Dave Clements | 7 Jun 01:58 2014

Galaxy-User has moved to Galaxy Biostar

Hello all,

After 8+ years and more than 8100 posts, the Galaxy-User mailing list has been retired.  But, don't worry, you can still get Galaxy user support at Galaxy Biostar (https://biostar.usegalaxy.org/), an online user support forum that has replaced this list.

Past postings to this list are available at Galaxy Biostar.  All existing archives of this list will also remain available. 

See the Galaxy Support page (https://wiki.galaxyproject.org/Support) and the Galaxy Mailing List page (https://wiki.galaxyproject.org/MailingLists) for all support options.

Thanks for making Galaxy-User, and Galaxy Biostar, such great resources.

See you online,

Dave C and the Galaxy Team
<div><div dir="ltr">Hello all,<div><br></div>
<div>After 8+ years and more than 8100 posts, the Galaxy-User mailing list has been retired. &nbsp;But, don't worry, you can still get Galaxy user support at Galaxy Biostar (<a href="https://biostar.usegalaxy.org/">https://biostar.usegalaxy.org/</a>), an online user support forum that has replaced this list.</div>

<div><br></div>
<div>Past postings to this list are available at Galaxy Biostar. &nbsp;All existing archives of this list will also remain available.&nbsp;</div>
<div><br></div>
<div>See the Galaxy Support page (<a href="https://wiki.galaxyproject.org/Support">https://wiki.galaxyproject.org/Support</a>) and the Galaxy Mailing List page (<a href="https://wiki.galaxyproject.org/MailingLists">https://wiki.galaxyproject.org/MailingLists</a>) for all support options.</div>

<div><br></div>
<div>Thanks for making Galaxy-User, and Galaxy Biostar, such great resources.</div>
<div><br></div>
<div>See you online,</div>
<div><br></div>
<div>Dave C and the Galaxy Team</div>
<div>-- <br><div dir="ltr">
<div>

<a href="http://galaxyproject.org/GCC2014" target="_blank">http://galaxyproject.org/GCC2014</a>
</div>
<a href="http://galaxyproject.org/" target="_blank">http://galaxyproject.org/</a><br><a href="http://getgalaxy.org/" target="_blank">http://getgalaxy.org/</a><br><a href="http://usegalaxy.org/" target="_blank">http://usegalaxy.org/</a><br><a href="https://wiki.galaxyproject.org/" target="_blank">https://wiki.galaxyproject.org/</a><br>
</div>
</div>
</div></div>
Ganote, Carrie L | 2 Jun 23:57 2014
Picon

CummeRbund on Galaxy

Hi list,

Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates that I'm trying to test for a
user on our local Galaxy, but I just can't get the program to behave.

Using cuffdiff v2.2.0 604fa75232a2 
cummeRbund version 0.0.7, 137aab1d9ac1
R 2.15.2 and 3.0.1 (tried both)
Last galaxy-dist/stable changeset: 7a7985a007fb

I ran cuffdiff like so:
Transcripts 	83: Cuffmerge on data 6, data 67, and others: merged transcripts 	
Name 	control 	
Add replicate 	44: Tophat2 on data 1 and data 6: accepted_hits (ran as single-end fastq)
Add replicate 	54: Tophat2 on data 2 and data 6: accepted_hits (ran as single-end fastq)
Name 	sample 	
Add replicate 	59: Tophat2 on data 3 and data 6: accepted_hits (ran as single-end fastq)
Add replicate 	64: Tophat2 on data 4 and data 6: accepted_hits (ran as single-end fastq)
Library normalization method 	geometric 	
Dispersion estimation method 	pooled 	
False Discovery Rate 	0.05 	
Min Alignment Count 	10 	
Use multi-read correct 	No 	
Perform Bias Correction 	No 	
Include Read Group Datasets 	No 	
Set Additional Parameters? (not recommended for paired-end reads) 	No

Here's what I get when I run cummeRbund:
(From Galaxy, with R 2.15.2)
Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat
Reading //path/dataset_files/009/dataset_9861.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9861.dat
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous>
Execution halted

(From R interpreter on command line, R = 3.0.1)
Reading //path/dataset_files/009/dataset_9842.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9842.dat
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
In addition: Warning message:
attributes are not identical across measure variables; they will be dropped 

I tried changing the group names in cuffdiff but no luck. No spaces or funny characters.

Thanks for any insight,

Carrie Ganote

Ianiri, Giuseppe | 2 Jun 17:54 2014
Picon

(no subject)

Hi,
I uploaded some file that resulted to be too big and my history showed that that was not more space available. Now I deleted few file, and  I should have 80 GB available, but my history shows still that I have no more space available for analysis. Can anyone from the Galaxy team check this for me?

Giuseppe 

<div>
<div>Hi,
<div>I uploaded some file that resulted to be too big and my history showed that that was not more space available. Now I deleted few file, and&nbsp;&nbsp;I should have 80 GB available, but&nbsp;<span>my history shows still that I have no more space
 available for analysis. Can anyone from the Galaxy team check this for me?</span>
<div>
<div>
<br><div>
<div>
<div>
<p class="MsoNoSpacing"></p>
<p class="MsoNoSpacing"></p>
<p class="MsoNoSpacing"><span>Giuseppe&nbsp;</span></p>
<p></p>
<p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
Dave Clements | 30 May 18:47 2014

Galaxy User List Being Retired on June 6, 2014.

Hello all,

In case you didn't see this it the June Galaxy Newsletter that went out today:


Galaxy-User Being Retired June 6

Join the conversation! Learn how here.

The Galaxy Biostar online forum was launched April 23 as a replacement for the Galaxy-User mailing list.

During the past 5 weeks, Galaxy Biostar has been wildly successful with over 125 active threads, more than 5 times the number of active threads on Galaxy-user in the 5 weeks before the switch.

Galaxy-User has remained open during the transition, but now it's time to retire it. All new posting to Galaxy-User will be stopped on Friday, June 6, some 101 months, and 8,100 postings after it was launched. All those postings will remain available both in Galaxy Biostar (where they have been imported), and in the online list archives.

Thanks for making Galaxy Biostar, and Galaxy-User before it, such a great resource.


Thanks again,

Dave C



--
<div><div dir="ltr">
<div>Hello all,</div>
<div><br></div>
<div>In case you didn't see this it the <a href="http://bit.ly/SX3MuS">June Galaxy Newsletter</a> that went out today:</div>
<div><br></div>
<div><br></div>
<blockquote>

<div><span>Galaxy-User Being Retired June 6</span></div>
<div><span><br></span></div>
<div>
<div class=""><a class="" href="https://biostar.usegalaxy.org/"></a></div>

</div>
<div>
<div class="">Join the conversation! Learn how&nbsp;<a href="https://wiki.galaxyproject.org/Support/Biostar">here</a>.</div>

</div>
<div><br></div>
<div>
<p class="">

The&nbsp;<a class="" href="https://biostar.usegalaxy.org/">Galaxy Biostar</a>&nbsp;online forum was launched April 23 as a replacement for the Galaxy-User&nbsp;<a href="https://wiki.galaxyproject.org/MailingLists">mailing list</a>.</p>

</div>
<div>
<p class="">During the past 5 weeks, Galaxy Biostar has been wildly successful with over 125 active threads,&nbsp;more than 5 times the number of active threads on Galaxy-user in the 5 weeks before the switch.</p>

</div>
<div>
<p class="">Galaxy-User has remained open during the transition, but now it's time to retire it. All new posting to Galaxy-User will be stopped on Friday, June 6,&nbsp;some 101 months, and 8,100 postings&nbsp;after it was launched. All those postings will remain available both in Galaxy Biostar (where they have been imported), and in the&nbsp;<a class="" href="http://user.list.galaxyproject.org/">online list archives</a>.</p>

</div>
<div>
<p class="">Thanks for making Galaxy Biostar, and Galaxy-User before it, such a great resource.</p>

</div>
</blockquote>
<div>
<span class=""></span><span class=""></span><p class="">

</p>
<span class=""></span><span class=""></span><span class=""></span><p class="">

<span class=""></span></p>
<p class="">

<span class=""></span></p>
<p class="">

<span class=""></span></p>
</div>
<div><br></div>
<div>Thanks again,</div>
<div><br></div>
<div>Dave C</div>
<div><br></div>
<br clear="all"><div><br></div>
-- <br><div dir="ltr">
<div><a href="http://galaxyproject.org/GCC2014" target="_blank">http://galaxyproject.org/GCC2014</a></div>
<a href="http://galaxyproject.org/" target="_blank">http://galaxyproject.org/</a><br><a href="http://getgalaxy.org/" target="_blank">http://getgalaxy.org/</a><br><a href="http://usegalaxy.org/" target="_blank">http://usegalaxy.org/</a><br><a href="https://wiki.galaxyproject.org/" target="_blank">https://wiki.galaxyproject.org/</a><br>
</div>
</div></div>
Emmanuelle Lerat | 27 May 12:58 2014
Picon

slow running

Hi everyone,

I am currently running a fastqgroomer on some data (about 7Go big). I am 
surprise because I launched the analysis several hours ago and it is 
still running. I am wondering if everything is alright since usually it 
is faster than that, even on bigger dataset. I had the same problem 
yesterday with fastQC that was not finished after 24h also it was 
indicated as running (I finally discarded this job)

Is the galaxy sever busy or do you think it is because of my data?

thank you in advance for your help

Sincerely

Emmanuelle Lerat

--

-- 
Dr. Emmanuelle LERAT, CR1 CNRS, HDR

Laboratoire Biometrie et Biologie Evolutive
Universite Claude Bernard - Lyon 1
UMR-CNRS 5558 - Bat. Mendel
43 bd du 11 novembre 1918
69622 Villeurbanne cedex
France

Phone: 33+ 4.72.43.29.18
Fax:   33+ 4.72.43.13.88

http://lbbe.univ-lyon1.fr/-Lerat-Emmanuelle-.html

Les Dethlefsen | 25 May 03:41 2014
Picon

Re: galaxy-user Digest, Vol 95, Issue 9

Actually, if the ones I ordered last year are expiring soon, I'd suggest people continue to use those before
recently ordered kits.

Les

----- Original Message -----
> Send galaxy-user mailing list submissions to
> 	galaxy-user@...
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> To subscribe or unsubscribe via the World Wide Web, visit
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> 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to
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> Why?
> 1. This will keep the subject meaningful.  People will have some idea from
> the subject line if they should read it or not.
> 2. Not doing this greatly increases the number of emails that match search
> queries, but that aren't actually informative.
> 
> Today's Topics:
> 
>    1. Re: Urgent Question about PostgreSQL Compatibility
>       (Paniagua, Eric)
>    2. Re: Urgent Question about PostgreSQL Compatibility (Dannon Baker)
>    3. Re: Urgent Question about PostgreSQL Compatibility
>       (Paniagua, Eric)
>    4. Re: Urgent Question about PostgreSQL Compatibility
>       (Paniagua, Eric)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 23 May 2014 19:49:02 +0000
> From: "Paniagua, Eric" <epaniagu@...>
> To: Dannon Baker <dannon.baker@...>
> Cc: Galaxy ?[galaxy-user@...]? 	<galaxy-user@...>
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL
> 	Compatibility
> Message-ID:
> 	<759E5BE3A1277B48ADEE4096E39269CBB22248AD@...>
> Content-Type: text/plain; charset="windows-1256"
> 
> Hi Dannon,
> 
> There have been some developments, and I would like to update my question
> accordingly.
> 
> I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and
> ferried the database contents over.  My question is this:
> 
> What is the appropriate syntax to use for the parameter "database_connection"
> in universe_wsgi.ini to use a remote database server?  Specifically:
> 
> Galaxy host: genomics.cshl.edu
> Database host: wigserv5.cshl.edu
> Database name: glxeric
> Database user/role: glxeric
> Database port: 5432 (postgresql default port)
> Database password: not required under the current configuration.
> 
> Can someone please explain how to fill in the "database_connection" parameter
> appropriately?
> 
> Many thanks,
> Eric
> 
> ________________________________________
> From: galaxy-user-bounces@...
> [galaxy-user-bounces@...] on behalf of Paniagua, Eric
> [epaniagu@...]
> Sent: Thursday, May 22, 2014 1:38 PM
> To: Dannon Baker
> Cc: Galaxy ?[galaxy-user@...]?
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hi Dannon,
> 
> I have attached a screenshot of the error as it appears in the Galaxy web
> site and a screenshot of the log.
> 
> Please let me know if I can provide any more information.
> 
> Also, please note that the version information I gave for PostgreSQL before
> was incorrect.  I am actually running PostgreSQL 8.1.22.
> 
> Thanks for your assistance,
> Eric
> 
> ________________________________________
> From: galaxy-user-bounces@...
> [galaxy-user-bounces@...] on behalf of Paniagua, Eric
> [epaniagu@...]
> Sent: Thursday, May 22, 2014 11:14 AM
> To: Dannon Baker
> Cc: Galaxy ?[galaxy-user@...]?
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hi Dannon,
> 
> I am in a meeting right now.  I should be done at noon.  I'll send you more
> info then.  Thank you for your assistance!
> 
> Best,
> Eric
> 
> 
> -------- Original message --------
> From: Dannon Baker
> Date:2014/05/22 11:08 (GMT-05:00)
> To: "Paniagua, Eric"
> Cc: "Galaxy ?[galaxy-user@...]?"
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hey Eric,
> 
> Looking into this.  Can you send the exact error/trace if available?
> 
> -Dannon
> 
> 
> On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric
> <epaniagu@...<mailto:epaniagu@...>> wrote:
> Hi,
> 
> I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the
> process of preparing an update I have encountered some problems.  When I try
> to create a new dataset (e.g. by running a tool), I receive an error message
> indicating a syntactic problem with backend database commands.
> Specifically, the error mentions a read-only cursor and occurs when the
> system is trying to look up the history hid number for the new dataset, a
> value which (as far as I understand it) should be an autoincrementing
> primary key.
> 
> My codebase is the 68a8b0397947 commit on the stable branch, plus some custom
> tool definitions, but no real modification to any core Galaxy code.  The
> database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In the
> target (production) environment, we run with 3 web server processes and 3
> job runner processes, but I am encountering this error in a
> single-Galaxy-process test instance.  The error is reported both in the logs
> (with a traceback originating in the bowels of SQLAlchemy) and via the web
> interface.
> 
> I dug through the commit history and found a comit (e1bc855165bc) with the
> comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)."
> on Sep 23, 2013.  I am wondering if this means I need to upgrade my database
> backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that I need to
> keep 2 parallel Galaxy instances running for an extended time period (~1
> month).  The first is the current (not updated) local Galaxy instance, and
> the second is the new (updated) Galaxy instance, which naturally implies
> diverging databases.  Does this mean I will need to maintain parallel
> installations of PostgreSQL 9.1 and 9.2.x?  How would I go about setting up
> that configuration?
> 
> Any assistance on debugging this error would be greatly appreciated.  Our
> initial goal was to roll out this update tomorrow afternoon, but that may
> need to be delayed because of this show-stopper.  If I can provide any
> further useful information, please let me know, and I will be happy to do
> so.
> 
> Best,
> Eric Paniagua
> 
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
> 
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
> 
> 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/
> 
> To search Galaxy mailing lists use the unified search at:
> 
>   http://galaxyproject.org/search/mailinglists/
> 
> 
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
> 
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
> 
> 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/
> 
> To search Galaxy mailing lists use the unified search at:
> 
>   http://galaxyproject.org/search/mailinglists/
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 23 May 2014 16:02:41 -0400
> From: Dannon Baker <dannon.baker@...>
> To: "Paniagua, Eric" <epaniagu@...>
> Cc: Galaxy ?[galaxy-user@...]? 	<galaxy-user@...>
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL
> 	Compatibility
> Message-ID:
> 	<CAGn_WZnY9BV9HAsMSekCDdrqUbtSGjTieRG=s75_oHxewnHrXQ@...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hey Eric,
> 
> We use sqlalchemy, and the detailed documentation is here:
> 
> http://docs.sqlalchemy.org/en/rel_0_7/core/engines.html#postgresql
> 
> That said, the basic format is:  dialect+driver://username:password <at> host
> :port/database
> 
> So, you're going to be looking at something like: postgres://
> glxeric@...:5432/glxeric
> 
> 
> 
> On Fri, May 23, 2014 at 3:49 PM, Paniagua, Eric <epaniagu@...> wrote:
> 
> > Hi Dannon,
> >
> > There have been some developments, and I would like to update my question
> > accordingly.
> >
> > I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and
> > ferried the database contents over.  My question is this:
> >
> > What is the appropriate syntax to use for the parameter
> > "database_connection" in universe_wsgi.ini to use a remote database server?
> >  Specifically:
> >
> > Galaxy host: genomics.cshl.edu
> > Database host: wigserv5.cshl.edu
> > Database name: glxeric
> > Database user/role: glxeric
> > Database port: 5432 (postgresql default port)
> > Database password: not required under the current configuration.
> >
> > Can someone please explain how to fill in the "database_connection"
> > parameter appropriately?
> >
> > Many thanks,
> > Eric
> >
> > ________________________________________
> > From: galaxy-user-bounces@... [
> > galaxy-user-bounces@...] on behalf of Paniagua, Eric [
> > epaniagu@...]
> > Sent: Thursday, May 22, 2014 1:38 PM
> > To: Dannon Baker
> > Cc: Galaxy ?[galaxy-user@...]?
> > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> >
> > Hi Dannon,
> >
> > I have attached a screenshot of the error as it appears in the Galaxy web
> > site and a screenshot of the log.
> >
> > Please let me know if I can provide any more information.
> >
> > Also, please note that the version information I gave for PostgreSQL
> > before was incorrect.  I am actually running PostgreSQL 8.1.22.
> >
> > Thanks for your assistance,
> > Eric
> >
> > ________________________________________
> > From: galaxy-user-bounces@... [
> > galaxy-user-bounces@...] on behalf of Paniagua, Eric [
> > epaniagu@...]
> > Sent: Thursday, May 22, 2014 11:14 AM
> > To: Dannon Baker
> > Cc: Galaxy ?[galaxy-user@...]?
> > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> >
> > Hi Dannon,
> >
> > I am in a meeting right now.  I should be done at noon.  I'll send you
> > more info then.  Thank you for your assistance!
> >
> > Best,
> > Eric
> >
> >
> > -------- Original message --------
> > From: Dannon Baker
> > Date:2014/05/22 11:08 (GMT-05:00)
> > To: "Paniagua, Eric"
> > Cc: "Galaxy ?[galaxy-user@...]?"
> > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> >
> > Hey Eric,
> >
> > Looking into this.  Can you send the exact error/trace if available?
> >
> > -Dannon
> >
> >
> > On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric <epaniagu@...
> > <mailto:epaniagu@...>> wrote:
> > Hi,
> >
> > I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in
> > the process of preparing an update I have encountered some problems.  When
> > I try to create a new dataset (e.g. by running a tool), I receive an error
> > message indicating a syntactic problem with backend database commands.
> >  Specifically, the error mentions a read-only cursor and occurs when the
> > system is trying to look up the history hid number for the new dataset, a
> > value which (as far as I understand it) should be an autoincrementing
> > primary key.
> >
> > My codebase is the 68a8b0397947 commit on the stable branch, plus some
> > custom tool definitions, but no real modification to any core Galaxy code.
> >  The database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In
> > the target (production) environment, we run with 3 web server processes and
> > 3 job runner processes, but I am encountering this error in a
> > single-Galaxy-process test instance.  The error is reported both in the
> > logs (with a traceback originating in the bowels of SQLAlchemy) and via the
> > web interface.
> >
> > I dug through the commit history and found a comit (e1bc855165bc) with the
> > comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL
> > 9.2.4)." on Sep 23, 2013.  I am wondering if this means I need to upgrade
> > my database backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that
> > I need to keep 2 parallel Galaxy instances running for an extended time
> > period (~1 month).  The first is the current (not updated) local Galaxy
> > instance, and the second is the new (updated) Galaxy instance, which
> > naturally implies diverging databases.  Does this mean I will need to
> > maintain parallel installations of PostgreSQL 9.1 and 9.2.x?  How would I
> > go about setting up that configuration?
> >
> > Any assistance on debugging this error would be greatly appreciated.  Our
> > initial goal was to roll out this update tomorrow afternoon, but that may
> > need to be delayed because of this show-stopper.  If I can provide any
> > further useful information, please let me know, and I will be happy to do
> > so.
> >
> > Best,
> > Eric Paniagua
> >
> > ___________________________________________________________
> > The Galaxy User List is being replaced by the Galaxy Biostar
> > User Support Forum at https://biostar.usegalaxy.org/
> >
> > Posts to this list will be disabled in May 2014.  In the
> > meantime, you are encouraged to post all new questions to
> > Galaxy Biostar.
> >
> > 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/
> >
> > To search Galaxy mailing lists use the unified search at:
> >
> >   http://galaxyproject.org/search/mailinglists/
> >
> >
> > ___________________________________________________________
> > The Galaxy User List is being replaced by the Galaxy Biostar
> > User Support Forum at https://biostar.usegalaxy.org/
> >
> > Posts to this list will be disabled in May 2014.  In the
> > meantime, you are encouraged to post all new questions to
> > Galaxy Biostar.
> >
> > 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/
> >
> > To search Galaxy mailing lists use the unified search at:
> >
> >   http://galaxyproject.org/search/mailinglists/
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> <http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20140523/936cf4f1/attachment-0001.html>
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 23 May 2014 20:04:44 +0000
> From: "Paniagua, Eric" <epaniagu@...>
> To: Dannon Baker <dannon.baker@...>
> Cc: Galaxy ?[galaxy-user@...]? 	<galaxy-user@...>
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL
> 	Compatibility
> Message-ID:
> 	<759E5BE3A1277B48ADEE4096E39269CBB22249CF@...>
> Content-Type: text/plain; charset="windows-1256"
> 
> Hi Dannon,
> 
> I just wanted to provide you with some new information regarding the
> situation.  I have installed PostgreSQL 9.1 on another box and migrated the
> database.  I have Galaxy communicating with the remote database.
> 
> However, I still see the same error I originally reported.  So using a newer
> version of PostgreSQL (at least 9.1) didn't fix the problem.
> 
> Thanks for your help!
> 
> Thanks,
> Eric
> 
> ________________________________________
> From: Paniagua, Eric
> Sent: Thursday, May 22, 2014 1:36 PM
> To: Dannon Baker
> Cc: Galaxy ?[galaxy-user@...]?
> Subject: RE: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hi Dannon,
> 
> I have attached a screenshot of the error as it appears in the Galaxy web
> site and a screenshot of the log.
> 
> Please let me know if I can provide any more information.
> 
> Also, please note that the version information I gave for PostgreSQL before
> was incorrect.  I am actually running PostgreSQL 8.1.22.
> 
> Thanks for your assistance,
> Eric
> 
> ________________________________________
> From: galaxy-user-bounces@...
> [galaxy-user-bounces@...] on behalf of Paniagua, Eric
> [epaniagu@...]
> Sent: Thursday, May 22, 2014 11:14 AM
> To: Dannon Baker
> Cc: Galaxy ?[galaxy-user@...]?
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hi Dannon,
> 
> I am in a meeting right now.  I should be done at noon.  I'll send you more
> info then.  Thank you for your assistance!
> 
> Best,
> Eric
> 
> 
> -------- Original message --------
> From: Dannon Baker
> Date:2014/05/22 11:08 (GMT-05:00)
> To: "Paniagua, Eric"
> Cc: "Galaxy ?[galaxy-user@...]?"
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hey Eric,
> 
> Looking into this.  Can you send the exact error/trace if available?
> 
> -Dannon
> 
> 
> On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric
> <epaniagu@...<mailto:epaniagu@...>> wrote:
> Hi,
> 
> I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the
> process of preparing an update I have encountered some problems.  When I try
> to create a new dataset (e.g. by running a tool), I receive an error message
> indicating a syntactic problem with backend database commands.
> Specifically, the error mentions a read-only cursor and occurs when the
> system is trying to look up the history hid number for the new dataset, a
> value which (as far as I understand it) should be an autoincrementing
> primary key.
> 
> My codebase is the 68a8b0397947 commit on the stable branch, plus some custom
> tool definitions, but no real modification to any core Galaxy code.  The
> database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In the
> target (production) environment, we run with 3 web server processes and 3
> job runner processes, but I am encountering this error in a
> single-Galaxy-process test instance.  The error is reported both in the logs
> (with a traceback originating in the bowels of SQLAlchemy) and via the web
> interface.
> 
> I dug through the commit history and found a comit (e1bc855165bc) with the
> comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)."
> on Sep 23, 2013.  I am wondering if this means I need to upgrade my database
> backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that I need to
> keep 2 parallel Galaxy instances running for an extended time period (~1
> month).  The first is the current (not updated) local Galaxy instance, and
> the second is the new (updated) Galaxy instance, which naturally implies
> diverging databases.  Does this mean I will need to maintain parallel
> installations of PostgreSQL 9.1 and 9.2.x?  How would I go about setting up
> that configuration?
> 
> Any assistance on debugging this error would be greatly appreciated.  Our
> initial goal was to roll out this update tomorrow afternoon, but that may
> need to be delayed because of this show-stopper.  If I can provide any
> further useful information, please let me know, and I will be happy to do
> so.
> 
> Best,
> Eric Paniagua
> 
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
> 
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
> 
> 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/
> 
> To search Galaxy mailing lists use the unified search at:
> 
>   http://galaxyproject.org/search/mailinglists/
> 
> 
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
> 
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
> 
> 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/
> 
> To search Galaxy mailing lists use the unified search at:
> 
>   http://galaxyproject.org/search/mailinglists/
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 23 May 2014 20:09:19 +0000
> From: "Paniagua, Eric" <epaniagu@...>
> To: Dannon Baker <dannon.baker@...>
> Cc: Galaxy ?[galaxy-user@...]? 	<galaxy-user@...>
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL
> 	Compatibility
> Message-ID: <lcqka37094c1iq6x1d969210.1400875650627@...>
> Content-Type: text/plain; charset="windows-1256"
> 
> Thank you!
> 
> -------- Original message --------
> From: Dannon Baker
> Date:2014/05/23 16:02 (GMT-05:00)
> To: "Paniagua, Eric"
> Cc: "Galaxy ?[galaxy-user@...]?"
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hey Eric,
> 
> We use sqlalchemy, and the detailed documentation is here:
> 
> http://docs.sqlalchemy.org/en/rel_0_7/core/engines.html#postgresql
> 
> That said, the basic format is:
> dialect+driver://username:password <at> host:port/database
> 
> So, you're going to be looking at something like:
> postgres://glxeric@...:5432/glxeric<http://glxeric-Gxze+4rIJ/w1u5t9mutDEIdd74u8MsAO <at> public.gmane.org:5432/glxeric>
> 
> 
> 
> On Fri, May 23, 2014 at 3:49 PM, Paniagua, Eric
> <epaniagu@...<mailto:epaniagu@...>> wrote:
> Hi Dannon,
> 
> There have been some developments, and I would like to update my question
> accordingly.
> 
> I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and
> ferried the database contents over.  My question is this:
> 
> What is the appropriate syntax to use for the parameter "database_connection"
> in universe_wsgi.ini to use a remote database server?  Specifically:
> 
> Galaxy host: genomics.cshl.edu<http://genomics.cshl.edu>
> Database host: wigserv5.cshl.edu<http://wigserv5.cshl.edu>
> Database name: glxeric
> Database user/role: glxeric
> Database port: 5432 (postgresql default port)
> Database password: not required under the current configuration.
> 
> Can someone please explain how to fill in the "database_connection" parameter
> appropriately?
> 
> Many thanks,
> Eric
> 
> ________________________________________
> From:
> galaxy-user-bounces@...<mailto:galaxy-user-bounces@...>
> [galaxy-user-bounces@...<mailto:galaxy-user-bounces@...>]
> on behalf of Paniagua, Eric [epaniagu@...<mailto:epaniagu@...>]
> Sent: Thursday, May 22, 2014 1:38 PM
> To: Dannon Baker
> Cc: Galaxy ?[galaxy-user@...<mailto:galaxy-user@...>]?
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hi Dannon,
> 
> I have attached a screenshot of the error as it appears in the Galaxy web
> site and a screenshot of the log.
> 
> Please let me know if I can provide any more information.
> 
> Also, please note that the version information I gave for PostgreSQL before
> was incorrect.  I am actually running PostgreSQL 8.1.22.
> 
> Thanks for your assistance,
> Eric
> 
> ________________________________________
> From:
> galaxy-user-bounces@...<mailto:galaxy-user-bounces@...>
> [galaxy-user-bounces@...<mailto:galaxy-user-bounces@...>]
> on behalf of Paniagua, Eric [epaniagu@...<mailto:epaniagu@...>]
> Sent: Thursday, May 22, 2014 11:14 AM
> To: Dannon Baker
> Cc: Galaxy ?[galaxy-user@...<mailto:galaxy-user@...>]?
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hi Dannon,
> 
> I am in a meeting right now.  I should be done at noon.  I'll send you more
> info then.  Thank you for your assistance!
> 
> Best,
> Eric
> 
> 
> -------- Original message --------
> From: Dannon Baker
> Date:2014/05/22 11:08 (GMT-05:00)
> To: "Paniagua, Eric"
> Cc: "Galaxy ?[galaxy-user@...<mailto:galaxy-user@...>]?"
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
> 
> Hey Eric,
> 
> Looking into this.  Can you send the exact error/trace if available?
> 
> -Dannon
> 
> 
> On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric
> <epaniagu@...<mailto:epaniagu@...><mailto:epaniagu@...<mailto:epaniagu@...>>>
> wrote:
> Hi,
> 
> I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the
> process of preparing an update I have encountered some problems.  When I try
> to create a new dataset (e.g. by running a tool), I receive an error message
> indicating a syntactic problem with backend database commands.
> Specifically, the error mentions a read-only cursor and occurs when the
> system is trying to look up the history hid number for the new dataset, a
> value which (as far as I understand it) should be an autoincrementing
> primary key.
> 
> My codebase is the 68a8b0397947 commit on the stable branch, plus some custom
> tool definitions, but no real modification to any core Galaxy code.  The
> database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In the
> target (production) environment, we run with 3 web server processes and 3
> job runner processes, but I am encountering this error in a
> single-Galaxy-process test instance.  The error is reported both in the logs
> (with a traceback originating in the bowels of SQLAlchemy) and via the web
> interface.
> 
> I dug through the commit history and found a comit (e1bc855165bc) with the
> comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)."
> on Sep 23, 2013.  I am wondering if this means I need to upgrade my database
> backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that I need to
> keep 2 parallel Galaxy instances running for an extended time period (~1
> month).  The first is the current (not updated) local Galaxy instance, and
> the second is the new (updated) Galaxy instance, which naturally implies
> diverging databases.  Does this mean I will need to maintain parallel
> installations of PostgreSQL 9.1 and 9.2.x?  How would I go about setting up
> that configuration?
> 
> Any assistance on debugging this error would be greatly appreciated.  Our
> initial goal was to roll out this update tomorrow afternoon, but that may
> need to be delayed because of this show-stopper.  If I can provide any
> further useful information, please let me know, and I will be happy to do
> so.
> 
> Best,
> Eric Paniagua
> 
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
> 
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
> 
> 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/
> 
> To search Galaxy mailing lists use the unified search at:
> 
>   http://galaxyproject.org/search/mailinglists/
> 
> 
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
> 
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
> 
> 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/
> 
> To search Galaxy mailing lists use the unified search at:
> 
>   http://galaxyproject.org/search/mailinglists/
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
> 
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
> 
> galaxy-user mailing list
> galaxy-user@...
> http://lists.bx.psu.edu/listinfo/galaxy-user
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> 
> End of galaxy-user Digest, Vol 95, Issue 9
> ******************************************
> 
Enis Afgan | 24 May 22:45 2014
Picon

Re: Asking for help from China about Galaxy Project

You can upload the required genome into your history and then from the "Use a built in reference genome or own from your history:" dropdown choose "use a genome from history" option of the Tophat tool. Tophat will then run using the desired reference genome.

BTW, these types of questions are best asked on the Biostar Q&A site for Galaxy (https://biostar.usegalaxy.org/) or the user mailing list (CC'd). That will give you better exposure to the community and hence a better chance for an answer.

Hope this help,
Enis


On Sat, May 24, 2014 at 9:43 AM, shiny <shishishiny-H32Fclmsjq1BDgjK7y7TUQ@public.gmane.org> wrote:
Hello,Enis Afgan.
I wonna run TOPHAT through the Galaxy project.Well, I can't find the reference genome of Carica papaya.So should I ask for help as it shows on the website,or it is easier should I turn to use Linux shell for me?
Shiny

<div>
<div dir="ltr">You can upload the required genome into your history and then from the "Use a built in reference genome or own from your history:" dropdown choose "use a genome from history" option of the Tophat tool. Tophat will then run using the desired reference genome.<div>

<br>
</div>
<div>BTW, these types of questions are best asked on the Biostar Q&amp;A site for Galaxy (<a href="https://biostar.usegalaxy.org/">https://biostar.usegalaxy.org/</a>) or the user mailing list (CC'd). That will give you better exposure to the community and hence a better chance for an answer.</div>

<div><br></div>
<div>Hope this help,</div>
<div>Enis</div>
</div>
<div class="gmail_extra">
<br><br><div class="gmail_quote">On Sat, May 24, 2014 at 9:43 AM, shiny <span dir="ltr">&lt;<a href="mailto:shishishiny@...m" target="_blank">shishishiny@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">
<div><span>Hello,Enis Afgan.</span></div>

<div><span>I wonna run TOPHAT through the Galaxy project.Well, I can't find the reference genome of Carica papaya.So should I ask for help as it shows on the website,or it is easier should I turn to use Linux shell for me?</span></div>

<span class="HOEnZb"><div><span>Shiny</span></div></span>
</blockquote>
</div>
<br>
</div>
</div>
Jennifer Jackson | 16 May 20:10 2014
Picon

Re: problems with MAF alignment file in Galaxy

Hi Amit,

The problem has to do with the MAF files themselves - they are truncated. This occurs when MAF data is extracted from the Table browser (or any data in excess of ~100k lines). This data greatly exceeds that:
Database: dm3    Primary Table: multiz15way    Row Count: 1,633,505

The ends of both dataset #1 and dataset #3 have this warning:
---------------------------------------------------------------------------
procedures have exceeded timeout: 1200 seconds, function has ended. ---------------------------------------------------------------------------

Instead, you have two options:

1 - obtain the MAF files from the UCSC downloads area. Go to http://genome.ucsc.edu, then in the left blue side bar select "Downloads", then navigate to the data for dm3. The multiz (MAF) will be under the Conservation track data.

2 - this same MAF data is cashed as a local data source on usegalaxy.org. If you queried the blocks using an interval/bed file of coordinates (assigned with database "dm3"), you could obtain the intervals that way. UCSC has the chromsome names and lengths on the D. Mel home page in a table found by clicking on the link near the top named "Sequences". Simple files from this info can be pasted into the "Get Data -> Upload file" tool form to create one-line query datasets, like this one:




I was able to run " Extract MAF blocks" then "MAF to Interval" with no problems. I don't know if doing this one chromosome at time is required, but it certainly will work and not exceed any resources. I suggested doing this once, building a workflow, then running on the rest in batch.

Hopefully one of these options works out for you!

Jen
Galaxy team

On 5/16/14 6:59 AM, Amit Pande wrote:
Dear Jennifer,

I uploaded the data both the ways i.e via the FTP and through the UCSC browser, but all the attempts to extract MAF blocks between insect species has failed.
I need your help in this regard, so I have shared my history with you.
warm regards,
Amit. 


On Thu, May 15, 2014 at 5:07 PM, Jennifer Jackson <jen-dukY5rQBki03uPMLIKxrzw@public.gmane.org> wrote:
Hi Amit,

This is occurring when you are uploading a MAF "multizXXway" file obtained from UCSC downloads (genome.ucsc.edu) to Galaxy main (usegalaxy.org)? Upload using FTP? https://wiki.galaxyproject.org/Support#Loading_data

The table browser is generally a poor choice to extract more than a few regions with MAF data (per query) as there are limits on how many lines of output will be sent over. Incomplete transfers are a common. This error could be related to a format or datatype assignment issue from that type of issue.

Please give FTP loading a try if you have not already. Then if problems continue, you can share a history link with me. Note which dataset was the MAF uploaded via FTP. This is how to share: https://wiki.galaxyproject.org/Learn/Share

Best,

Jen
Galaxy team

Going forward, please ask questions on our new forum that is replacing this list (very soon now):
https://wiki.galaxyproject.org/Support#Biostar


On 5/14/14 10:52 PM, Amit Pande wrote:
Dear Galaxy,

I am trying to import a multiz alignment file for all the insect species from the UCSC
genome browser.
Galaxy does not recognize number of blocks in the multiz file as there is a question mark in the file format view (? blocks).
Then when I am trying to use the tool ( Extract MAF blocks given a set of genomic intervals) then there is an error saying
 
"An error occurred with this dataset:191757 MAF blocks converted to Genomic Intervals for species dm3. There was a problem processing your input: exceptions must be old-style classes or derived from BaseException, not str" and even when the tool runs it shows the following message "
This is a new dataset and not all of its data are available yet "

Please look into the problem.

warm regards,
Amit.


___________________________________________________________ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

-- Jennifer Hillman-Jackson http://galaxyproject.org


-- Jennifer Hillman-Jackson http://galaxyproject.org
<div>
    Hi Amit,<br><br>
    The problem has to do with the MAF files themselves - they are
    truncated. This occurs when MAF data is extracted from the Table
    browser (or any data in excess of ~100k lines). This data greatly
    exceeds that:<br>Database:<span><span class="Apple-converted-space">&nbsp;</span>dm3&nbsp;&nbsp;&nbsp;&nbsp;</span>Primary Table:<span><span class="Apple-converted-space">&nbsp;</span>multiz15way&nbsp;&nbsp;&nbsp;&nbsp;</span>Row Count:<span><span class="Apple-converted-space">&nbsp;</span>1,633,505</span><br><br>
    The ends of both dataset #1 and dataset #3 have this warning:<br>
---------------------------------------------------------------------------
    <br>
    procedures have exceeded timeout: 1200 seconds, function has ended.
---------------------------------------------------------------------------<br><br>
    Instead, you have two options:<br><br>
    1 - obtain the MAF files from the UCSC downloads area. Go to
    <a class="moz-txt-link-freetext" href="http://genome.ucsc.edu">http://genome.ucsc.edu</a>, then in the left blue side bar select
    "Downloads", then navigate to the data for dm3. The multiz (MAF)
    will be under the Conservation track data. <br><br>
    2 - this same MAF data is cashed as a local data source on
    usegalaxy.org. If you queried the blocks using an interval/bed file
    of coordinates (assigned with database "dm3"), you could obtain the
    intervals that way. UCSC has the chromsome names and lengths on the
    D. Mel home page in a table found by clicking on the link near the
    top named "Sequences". Simple files from this info can be pasted
    into the "Get Data -&gt; Upload file" tool form to create one-line
    query datasets, like this one:<br><br><br><br><br>
    I was able to run "

    Extract MAF blocks" then "MAF to Interval" with no problems. I don't
    know if doing this one chromosome at time is required, but it
    certainly will work and not exceed any resources. I suggested doing
    this once, building a workflow, then running on the rest in batch.<br><br>
    Hopefully one of these options works out for you!<br><br>
    Jen<br>
    Galaxy team<br><br><div class="moz-cite-prefix">On 5/16/14 6:59 AM, Amit Pande wrote:<br>
</div>
    <blockquote cite="mid:CAMWn8txMO5rrbz1jkF_igKgrbgqhuWWAmpbgsCpQ=jWPPFR+uA@...ail.com" type="cite">
      <div dir="ltr">
        <div>
          <div>
            <div>
              <div>Dear Jennifer,<br><br>
</div>
              I uploaded the data both the ways i.e via the FTP and
              through the UCSC browser, but all the attempts to extract
              MAF blocks between insect species has failed.<br>
</div>
            I need your help in this regard, so I have shared my history
            with you.<br>
</div>
          warm regards,<br>
</div>
        Amit.&nbsp; <br>
</div>
      <div class="gmail_extra">
<br><br><div class="gmail_quote">On Thu, May 15, 2014 at 5:07 PM,
          Jennifer Jackson <span dir="ltr">&lt;<a moz-do-not-send="true" href="mailto:jen@..." target="_blank">jen@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">
            <div bgcolor="#FFFFFF" text="#000000"> Hi Amit,<br><br>
              This is occurring when you are uploading a MAF
              "multizXXway" file obtained from UCSC downloads (<a moz-do-not-send="true" href="http://genome.ucsc.edu" target="_blank">genome.ucsc.edu</a>) to Galaxy main (<a moz-do-not-send="true" href="http://usegalaxy.org" target="_blank">usegalaxy.org</a>)? Upload using FTP? <a moz-do-not-send="true" href="https://wiki.galaxyproject.org/Support#Loading_data" target="_blank">https://wiki.galaxyproject.org/Support#Loading_data</a><br><br>
              The table browser is generally a poor choice to extract
              more than a few regions with MAF data (per query) as there
              are limits on how many lines of output will be sent over.
              Incomplete transfers are a common. This error could be
              related to a format or datatype assignment issue from that
              type of issue.<br><br>
              Please give FTP loading a try if you have not already.
              Then if problems continue, you can share a history link
              with me. Note which dataset was the MAF uploaded via FTP.
              This is how to share: <a moz-do-not-send="true" href="https://wiki.galaxyproject.org/Learn/Share" target="_blank">https://wiki.galaxyproject.org/Learn/Share</a><br><br>
              Best,<br><br>
              Jen<br>
              Galaxy team<br><br>
              Going forward, please ask questions on our new forum that
              is replacing this list (very soon now): <br><a moz-do-not-send="true" href="https://wiki.galaxyproject.org/Support#Biostar" target="_blank">https://wiki.galaxyproject.org/Support#Biostar</a>
              <div>
                <div class="h5">
<br><br><div>On 5/14/14 10:52 PM, Amit Pande wrote:<br>
</div>
                </div>
              </div>
              <blockquote type="cite">
                <div>
                  <div class="h5">
                    <div dir="ltr">
                      <div>
                        <div>
                          <div>
                            <div>Dear Galaxy,<br><br>
</div>
                            I am trying to import a multiz alignment
                            file for all the insect species from the
                            UCSC<br>
</div>
                          genome browser.<br>
</div>
                        Galaxy does not recognize number of blocks in
                        the multiz file as there is a question mark in
                        the file format view (<span>? blocks).<br></span>
</div>
                      <span>Then when I am trying to use the tool ( </span><a moz-do-not-send="true" href="https://usegalaxy.org/tool_runner?tool_id=Interval2Maf1" target="_blank">Extract MAF blocks</a> given a
                      set of genomic intervals) then there is an error
                      saying<br>
                      &nbsp;<br>
                      "An error occurred with this dataset:191757 MAF
                      blocks converted to Genomic Intervals for species
                      dm3. There was a problem processing your input:
                      exceptions must be old-style classes or derived
                      from BaseException, not str" and even when the
                      tool runs it shows the following message "<span></span>
                      <div>
                        <div>
                          <div>This is a new dataset and not all of its
                            data are available yet "<br>
</div>
                        </div>
                      </div>
                      <div>
                        <div><br></div>
                        Please look into the problem.<br><br>
</div>
                      <div>warm regards,<br>
</div>
                      <div>Amit.<br>
</div>
                    </div>
                    <br><br>
</div>
                </div>
                ___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at <a moz-do-not-send="true" href="https://biostar.usegalaxy.org/" target="_blank">https://biostar.usegalaxy.org/</a>

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  <a moz-do-not-send="true" href="http://lists.bx.psu.edu/listinfo/galaxy-dev" target="_blank">http://lists.bx.psu.edu/listinfo/galaxy-dev</a>

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

  <a moz-do-not-send="true" href="http://lists.bx.psu.edu/" target="_blank">http://lists.bx.psu.edu/</a>

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                <span class="HOEnZb"> </span>
</blockquote>
              <span class="HOEnZb"> <br>-- 
Jennifer Hillman-Jackson
<a moz-do-not-send="true" href="http://galaxyproject.org" target="_blank">http://galaxyproject.org</a>
                </span>
</div>
          </blockquote>
        </div>
        <br>
</div>
    </blockquote>
    <br>-- 
Jennifer Hillman-Jackson
<a class="moz-txt-link-freetext" href="http://galaxyproject.org">http://galaxyproject.org</a>
  </div>
Antoine Buetti-Dinh | 16 May 11:10 2014
Picon

cuffcompare MPI error


Hi,

sorry to bother but now it's the 3rd time I get a message saying that if the problem persists I should contact the galaxy staff.

It occurs while running cuffcompare of total RNA to a genomic reference that I uploaded myself (Sulfolobus acidocaldarius). It's about MPI processes terminated incorrectly if I understood it correctly.

Just to let you know...

These are the details of the generated error:
---------------------------------------------------------------
user   
username    twincacca
quota_percent    32
total_disk_usage    86918246471
nice_total_disk_usage    80.9 GB
email    antoine.buetti-+t3nrxhBqL8@public.gmane.org
is_admin    false
tags_used   
model_class    User
id    3e934cb0877d45db
source    HDACollection(8fb8cc6fa23b1dbe,99)
xhr   
readyState    4
responseText    {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
responseJSON   
err_msg    Uncaught exception in exposed API method:
err_code    0
status    500
statusText    Internal Server Error
responseHeaders   
Server    nginx/1.4.7
Date    Fri, 16 May 2014 08:58:57 GMT
Content-Type    application/json
Transfer-Encoding    chunked
Connection    keep-alive
Cache-Control    max-age=0,no-cache,no-store
options   
data   
parse    true
emulateHTTP    false
emulateJSON    false
---------------------------------------------------------------END


<div>
<div>
<br>
Hi, <br><br>
sorry to bother but now it's the 3rd time I get a message saying that if the problem persists I should contact the galaxy staff.
<br><br>
It occurs while running cuffcompare of total RNA to a genomic reference that I uploaded myself (Sulfolobus acidocaldarius). It's about MPI processes terminated incorrectly if I understood it correctly.
<br><br>
Just to let you know... <br><br>
These are the details of the generated error: <br>
---------------------------------------------------------------<br>
user&nbsp;&nbsp;&nbsp; <br>
username&nbsp;&nbsp;&nbsp; twincacca<br>
quota_percent&nbsp;&nbsp;&nbsp; 32<br>
total_disk_usage&nbsp;&nbsp;&nbsp; 86918246471<br>
nice_total_disk_usage&nbsp;&nbsp;&nbsp; 80.9 GB<br>
email&nbsp;&nbsp;&nbsp; antoine.buetti@...<br>
is_admin&nbsp;&nbsp;&nbsp; false<br>
tags_used&nbsp;&nbsp;&nbsp; <br>
model_class&nbsp;&nbsp;&nbsp; User<br>
id&nbsp;&nbsp;&nbsp; 3e934cb0877d45db<br>
source&nbsp;&nbsp;&nbsp; HDACollection(8fb8cc6fa23b1dbe,99)<br>
xhr&nbsp;&nbsp;&nbsp; <br>
readyState&nbsp;&nbsp;&nbsp; 4<br>
responseText&nbsp;&nbsp;&nbsp; {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}<br>
responseJSON&nbsp;&nbsp;&nbsp; <br>
err_msg&nbsp;&nbsp;&nbsp; Uncaught exception in exposed API method:<br>
err_code&nbsp;&nbsp;&nbsp; 0<br>
status&nbsp;&nbsp;&nbsp; 500<br>
statusText&nbsp;&nbsp;&nbsp; Internal Server Error<br>
responseHeaders&nbsp;&nbsp;&nbsp; <br>
Server&nbsp;&nbsp;&nbsp; nginx/1.4.7<br>
Date&nbsp;&nbsp;&nbsp; Fri, 16 May 2014 08:58:57 GMT<br>
Content-Type&nbsp;&nbsp;&nbsp; application/json<br>
Transfer-Encoding&nbsp;&nbsp;&nbsp; chunked<br>
Connection&nbsp;&nbsp;&nbsp; keep-alive<br>
Cache-Control&nbsp;&nbsp;&nbsp; max-age=0,no-cache,no-store<br>
options&nbsp;&nbsp;&nbsp; <br>
data&nbsp;&nbsp;&nbsp; <br>
parse&nbsp;&nbsp;&nbsp; true<br>
emulateHTTP&nbsp;&nbsp;&nbsp; false<br>
emulateJSON&nbsp;&nbsp;&nbsp; false<br>
---------------------------------------------------------------END<br><br><br>
</div>
</div>
Ay Ayy | 16 May 03:23 2014
Picon

Re: edit file in galaxy

過去18年力抗抑鬱病折磨,時刻鼓勵自己努力、加油的女子,終因難敵頭痛失眠,昨午在灣仔軒尼詩道向上班僅兩個月的餐廳請辭後,突由大廈31樓天台躍下,身體倒插在餐廳窗外的大廈一樓玻璃簷篷,消防員到場將她救下送院,證實死亡。

難敵抑鬱辭職即跳樓

死者鍾巧盈(28歲),暱稱小巧,生前與父母及兩名胞妹同住香港仔華貴邨,兩個月前獲軒尼詩道彰顯大廈一樓樂農素食餐廳聘任兼職收銀員。據悉,小巧10歲那年患上抑鬱症,多年來飽受折磨,需經常往醫院接受治療。但她性格樂天,一旦身體狀況不錯,便外出工作,早前曾在一家精品店工作。消息稱小巧最近病情反覆,連續多日頭痛失眠,昨晨11時上班後,向經理辭職。下午2時半落場時她又頭痛不適,經理批准她即時離職休養。怎料,小巧離開餐廳25分鐘後,即被人發現從大廈高處墮下,身體倒插在餐廳對開玻璃簷篷上,嚇得途人立即報警,消防員將她救下送院,但證實不治。
小巧母親趕往醫院,傷心痛哭。警方相信事件無可疑。小巧任職的樂農是本港首家社會企業素食餐廳,經理說小巧對人有禮,對她去世感惋惜。資料顯示,去年約6,700名兒童及青少年患抑鬱等精神病,醫生指有年輕化趨勢。

Ibrahim YU; wilson (cuhk)
ay73ay-YDxpq3io04c@public.gmane.org
Find me at about.me/uy73


-----Original Message-----
From: Koehorst, Jasper <jasper.koehorst-kYp8Ca87YEA@public.gmane.org>
To: galaxy-user <galaxy-user-btkOtGxnL5087WB9TwDe4A@public.gmane.org>
Sent: Tue, May 13, 2014 3:18 pm
Subject: [galaxy-user] edit file in galaxy

Hello, I am generating files but sometimes I want to add something to the text file generated. I would like to do this within galaxy instead of downloading, modifying, uploading the file. Is this possible? Thanks, jasper ___________________________________________________________ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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<br><div>Ibrahim YU; wilson (cuhk)<br>
ay73ay@...<br>
Find me at <a href="http://about.me/uy73" target="_blank">about.me/uy73</a>
</div>
<br><br><div>-----Original Message-----<br>
From: Koehorst, Jasper &lt;jasper.koehorst@...&gt;<br>
To: galaxy-user &lt;galaxy-user@...&gt;<br>
Sent: Tue, May 13, 2014 3:18 pm<br>
Subject: [galaxy-user] edit file in galaxy<br><br><div>

<div>
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</div>

<div>

Hello,

I am generating files but sometimes I want to add something to the text file 
generated. I would like to do this within galaxy instead of downloading, 
modifying, uploading the file.

Is this possible?

Thanks,

jasper

___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at <a href="https://biostar.usegalaxy.org/" target="_blank">https://biostar.usegalaxy.org/</a>

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  <a href="http://lists.bx.psu.edu/listinfo/galaxy-dev" target="_blank">http://lists.bx.psu.edu/listinfo/galaxy-dev</a>

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

  <a href="http://lists.bx.psu.edu/" target="_blank">http://lists.bx.psu.edu/</a>

To search Galaxy mailing lists use the unified search at:

  <a href="http://galaxyproject.org/search/mailinglists/" target="_blank">http://galaxyproject.org/search/mailinglists/</a>

</div>

</div>
</div>
Amit Pande | 15 May 07:52 2014
Picon

problems with MAF alignment file in Galaxy

Dear Galaxy,

I am trying to import a multiz alignment file for all the insect species from the UCSC
genome browser.
Galaxy does not recognize number of blocks in the multiz file as there is a question mark in the file format view (? blocks).
Then when I am trying to use the tool ( Extract MAF blocks given a set of genomic intervals) then there is an error saying
 
"An error occurred with this dataset:191757 MAF blocks converted to Genomic Intervals for species dm3. There was a problem processing your input: exceptions must be old-style classes or derived from BaseException, not str" and even when the tool runs it shows the following message "
This is a new dataset and not all of its data are available yet "

Please look into the problem.

warm regards,
Amit.
<div><div dir="ltr">
<div>
<div>
<div>
<div>Dear Galaxy,<br><br>
</div>I am trying to import a multiz alignment file for all the insect species from the UCSC<br>
</div>genome browser.<br>
</div>Galaxy does not recognize number of blocks in the multiz file as there is a question mark in the file format view (<span class="">? blocks).<br></span>
</div>
<span class="">Then when I am trying to use the tool ( </span><a class="" href="https://usegalaxy.org/tool_runner?tool_id=Interval2Maf1" target="galaxy_main">Extract MAF blocks</a> given a set of genomic intervals) then there is an error saying<br>
&nbsp;<br>"An error occurred with this dataset:191757 MAF blocks converted to Genomic Intervals for species dm3.
There was a problem processing your input: exceptions must be old-style classes or derived from BaseException, not str" and even when the tool runs it shows the following message "<span class=""></span><div class="">
<div class=""><div>This is a new dataset and not all of its data are available yet "<br>
</div></div>
</div>
<div class="">
<div class=""><br></div>Please look into the problem.<br><br>
</div>
<div class="">warm regards,<br>
</div>
<div class="">Amit.<br>
</div>
</div></div>

Gmane