Re: [galaxy-user] Installing galaxy with Apache ...

[Neil.Burdett]

Thanks very much. This did in fact solve the issue. For those following the 
thread the "Rewrite" statements have to be added to 
/etc/apache2/sites-available/defaults.

Thanks
Again
Neil

-Original Message-
From: Carlos Borroto [mailto:carlos.borr...@gmail.com] 
Sent: Tuesday, 28 August 2012 6:14 AM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Installing galaxy with Apache ...

This thread my help you:
http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.html

On Thu, Aug 23, 2012 at 5:48 PM,   wrote:
> Hi Jelle,
>I'm still having issues with Apache. I've moved
>
> RewriteEngine on
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*) 
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] 
> RewriteRule ^/galaxy/static/scripts/(.*) 
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule 
> ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] 
> RewriteRule ^/galaxy/favicon.ico 
> /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule 
> ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] 
> RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
>
> from /var/www/.htaccess to /etc/apache2/httpd.conf
>
> I still get a "404 Not found" error when trying to access galaxy 
> (http://140.253.78.44/galaxy )
>
> http://140.253.78.44 still gets the "It Works!" Apache default 
> index.html
>
> and http://140.253.78.44:8080 gets the galaxy page
>
> /var/log/apache2/error.log states...
>
> [Fri Aug 24 07:35:27 2012] [error] [client 140.253.78.44] File does 
> not exist: /var/www/favicon.ico [Fri Aug 24 07:36:25 2012] [error] 
> [client 140.253.78.44] File does not exist: /var/www/galaxy
>
> Now if I change httpd.conf and add the vitrtualHost tags to:
>
> ServerName localhost
> 
>   RewriteEngine on
>   RewriteRule ^/galaxy$ /galaxy/ [R]
>   RewriteRule ^/galaxy/static/style/(.*) 
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
>   RewriteRule ^/galaxy/static/scripts/(.*) 
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
>   RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
>   RewriteRule ^/galaxy/favicon.ico 
> /home/galaxy/galaxy-dist/static/favicon.ico [L]
>   RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt 
> [L]
>   RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] 
>
> I now get a "403 Forbidden" error when trying to access 
> (http://140.253.78.44/galaxy ) You don't have permission to access /galaxy/ 
> on this server, and /var/log/apache2/error.log states..
>
> [Fri Aug 24 07:45:33 2012] [error] [client 140.253.78.44] attempt to 
> make remote request from mod_rewrite without proxy enabled: 
> proxy:http://localhost:8080/ [Fri Aug 24 07:45:34 2012] [error] 
> [client 140.253.78.44] File does not exist: /etc/apache2/htdocs
>
> Any help much appreciated
>
> Neil
> 
> From: Jelle Scholtalbers [j.scholtalb...@gmail.com]
> Sent: Thursday, August 23, 2012 8:20 PM
> To: Burdett, Neil (ICT Centre, Herston - RBWH)
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Installing galaxy with Apache ...
>
> Hi Neil,
>
> with your current apache configuration, you should probably see Galaxy 
> at http://yourip/galaxy This is due to your Rewriterule /galaxy and 
> for that you have also set proxy_prefix = /galaxy in your 
> universe_wsgi.ini
>
> You should probably remove the empty galaxy directory under /var/www 
> Furthermore, most of the time you will not need a directory with 777 
> in your apache web/documentroot..
>
> Cheers,
> Jelle
>
> On Thu, Aug 23, 2012 at 8:34 AM,   wrote:
>> Hi
>>I've installed galaxy with the default settings and it works fine.
>>
>> On a new Ubuntu machine I am trying to get galaxy running with Apache. But I 
>> am having problems, I've followed the documentation.
>>
>> After installing Apache I can put my ip address into a browser and I 
>> get message saying Apache is working fine. It displays a message from 
>> /var/www/index.html
>>
>> Now when I start galaxy I was assuming I would get redirected to the galaxy 
>> welcome page, but this doesn't happen and it remains at /var/www/index.html. 
>> To view the welcome page I have to add ":8080" after the ip address. Is this 
>> still required? I thought that Apache would know to redirect to my 
>> distributionWhat am I doing wrong?
>>
>> /etc/apache2/sites-available/default-ssl and 
>> /etc/apache2/sites-available/default look like this ...
>>
>> DocumentRoot /var/www
>> 
>> Options FollowSymLinks
>> AllowOverride None
>> 
>> 
>> Options Indexes FollowSymLinks MultiViews
>> AllowOverride None
>> Order allow,deny
>> allow from all
>> 
>>
>>  etc ...
>>
>> /var/www/.htaccess
>>
>> RewriteEngine on
>> RewriteRule ^

Re: [galaxy-user] Text Manipulation

[Lee M. Silver]

Thanks Jen,

Yes, I am working with codingDbSnp files.  The solutions you suggest do the 
work, but they're clunky in requiring a bunch of operations to extract a whole 
codon or to determine whether a particular interval has two or three codons.  
So if someone has a one or two line solution, it would be much appreciated.

Lee


On Aug 27, 2012, at 2:04 PM, Jennifer Jackson  wrote:

> Hi Lee,
> 
> There are a few options .. my guess is you are working with files like 
> snpXXXCodingDbSnp?
> 
> 1 - Using an expression such as this one will extract individual characters 
> from the column, including the commas (treating the column's data like a 
> string)
> 
>  c5.pop(1)
> 
>  = extracts the second character from the column
> 
> 2 - Or, if you want to work with the entire codons, you could use the tool 
> "Convert delimiters to TAB" to fully expand the data. You might want to use 
> other Text Manipulation tools such as "Cut" with this option to get access to 
> specific columns. Or "Condense consecutive characters" if the extra trailing 
> commas in some of these datasets create empty columns (after converting to 
> tabs).
> 
> Hopefully this helps! If there is more feedback from our developers, we'll 
> post more. Others on the list are also welcome to add in comments.
> 
> Best,
> 
> Jen
> Galaxy team
> 
> On 8/27/12 9:44 AM, Jennifer Jackson wrote:
>> Post to mailing list
>> 
>> On 8/26/12 11:38 AM, leemsil...@genepeeks.com wrote:
>>> Hi Jen,
>>> 
>>> The ability to use Python commands with the Compute tool seems to be a
>>> very well-hidden gem in Galaxy.  The problem with this nearly
>>> unmentioned gem is the sheer frustration felt when something that
>>> works on the Python command line fails on the Galaxy Compute tool.
>>> 
>>> What I would like to do is manipulate a column from a UCSC download
>>> that lists two or three codons separated by a comma, e.g.AAC,GCG,
>>> or  GGT, CAC, TAT,  .   The string-based split command  <
>>> c5.split(",").pop(1) > fails on this data because Galaxy assigned it a
>>>  type automatically. All of my attempts to change the data type
>>> to "string" have failed.
>>> 
>>> Any suggestions?
>>> 
>>> Lee
>>> leemsil...@genepeeks.com
> 
> -- 
> Jennifer Jackson
> http://galaxyproject.org


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[galaxy-user] How to decide if the deference is significant

[Du, Jianguang]

Dear All,

I am looking for the deferential splicing events between cell types. I have run 
the Cuffdiff and I am going through the output file "splicing differential 
expression testing". I have read the documentation and protocols about how 
Cuffdiff test for differential expression and regulation. However although I 
know the changes in relative abundance are quantified by the square root of the 
Jensen-Shannon divergence, I still could not understand the concept of it 
(unfortunately I am not good at math and statistics). Is there any way to 
convert "the square root of the Jensen-Shannon divergence" into "fold of 
diference"? How much of "the square root of the Jensen-Shannon divergence" 
equals to 2 fold of difference?

Thanks.

Jianguang
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Re: [galaxy-user] Is there web-based CummeRbund?

[Carlos Borroto]

Hi Jianguang,

I'm the author of cummeRbund wrapper in the test Galaxy Tool Shed. I
never got around to quite finish it, that's why I never submitted to
main. Also cummeRbund received a big update since the time I was
writing this wrapper. I don't think I can recommend using the wrapper
in its current state at all.

In any case, even if the wrapper could help you, you would need to
deploy a local or a cloud instance of Galaxy,  as is not clear to me
that this wrapper would make its way to Galaxy Main server any time
soon. You would probably be better of by dealing with R and
cummeRbund, which by the way you should be able to use in Windows.

If I find the time to play with the cummeRbund Galaxy wrapper again,
I'll make sure to comment about it in this list.

Best,
Carlos

On Sat, Aug 25, 2012 at 8:09 PM, Dave Clements
 wrote:
> Hi Jianguang,
>
> I went to http://galaxy.psu.edu/search/web/ and searched for cummerbund.
>
> It looks like there is a cummerbund wrapper in the test Galaxy Tool Shed,
> but that is about it.
>
> Dave C
>
> On Fri, Aug 24, 2012 at 3:23 PM, Du, Jianguang  wrote:
>>
>> Dear All,
>>
>> I am going to visualize Cuffdiff outputs. I understand that CummeRbund can
>> be used to visualize Cuffdiff outputs. However, I am not good at Linux
>> system and feel difficult to understand CummeRbund manual. Is there
>> web-based CummeRbund program (like Tophat and Cufflink) available for use?
>>
>> If web-based CummeRbund does not exist, is there other web-based program
>> can be used to visualize Cuffdiff outputs?
>>
>> Thanks.
>>
>> Jianguang
>>
>>
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>
>
>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> http://galaxyproject.org/wiki/
>
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] Installing galaxy with Apache ...

[Carlos Borroto]

This thread my help you:
http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.html

On Thu, Aug 23, 2012 at 5:48 PM,   wrote:
> Hi Jelle,
>I'm still having issues with Apache. I've moved
>
> RewriteEngine on
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*) 
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*) 
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico 
> [L]
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
> RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
>
> from /var/www/.htaccess to /etc/apache2/httpd.conf
>
> I still get a "404 Not found" error when trying to access galaxy 
> (http://140.253.78.44/galaxy )
>
> http://140.253.78.44 still gets the "It Works!" Apache default index.html
>
> and http://140.253.78.44:8080 gets the galaxy page
>
> /var/log/apache2/error.log states...
>
> [Fri Aug 24 07:35:27 2012] [error] [client 140.253.78.44] File does not 
> exist: /var/www/favicon.ico
> [Fri Aug 24 07:36:25 2012] [error] [client 140.253.78.44] File does not 
> exist: /var/www/galaxy
>
> Now if I change httpd.conf and add the vitrtualHost tags to:
>
> ServerName localhost
> 
>   RewriteEngine on
>   RewriteRule ^/galaxy$ /galaxy/ [R]
>   RewriteRule ^/galaxy/static/style/(.*) 
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
>   RewriteRule ^/galaxy/static/scripts/(.*) 
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
>   RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
>   RewriteRule ^/galaxy/favicon.ico 
> /home/galaxy/galaxy-dist/static/favicon.ico [L]
>   RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt 
> [L]
>   RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
> 
>
> I now get a "403 Forbidden" error when trying to access 
> (http://140.253.78.44/galaxy ) You don't have permission to access /galaxy/ 
> on this server, and /var/log/apache2/error.log states..
>
> [Fri Aug 24 07:45:33 2012] [error] [client 140.253.78.44] attempt to make 
> remote request from mod_rewrite without proxy enabled: 
> proxy:http://localhost:8080/
> [Fri Aug 24 07:45:34 2012] [error] [client 140.253.78.44] File does not 
> exist: /etc/apache2/htdocs
>
> Any help much appreciated
>
> Neil
> 
> From: Jelle Scholtalbers [j.scholtalb...@gmail.com]
> Sent: Thursday, August 23, 2012 8:20 PM
> To: Burdett, Neil (ICT Centre, Herston - RBWH)
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Installing galaxy with Apache ...
>
> Hi Neil,
>
> with your current apache configuration, you should probably see Galaxy
> at http://yourip/galaxy
> This is due to your Rewriterule /galaxy and for that you have also set
> proxy_prefix = /galaxy in your universe_wsgi.ini
>
> You should probably remove the empty galaxy directory under /var/www
> Furthermore, most of the time you will not need a directory with 777
> in your apache web/documentroot..
>
> Cheers,
> Jelle
>
> On Thu, Aug 23, 2012 at 8:34 AM,   wrote:
>> Hi
>>I've installed galaxy with the default settings and it works fine.
>>
>> On a new Ubuntu machine I am trying to get galaxy running with Apache. But I 
>> am having problems, I've followed the documentation.
>>
>> After installing Apache I can put my ip address into a browser and I get 
>> message saying Apache is working fine. It displays a message from 
>> /var/www/index.html
>>
>> Now when I start galaxy I was assuming I would get redirected to the galaxy 
>> welcome page, but this doesn't happen and it remains at /var/www/index.html. 
>> To view the welcome page I have to add ":8080" after the ip address. Is this 
>> still required? I thought that Apache would know to redirect to my 
>> distributionWhat am I doing wrong?
>>
>> /etc/apache2/sites-available/default-ssl and 
>> /etc/apache2/sites-available/default look like this ...
>>
>> DocumentRoot /var/www
>> 
>> Options FollowSymLinks
>> AllowOverride None
>> 
>> 
>> Options Indexes FollowSymLinks MultiViews
>> AllowOverride None
>> Order allow,deny
>> allow from all
>> 
>>
>>  etc ...
>>
>> /var/www/.htaccess
>>
>> RewriteEngine on
>> RewriteRule ^/galaxy$ /galaxy/ [R]
>> RewriteRule ^/galaxy/static/style/(.*) 
>> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
>> RewriteRule ^/galaxy/static/scripts/(.*) 
>> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
>> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
>> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico 
>> [L]
>> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static

Re: [galaxy-user] Please help with the settings for Cufflink, Cuffmerge and Cuffdiff

[Jennifer Jackson]

Jianguang,

If your input dataset(s) have a genome assigned ("database") and that 
genome is local to Galaxy (I believe this is true for your data, mm9, 
correct?), then using bias correction would be an advantageous option to 
make use of according to our experience and the tool authors in the 
Cufflinks manuals/protocols/publications.


That said, the choice of whether or not to use Bias correction would be 
ultimately up to you (a test using and not using could help with this 
decision). From what I know, it is generally considered best practice to 
use it when available.


Custom genomes can also be used with bias correction, but require a 
different way of setting options and database assignments. Using no 
reference genome is also possible (and therefore no bias correction), 
again with different settings. The tool form has general instructions 
around this as does the RNA-seq FAQ under Shared Data -> Published Pages 
and the Custom genome wiki. In addition, there are several prior posts 
with Q/A on the topic on the mailing list (a search would bring up the 
settings for others reading this post that are curious). Anything that 
remains unclear we can help with (send a new Q to the list) and we can 
adjust the wiki, etc. to be more specific if not covered already.

http://galaxyproject.org/search/mailinglists

Take care,

Jen
Galaxy team

On 8/27/12 12:03 PM, Du, Jianguang wrote:

Dear All,

I am looking for the differential splicing events between cell types.

Although I got a lot of helps from Jen and from protocols found online,
I am still not sure about some settings for Cufflink, Cuffmerge and
Cuffdiff.

1) For Cufflink:

There is a setting for Bias Correction. I made the setting as below:

Perform Bias Correction:Yes

Reference sequence data:Locally cached

Did I make the right settings?

2) For Cuffmerge:

As for whether use sequence data, I made the setting as below:

Use Sequence Data: Yes

Choose the source for the reference list: Locally cached

Did I make the right settings?

3) For Cuffdiff:

There is another choice whether perform Bias Correction, I made the
setting as below:

Perform Bias Correction:Yes

Reference sequence data:Locally cached

Did I make the right settings?

Thanks.

Jianguang



___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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--
Jennifer Jackson
http://galaxyproject.org
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[galaxy-user] Calling SNP

[Francesco Vitiello]

Hi everyone,
I'ha a dataset from a sample in Illumina format. I've already groomed the
file and aligned to hg19. How can I call SNPs and remove the most common
and generally not dangerous?
Thank a lot.
Francesco

-- 




--
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[galaxy-user] Please help with the settings for Cufflink, Cuffmerge and Cuffdiff

[Du, Jianguang]

Dear All,
I am looking for the differential splicing events between cell types.
Although I got a lot of helps from Jen and from protocols found online, I am 
still not sure about some settings for Cufflink, Cuffmerge and Cuffdiff.

1) For Cufflink:
There is a setting for Bias Correction. I made the setting as below:

Perform Bias Correction:  Yes
Reference sequence data:  Locally cached

Did I make the right settings?

2) For Cuffmerge:
As for whether use sequence data, I made the setting as below:

Use Sequence Data:  Yes
Choose the source for the reference list:   Locally cached

Did I make the right settings?

3) For Cuffdiff:
There is another choice whether perform Bias Correction, I made the setting as 
below:

Perform Bias Correction:   Yes
Reference sequence data:   Locally cached

Did I make the right settings?

Thanks.
Jianguang


___
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
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Re: [galaxy-user] Text Manipulation

[Jennifer Jackson]

Hi Lee,

There are a few options .. my guess is you are working with files like 
snpXXXCodingDbSnp?


1 - Using an expression such as this one will extract individual 
characters from the column, including the commas (treating the column's 
data like a string)


  c5.pop(1)

  = extracts the second character from the column

2 - Or, if you want to work with the entire codons, you could use the 
tool "Convert delimiters to TAB" to fully expand the data. You might 
want to use other Text Manipulation tools such as "Cut" with this option 
to get access to specific columns. Or "Condense consecutive characters" 
if the extra trailing commas in some of these datasets create empty 
columns (after converting to tabs).


Hopefully this helps! If there is more feedback from our developers, 
we'll post more. Others on the list are also welcome to add in comments.


Best,

Jen
Galaxy team

On 8/27/12 9:44 AM, Jennifer Jackson wrote:

Post to mailing list

On 8/26/12 11:38 AM, leemsil...@genepeeks.com wrote:

Hi Jen,

The ability to use Python commands with the Compute tool seems to be a
very well-hidden gem in Galaxy.  The problem with this nearly
unmentioned gem is the sheer frustration felt when something that
works on the Python command line fails on the Galaxy Compute tool.

What I would like to do is manipulate a column from a UCSC download
that lists two or three codons separated by a comma, e.g.AAC,GCG,
or  GGT, CAC, TAT,  .   The string-based split command  <
c5.split(",").pop(1) > fails on this data because Galaxy assigned it a
 type automatically. All of my attempts to change the data type
to "string" have failed.

Any suggestions?

Lee
leemsil...@genepeeks.com


--
Jennifer Jackson
http://galaxyproject.org
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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 http://lists.bx.psu.edu/listinfo/galaxy-dev

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[galaxy-user] Galaxy-France -- Communauté française de Galaxy (French Galaxy Community)

[Dave Clements]

Bonjour à tous,

Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en
ligne la liste de diffusion Galaxy France.

Cette liste a pour but de partager et communiquer sur nos différentes
expériences avec Galaxy au sein de l'hexagone.

La langue officielle de cette liste est le français.

Vous avez besoin d'aide dans l'utilisation de Galaxy,
Vous hébergez un serveur public Galaxy,
Vous maintenez une instance locale de Galaxy,
Vous venez de déposer un outil sur le toolshed,
Vous avez des trucs et astuces pouvant interresser la communauté,
Vous organisez des formations avec Galaxy,

Rejoignez nous en vous inscrivant à
http://lists.bx.psu.edu/listinfo/galaxy-france

Les archives de cette liste sont disponibles à
http://france.list.galaxyproject.org

A très bientôt sur la liste Galaxy France,

Les administrateurs:

Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer
Jackson


--
-

Hi everyone,

With the help and the support of the Galaxy team, we just put online the
Galaxy French mailing list.

The aim of this list is to share and communicate on our different
experiences with Galaxy in France.

* The main language is French.
*
Topics include, but are not limited to:
  You need help in the use of Galaxy,
   You're hosting a Galaxy public server,
   You're maintaining a local instance of Galaxy,
   You just add a new tool on the toolshed,
   You have some tips that could interested the community,
   You organize workshops with Galaxy,

Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france

The list's archives are also available at
http://france.list.galaxyproject.org

See you soon on the Galaxy-France list,

The administrators:

Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer
Jackson


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Re: [galaxy-user] Please help me check the quality of the Tophat mapping to reference genome

[Du, Jianguang]

Hi Jen,
Thank you very much for your information. I will not worry about the Tophat 
outputs now. For this particular run, I used a single-end dataset. The whole 
experiment contains both paired-end datasets datasets and single-end datasets. 
I ran Tophat with paired-end setting for the paired-end datasets, and 
single-end setting for the single-end datasets. And then ran Cufflink, 
Cuffmerge, and Cuffdiff.
Jianguang


From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Monday, August 27, 2012 12:36 PM
To: Du, Jianguang
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Please help me check the quality of the Tophat 
mapping to reference genome

Hello Jianguang,

This is the expected output from this particular tool. Your TopHat
output file 'accepted hits' contains only mapped data.

I did notice this option for the TopHat run:
 > Is this library mate-paired?
 > Single-end

Your data was originally paired end - so this is unexpected. But perhaps
you are working with a different dataset(s) now? If you are running with
the original paired dataset, then this is would be an option to correct
- change to mate paired = yes and run TopHat with both the fwd and rev
reads in a single mapping process. (The same method as in the RNA-seq
tutorial).
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

Best,

Jen
Galaxy team


On 8/27/12 8:15 AM, Du, Jianguang wrote:
> Dear All,
>
> I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the
> Tophat output (the file of accepted hits).  I got the diagnosis results
> as follow:
>
> 9471730 + 0 in total (QC-passed reads + QC-failed reads)
> 0 + 0 duplicates
> 9471730 + 0 mapped (100.00%:-nan%)
> 0 + 0 paired in sequencing
> 0 + 0 read1
> 0 + 0 read2
> 0 + 0 properly paired (-nan%:-nan%)
> 0 + 0 with itself and mate mapped
> 0 + 0 singletons (-nan%:-nan%)
> 0 + 0 with mate mapped to a different chr
> 0 + 0 with mate mapped to a different chr (mapQ>=5)
>
> I ran Tophat with settings as shown below:
>
> Will you select a reference genome from your history or use a built-in
> index?
> Use a built-in index
> Select a reference genome
> /galaxy/data/mm9/bowtie_index/mm9
> Is this library mate-paired?
> Single-end
> TopHat settings to use
> Full parameter list
> Library Type
> FR Unstranded
> Anchor length (at least 3)
> 8
> Maximum number of mismatches that can appear in the anchor region of
> spliced alignment
> 0
> The minimum intron length
> 70
> The maximum intron length
> 50
> Allow indel search
> Yes
> Max insertion length.
> 3
> Max deletion length.
> 3
> Maximum number of alignments to be allowed
> 20
> Minimum intron length that may be found during split-segment (default)
> search
> 50
> Maximum intron length that may be found during split-segment (default)
> search
> 50
> Number of mismatches allowed in the initial read mapping
> 1
> Number of mismatches allowed in each segment alignment for reads mapped
> independently
> 1
> Minimum length of read segments
> 25
> Use Own Junctions
> Yes
> Use Gene Annotation Model
> Yes
> Gene Model Annotations
> /iGenome version of mm9 genes. GTF/
> Use Raw Junctions
> No
> Only look for supplied junctions
> No
> Use Closure Search
> No
> Use Coverage Search
> Yes
> Minimum intron length that may be found during coverage search
> 50
> Maximum intron length that may be found during coverage search
> 2
> Use Microexon Search
> No
>
> Please help me find out what is wrong with the Tophat.
>
> Thanks,
>
> Jianguang
>
>
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>http://lists.bx.psu.edu/
>

--
Jennifer Jackson
http://galaxyproject.org
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at usegalaxy.org.  Please keep all replies on the list by
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[galaxy-user] Text Manipulation

[Jennifer Jackson]

Post to mailing list

On 8/26/12 11:38 AM, leemsil...@genepeeks.com wrote:

Hi Jen,

The ability to use Python commands with the Compute tool seems to be a very 
well-hidden gem in Galaxy.  The problem with this nearly unmentioned gem is the 
sheer frustration felt when something that works on the Python command line 
fails on the Galaxy Compute tool.

What I would like to do is manipulate a column from a UCSC download that lists two or three codons separated by 
a comma, e.g.AAC,GCG,  or  GGT, CAC, TAT,  .   The string-based split command  <  
c5.split(",").pop(1) > fails on this data because Galaxy assigned it a  type 
automatically. All of my attempts to change the data type to "string" have failed.

Any suggestions?

Lee
leemsil...@genepeeks.com

--
Jennifer Jackson
http://galaxyproject.org
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Galaxy analysis and other features on the public server
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using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
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Re: [galaxy-user] Please help me check the quality of the Tophat mapping to reference genome

[Jennifer Jackson]

Hello Jianguang,

This is the expected output from this particular tool. Your TopHat 
output file 'accepted hits' contains only mapped data.


I did notice this option for the TopHat run:
> Is this library mate-paired?
> Single-end

Your data was originally paired end - so this is unexpected. But perhaps 
you are working with a different dataset(s) now? If you are running with 
the original paired dataset, then this is would be an option to correct 
- change to mate paired = yes and run TopHat with both the fwd and rev 
reads in a single mapping process. (The same method as in the RNA-seq 
tutorial).

http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

Best,

Jen
Galaxy team


On 8/27/12 8:15 AM, Du, Jianguang wrote:

Dear All,

I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the
Tophat output (the file of accepted hits).  I got the diagnosis results
as follow:

9471730 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
9471730 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

I ran Tophat with settings as shown below:

Will you select a reference genome from your history or use a built-in
index?
Use a built-in index
Select a reference genome
/galaxy/data/mm9/bowtie_index/mm9
Is this library mate-paired?
Single-end
TopHat settings to use
Full parameter list
Library Type
FR Unstranded
Anchor length (at least 3)
8
Maximum number of mismatches that can appear in the anchor region of
spliced alignment
0
The minimum intron length
70
The maximum intron length
50
Allow indel search
Yes
Max insertion length.
3
Max deletion length.
3
Maximum number of alignments to be allowed
20
Minimum intron length that may be found during split-segment (default)
search
50
Maximum intron length that may be found during split-segment (default)
search
50
Number of mismatches allowed in the initial read mapping
1
Number of mismatches allowed in each segment alignment for reads mapped
independently
1
Minimum length of read segments
25
Use Own Junctions
Yes
Use Gene Annotation Model
Yes
Gene Model Annotations
/iGenome version of mm9 genes. GTF/
Use Raw Junctions
No
Only look for supplied junctions
No
Use Closure Search
No
Use Coverage Search
Yes
Minimum intron length that may be found during coverage search
50
Maximum intron length that may be found during coverage search
2
Use Microexon Search
No

Please help me find out what is wrong with the Tophat.

Thanks,

Jianguang



___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

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please use the interface at:

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



--
Jennifer Jackson
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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

[galaxy-user] Please help me check the quality of the Tophat mapping to reference genome

[Du, Jianguang]

Dear All,

I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the Tophat 
output (the file of accepted hits).  I got the diagnosis results as follow:

9471730 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
9471730 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

I ran Tophat with settings as shown below:

Will you select a reference genome from your history or use a built-in index?
Use a built-in index
Select a reference genome
/galaxy/data/mm9/bowtie_index/mm9
Is this library mate-paired?
Single-end
TopHat settings to use
Full parameter list
Library Type
FR Unstranded
Anchor length (at least 3)
8
Maximum number of mismatches that can appear in the anchor region of spliced 
alignment
0
The minimum intron length
70
The maximum intron length
50
Allow indel search
Yes
Max insertion length.
3
Max deletion length.
3
Maximum number of alignments to be allowed
20
Minimum intron length that may be found during split-segment (default) search
50
Maximum intron length that may be found during split-segment (default) search
50
Number of mismatches allowed in the initial read mapping
1
Number of mismatches allowed in each segment alignment for reads mapped 
independently
1
Minimum length of read segments
25
Use Own Junctions
Yes
Use Gene Annotation Model
Yes
Gene Model Annotations
iGenome version of mm9 genes. GTF
Use Raw Junctions
No
Only look for supplied junctions
No
Use Closure Search
No
Use Coverage Search
Yes
Minimum intron length that may be found during coverage search
50
Maximum intron length that may be found during coverage search
2
Use Microexon Search
No

Please help me find out what is wrong with the Tophat.

Thanks,

Jianguang
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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[galaxy-user] interupted running jobs restart

[petr]

We are running galaxy on pbs cluster. In out setting some jobs can take
several weeks to finish and it is virtually impossible to wait for suitable
moment when server can be restarted or turn down without interrupting
running tasks. Is there an option on server setting which will enable jobs
which were interrupted because of the server maintenance to run again after
the cluster is back on?
best regards.
Petr
___
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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