>>>   method(arg)
>>> File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
>>> line
>>> 151, in queue_job
>>>   external_job_id = self.ds.runJob(jt)
>>> File
>>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py",
>>> line 331, in runJob
>>>   _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
>>> File
>>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py",
>>> line
>>> 213, in c
>>>   return f(*(args + (error_buffer, sizeof(error_buffer
>>> File
>>> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py",
>>> line
>>> 90, in error_check
>>>   raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
>>> InvalidAttributeValueException: code 14: Illegal attribute or resource
>>> value: Illegal attribute or resource value
>>>
>>>
>>> If I do
>>> qsub -q NGSq
>>> /opt/ngs/bin/galaxy-dist/database/job_working_
>>> directory/000/249/galaxy_249.sh
>>>
>>> however the qsub returns
>>>
>>> 12345.myserver
>>>
>>>
>>> and the corresponding
>>>
>>> qstat | grep -i galaxy
>>> 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq
>>>
>>> Is the above error message perhaps related with
>>> a) PBS 12.1
>>> b) drmaa-0.7-py2.6.egg
>>>
>>> I am trying to compile pbs-drmaa-1.0.17 but there are problems ...
>>>
>>> any advice ?
>>>
>>> any alternative ?
>>>
>>> Thanks
>>> luca
>>>
>>>
>>> ___
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>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>http://lists.bx.psu.edu/
>>>
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>>>http://galaxyproject.org/search/mailinglists/
>>>
>>>
>>
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
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>>
>>
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Re: [galaxy-dev] Problems submitting using PBS Pro 12.1

[Nate Coraor]

Hi Luca,

Are you passing any params to the runner for inclusion as PBS submit
parameters ( in job_conf.xml)?

--nate


On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo  wrote:

> Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
>
> galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
> exception calling queue_job
> Traceback (most recent call last):
>File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 62, in run_next
>  method(arg)
>File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
> 151, in queue_job
>  external_job_id = self.ds.runJob(jt)
>File
> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py",
> line 331, in runJob
>  _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
>File
> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", line
> 213, in c
>  return f(*(args + (error_buffer, sizeof(error_buffer
>File
> "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line
> 90, in error_check
>  raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
> InvalidAttributeValueException: code 14: Illegal attribute or resource
> value: Illegal attribute or resource value
>
>
> If I do
> qsub -q NGSq
> /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh
>
> however the qsub returns
>
> 12345.myserver
>
>
> and the corresponding
>
> qstat | grep -i galaxy
> 12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq
>
> Is the above error message perhaps related with
> a) PBS 12.1
> b) drmaa-0.7-py2.6.egg
>
> I am trying to compile pbs-drmaa-1.0.17 but there are problems ...
>
> any advice ?
>
> any alternative ?
>
> Thanks
> luca
>
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Björn Grüning]

Hi,

that means that the snpeff annotation is missing. You can install it 
with the snpeff datamanager under your Admin panel. Have a look at the 
wiki page about data-manager and the snpeff wrapper documentation.
You do not need to edit xml files. If so that is an bug in the wrapper 
and we should fix it :)


Cheers,
Bjoern

Am 02.04.2014 19:34, schrieb Wang, Xiaofei:

When I used SnpEff in local galaxy instance, I got an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at 
java.lang.ClassLoader.defineClass1(Native Method) at 
java.lang.ClassLoader.defineClassCond(ClassLoader.j






Which Java version do you use. Please make sure you are running Java 1.7.





Yes, it is figured, when I changed the java version to 1.7. Thank you so much!




But, I got another error for snpEff.




java.lang.RuntimeException: Property: 'dm5.30.genome' not found
 at ca.mcgill.mcb.pcingola.interval.Genome.(Genome.java:92)
 at 
ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
 at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
 at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
 at ca.mcgill.mcb.pcingola.snpEffect.Config.(Config.java:96)
 at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
 at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
 at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
 at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
 at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
 at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)








What does this mean? I found the similar error on this thead 
http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is 
no reply.




Does this mean I need to add genome to Galaxy? Following this webpage: 
http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an 
example how to edit the snpEffect.xml file in dm (Drosophila) case as below? 
(In fact, on the drap-down menu of Genome in snpEff, there is different options 
for genome. Why the error shows '*.genome' not found? )





Human (hg37)
Mouse (mm37.61)





From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, April 02, 2014 10:35 AM
To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,


Dear there,

When I used SnpEff in local galaxy instance, I got an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at 
java.lang.ClassLoader.defineClass1(Native Method) at 
java.lang.ClassLoader.defineClassCond(ClassLoader.j


Which Java version do you use. Please make sure you are running Java 1.7.


Also, when I used the FASTQ Summary Statistics, I got an error like this:
Traceback (most recent call last): File 
"/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
 line 48, in if __name__ == "__main__": main() File "/Users/...


Can you give us the complete error message. The important part is missing.

Ciao,
Bjoern


I tried to google and solve them by myself. But I really do not know how to do 
that. Could anybody give me some clue? Thanks a lot for your help!




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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Wang, Xiaofei]

>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
>> ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 
>> 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at 
>> java.lang.ClassLoader.defineClassCond(ClassLoader.j




>Which Java version do you use. Please make sure you are running Java 1.7.




Yes, it is figured, when I changed the java version to 1.7. Thank you so much!




But, I got another error for snpEff.




java.lang.RuntimeException: Property: 'dm5.30.genome' not found
        at ca.mcgill.mcb.pcingola.interval.Genome.(Genome.java:92)
        at 
ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.(Config.java:96)
        at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
        at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
        at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
        at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
        at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
        at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)








What does this mean? I found the similar error on this thead 
http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is 
no reply.




Does this mean I need to add genome to Galaxy? Following this webpage: 
http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an 
example how to edit the snpEffect.xml file in dm (Drosophila) case as below? 
(In fact, on the drap-down menu of Genome in snpEff, there is different options 
for genome. Why the error shows '*.genome' not found? )





Human (hg37)
Mouse (mm37.61)
 




From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, April 02, 2014 10:35 AM
To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

> Dear there,
>
> When I used SnpEff in local galaxy instance, I got an error:
> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
> ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 
> at java.lang.ClassLoader.defineClass1(Native Method) at 
> java.lang.ClassLoader.defineClassCond(ClassLoader.j

Which Java version do you use. Please make sure you are running Java 1.7.

> Also, when I used the FASTQ Summary Statistics, I got an error like this:
> Traceback (most recent call last): File 
> "/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
>  line 48, in if __name__ == "__main__": main() File "/Users/...

Can you give us the complete error message. The important part is missing.

Ciao,
Bjoern

> I tried to google and solve them by myself. But I really do not know how to 
> do that. Could anybody give me some clue? Thanks a lot for your help!
>
>
>
>
> ___
> 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:
>http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>http://galaxyproject.org/search/mailinglists/
>



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Re: [galaxy-dev] Galaxy unhandled exception checking jobs error

[Ravi Alla]

John,
Thanks for this. I am new to managing galaxy, but how do I go about updating my 
galaxy to reflect these changes? I found directions on 
https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about 
pulling changes from the bitbucket repository. Does this preserve my previous 
galaxy settings?
Do I have to back up before I do this? I spent considerable time to get galaxy 
to work on the cluster and don't want to ruin it.
Thank you
Ravi
On Apr 2, 2014, at 9:58 AM, John Chilton  wrote:

> This looks very to similar to an issue discussed here:
> http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html.
> 
> The default branch of Galaxy contains changeset that should address
> this issue - 
> https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0.
> 
> Hope this helps.
> 
> -John
> 
> On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla  wrote:
>> Hi guys,
>> I keep getting an error everytime I start up the galaxy server. I am
>> guessing this has to do with a job that galaxy is trying to resume and
>> cannot find.
>> 
>> galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception
>> checking active jobs
>> Traceback (most recent call last):
>>  File
>> "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>> line 366, in monitor
>>self.check_watched_items()
>>  File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
>> line 363, in check_watched_items
>>( failures, statuses ) = self.check_all_jobs()
>>  File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
>> line 452, in check_all_jobs
>>c = pbs.pbs_connect( pbs_server_name )
>> TypeError: in method 'pbs_connect', argument 1 of type 'char *'
>> 
>> Because of this error I cannot get any other jobs to run either. They just
>> sit queued on the cluster.
>> Any ideas?
>> Thanks
>> 
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
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>> 
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[galaxy-dev] Problems submitting using PBS Pro 12.1

[Luca Toldo]

Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers

galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
exception calling queue_job
Traceback (most recent call last):
   File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 62, in run_next
 method(arg)
   File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
151, in queue_job
 external_job_id = self.ds.runJob(jt)
   File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py",
line 331, in runJob
 _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
   File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", line
213, in c
 return f(*(args + (error_buffer, sizeof(error_buffer
   File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line
90, in error_check
 raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
InvalidAttributeValueException: code 14: Illegal attribute or resource
value: Illegal attribute or resource value


If I do
qsub -q NGSq
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh

however the qsub returns

12345.myserver


and the corresponding

qstat | grep -i galaxy
12345.myserver galaxy_249.shgalaxy00:00:00 E NGSq

Is the above error message perhaps related with
a) PBS 12.1
b) drmaa-0.7-py2.6.egg

I am trying to compile pbs-drmaa-1.0.17 but there are problems ...

any advice ?

any alternative ?

Thanks
luca
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Re: [galaxy-dev] Galaxy unhandled exception checking jobs error

[John Chilton]

This looks very to similar to an issue discussed here:
http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html.

The default branch of Galaxy contains changeset that should address
this issue - 
https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0.

Hope this helps.

-John

On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla  wrote:
> Hi guys,
> I keep getting an error everytime I start up the galaxy server. I am
> guessing this has to do with a job that galaxy is trying to resume and
> cannot find.
>
> galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception
> checking active jobs
> Traceback (most recent call last):
>   File
> "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 366, in monitor
> self.check_watched_items()
>   File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
> line 363, in check_watched_items
> ( failures, statuses ) = self.check_all_jobs()
>   File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
> line 452, in check_all_jobs
> c = pbs.pbs_connect( pbs_server_name )
> TypeError: in method 'pbs_connect', argument 1 of type 'char *'
>
> Because of this error I cannot get any other jobs to run either. They just
> sit queued on the cluster.
> Any ideas?
> Thanks
>
> ___
> 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:
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>
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[galaxy-dev] Galaxy unhandled exception checking jobs error

[Ravi Alla]

Hi guys,
I keep getting an error everytime I start up the galaxy server. I am guessing 
this has to do with a job that galaxy is trying to resume and cannot find.

galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking 
active jobs
Traceback (most recent call last):
  File 
"/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 
366, in monitor
self.check_watched_items()
  File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", 
line 363, in check_watched_items
( failures, statuses ) = self.check_all_jobs()
  File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", 
line 452, in check_all_jobs
c = pbs.pbs_connect( pbs_server_name )
TypeError: in method 'pbs_connect', argument 1 of type 'char *'

Because of this error I cannot get any other jobs to run either. They just sit 
queued on the cluster.
Any ideas?
Thanks___
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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Wang, Xiaofei]

Oh, yes, here it is:

Traceback (most recent call last):
  File 
"/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
 line 48, in 
if __name__ == "__main__": main()
  File 
"/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
 line 32, in main
base_counts = aggregator.get_base_counts_for_column( i )
  File 
"/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", 
line 397, in get_base_counts_for_column
return self.nuc_index_base[ column ]
IndexError: list index out of range

From: Daniel Blankenberg [d...@bx.psu.edu]
Sent: Wednesday, April 02, 2014 11:14 AM
To: Wang, Xiaofei
Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

To get the complete error message, can you click on the bug icon (left-most 
icon at the bottom of the expanded history item) of the error’d dataset and 
copy and paste from the page that loads in the middle pane?


Thanks for using Galaxy,

Dan


On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei  wrote:

>>> Can you give us the complete error message. The important part is missing.
>
> Here is the whole thing for the error:
>
> Traceback (most recent call last):
>  File 
> "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
>  line 48, in
>if __name__ == "__main__": main()
>  File "/Users/xiaofe
>
> I know it seems weird, but it is the complete message. May I ask a question 
> about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?
>
> Thanks a lot!
> 
> From: Björn Grüning [bjoern.gruen...@gmail.com]
> Sent: Wednesday, April 02, 2014 10:35 AM
> To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear there,
>>
>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
>> ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 
>> 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at 
>> java.lang.ClassLoader.defineClassCond(ClassLoader.j
>
> Which Java version do you use. Please make sure you are running Java 1.7.
>
>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> Traceback (most recent call last): File 
>> "/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
>>  line 48, in if __name__ == "__main__": main() File "/Users/...
>
> Can you give us the complete error message. The important part is missing.
>
> Ciao,
> Bjoern
>
>> I tried to google and solve them by myself. But I really do not know how to 
>> do that. Could anybody give me some clue? Thanks a lot for your help!
>>
>>
>>
>>
>> ___
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
>
> ___
> 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:
>  http://lists.bx.psu.edu/
>
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>  http://galaxyproject.org/search/mailinglists/
>




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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Daniel Blankenberg]

Hi Xiaofei,

To get the complete error message, can you click on the bug icon (left-most 
icon at the bottom of the expanded history item) of the error’d dataset and 
copy and paste from the page that loads in the middle pane?


Thanks for using Galaxy,

Dan


On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei  wrote:

>>> Can you give us the complete error message. The important part is missing.
> 
> Here is the whole thing for the error:
> 
> Traceback (most recent call last):
>  File 
> "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
>  line 48, in 
>if __name__ == "__main__": main()
>  File "/Users/xiaofe
> 
> I know it seems weird, but it is the complete message. May I ask a question 
> about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?
> 
> Thanks a lot!
> 
> From: Björn Grüning [bjoern.gruen...@gmail.com]
> Sent: Wednesday, April 02, 2014 10:35 AM
> To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
> 
> Hi Xiaofei,
> 
>> Dear there,
>> 
>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
>> ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 
>> 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at 
>> java.lang.ClassLoader.defineClassCond(ClassLoader.j
> 
> Which Java version do you use. Please make sure you are running Java 1.7.
> 
>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> Traceback (most recent call last): File 
>> "/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
>>  line 48, in if __name__ == "__main__": main() File "/Users/...
> 
> Can you give us the complete error message. The important part is missing.
> 
> Ciao,
> Bjoern
> 
>> I tried to google and solve them by myself. But I really do not know how to 
>> do that. Could anybody give me some clue? Thanks a lot for your help!
>> 
>> 
>> 
>> 
>> ___
>> 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:
>>   http://lists.bx.psu.edu/
>> 
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>> 
> 
> 
> 
> ___
> 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:
>  http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
> 


___
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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Wang, Xiaofei]

>>Can you give us the complete error message. The important part is missing.

Here is the whole thing for the error:

Traceback (most recent call last):
  File 
"/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
 line 48, in 
if __name__ == "__main__": main()
  File "/Users/xiaofe

I know it seems weird, but it is the complete message. May I ask a question 
about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?

Thanks a lot!

From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, April 02, 2014 10:35 AM
To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

> Dear there,
>
> When I used SnpEff in local galaxy instance, I got an error:
> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
> ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 
> at java.lang.ClassLoader.defineClass1(Native Method) at 
> java.lang.ClassLoader.defineClassCond(ClassLoader.j

Which Java version do you use. Please make sure you are running Java 1.7.

> Also, when I used the FASTQ Summary Statistics, I got an error like this:
> Traceback (most recent call last): File 
> "/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
>  line 48, in if __name__ == "__main__": main() File "/Users/...

Can you give us the complete error message. The important part is missing.

Ciao,
Bjoern

> I tried to google and solve them by myself. But I really do not know how to 
> do that. Could anybody give me some clue? Thanks a lot for your help!
>
>
>
>
> ___
> 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:
>http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>http://galaxyproject.org/search/mailinglists/
>



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Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Björn Grüning]

Hi Xiaofei,


Dear there,

When I used SnpEff in local galaxy instance, I got an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at 
java.lang.ClassLoader.defineClass1(Native Method) at 
java.lang.ClassLoader.defineClassCond(ClassLoader.j


Which Java version do you use. Please make sure you are running Java 1.7.


Also, when I used the FASTQ Summary Statistics, I got an error like this:
Traceback (most recent call last): File 
"/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
 line 48, in if __name__ == "__main__": main() File "/Users/...


Can you give us the complete error message. The important part is missing.

Ciao,
Bjoern


I tried to google and solve them by myself. But I really do not know how to do 
that. Could anybody give me some clue? Thanks a lot for your help!




___
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___
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[galaxy-dev] snpEff and FASTQ Summary Statistics errors

[Wang, Xiaofei]

Dear there,

When I used SnpEff in local galaxy instance, I got an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: 
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 
at java.lang.ClassLoader.defineClass1(Native Method) at 
java.lang.ClassLoader.defineClassCond(ClassLoader.j


Also, when I used the FASTQ Summary Statistics, I got an error like this:
Traceback (most recent call last): File 
"/Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py",
 line 48, in if __name__ == "__main__": main() File "/Users/...

I tried to google and solve them by myself. But I really do not know how to do 
that. Could anybody give me some clue? Thanks a lot for your help!

___
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[galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

[Janaki Rama Rao Gollapudi]

Hi,

I have implemented a custom tool called 'barcode-parse' and uploaded this
custom to into my local tool shed(which is running at http://localhost:9009).
Also able to install this custom tool from galaxy.

Then I have added simple repository dependency. I have created a xml file
'repository_dependencies.xml'. Then I created a new repository in the
toolShed called 'Test' and uploaded all necessary files(.py, definition xml
file and repository dependency xml file) into this repository. (I have
created another repository called 'string_occurrence' and uploaded
necessary files into toolShed which is used as dependency repository)



 http://localhost:9009"; name="string_occurrence"
owner="janakiram-t1" />


I tried to install custom tool 'barcode-parse' from galaxy, but I got below
error message.

The repository dependency definitions for this repository are invalid and
will be ignored.

I followed the steps mentioned in the galaxy
wiki

Am I doing anything wrong? Please suggest me on this.

Thanks,
JanakiRam
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[galaxy-dev] Problem with executing newly installed tools (via admin)

[Nicolas Cybulski]

Hi,

I have installed the Picard tools using the Tool-shed functionality in 
the admin tools.

The tools and requisites have been correctly installed and run correctly.
The insert statement to the event table fails however. I get the 
following error on screen:


|OperationalError: (OperationalError) (1241, 'Operand should contain 1 
column(s)') 'INSERT INTO event (create_time, update_time, history_id, 
user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s, 
%s)' (datetime.datetime(2014, 4, 2, 9, 32, 47, 823142), 
datetime.datetime(2014, 4, 2, 9, 32, 47, 823170), 35L, 4L, "Tool params: 
{'histWidth': u'0', 'deviations': u'10.0', 'malevel': u'ALL_READS', 
'input_file': u'5266', 'out_prefix': u'Insertion size metrics', 
'refresh': u'refresh', 'minPct': u'0.05', 'tool_state': 
u'800254cf01316164663833323133363237333739303833323639353065346362343762393730383966363664313a37623232363836393733373435373639363437343638323233613230323235633232333035633232323232633230323236343635373636393631373436393666366537333232336132303232356332323331333032653330356332323232326332303232363936653730373537343566363636393663363532323361323032323335333233363336323232633230323235663566373036313637363535663566323233613230333032633230323235663566373236353732373536653566373236353664363137303566366136663632356636393634356635663232336132303665373536633663326332303232366436313663363537363635366332323361323032323563323234313463346335663532343534313434353335633232323232633230323236663735373435663730373236353636363937383232336132303232356332323439366537333635373237343639366636653230373336393761363532303664363537343", 
1468L, 
[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', 
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0'])


|The problem seems to be a duplicate entry of the tool_id

|[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', 
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0']

|In the shed_tool_conf.xml the tools are generated as follows

file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml" 
guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0">


If I change this guid to something less complicated like

file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml" 
guid="testPicard">


and restart galaxy it works ...
for all tools (so not only the one that I've changed).

Does anyone have an idea as to why this is ?

kind regards,

Nicolas
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