Re: [galaxy-user] FTP upload problem

[Jennifer Jackson]

Hi Thanh,

I am glad the password reset worked. This new issue was on our side and 
has been corrected again. Please try the FTP upload now. Our apologies 
for the multiple problems confusing the process,


Jen
Galaxy team

On 6/11/13 3:42 PM, Hoang, Thanh wrote:

Hi all,
I just finished uploading 2 files via FTP and I have some more files 
to be uploaded. After an Internet  disconnection, I got the same 
problem like Delong had. I got this message:
 "530 Sorry, the maximum number of clients (3) for this user are 
already connected

Error:Critical error
Error:Could not connect to server"

I tried to re-connect but it still did not work. Could anyone please 
help me with this?

Regards
Thanh


On Tue, Jun 11, 2013 at 4:16 PM, Jennifer Jackson > wrote:


Hello Delong,

This was a temporary issue during a short time window yesterday.
Letting us know about it is always OK, but then going back in and
trying to connect again in the right solution, as it will
generally clear up. If you haven't been able to make the
connection by now (I just tested it again right now, and it is
functioning for me), please let us know,

Best,

Jen
Galaxy team

On 6/10/13 10:50 AM, Delong, Zhou wrote:

Hello,
I was using the ftp uploading via filezilla. It worked perfectly
this morning, but after a disconnection of the internet I can no
longer upload any file. This is the message I got:
530 Sorry, the maximum number of clients (3) for this user are
already connected
I restarted my computer and shut down the program for 30 minutes
hoping the server will reset the connection but it didnt work.
I've done some search on the internet but nothing helped.
I noticed that this problem has already been mentioned on the ML
but the solution was not given. Anyone could help please?
Thanks
Delong


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Galaxy Support and Training
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Re: [galaxy-user] FTP upload problem

[Hoang, Thanh]

Hi all,
I just finished uploading 2 files via FTP and I have some more files to be
uploaded. After an Internet  disconnection, I got the same problem like
Delong had. I got this message:
 "530 Sorry, the maximum number of clients (3) for this user are already
connected
Error: Critical error
Error: Could not connect to server"

I tried to re-connect but it still did not work. Could anyone please help
me with this?
Regards
Thanh


On Tue, Jun 11, 2013 at 4:16 PM, Jennifer Jackson  wrote:

>  Hello Delong,
>
> This was a temporary issue during a short time window yesterday. Letting
> us know about it is always OK, but then going back in and trying to connect
> again in the right solution, as it will generally clear up. If you haven't
> been able to make the connection by now (I just tested it again right now,
> and it is functioning for me), please let us know,
>
> Best,
>
> Jen
> Galaxy team
>
> On 6/10/13 10:50 AM, Delong, Zhou wrote:
>
> Hello,
> I was using the ftp uploading via filezilla. It worked perfectly this
> morning, but after a disconnection of the internet I can no longer upload
> any file. This is the message I got:
> 530 Sorry, the maximum number of clients (3) for this user are already
> connected
> I restarted my computer and shut down the program for 30 minutes hoping
> the server will reset the connection but it didnt work. I've done some
> search on the internet but nothing helped.
> I noticed that this problem has already been mentioned on the ML but the
> solution was not given. Anyone could help please?
> Thanks
> Delong
>
>
> ___
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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
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>
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> --
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> Galaxy Support and Traininghttp://galaxyproject.org
>
>
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Re: [galaxy-user] FTP upload problem

[Jennifer Jackson]

Hello Delong,

This was a temporary issue during a short time window yesterday. Letting 
us know about it is always OK, but then going back in and trying to 
connect again in the right solution, as it will generally clear up. If 
you haven't been able to make the connection by now (I just tested it 
again right now, and it is functioning for me), please let us know,


Best,

Jen
Galaxy team

On 6/10/13 10:50 AM, Delong, Zhou wrote:

Hello,
I was using the ftp uploading via filezilla. It worked perfectly this 
morning, but after a disconnection of the internet I can no longer 
upload any file. This is the message I got:
530 Sorry, the maximum number of clients (3) for this user are already 
connected
I restarted my computer and shut down the program for 30 minutes 
hoping the server will reset the connection but it didnt work. I've 
done some search on the internet but nothing helped.
I noticed that this problem has already been mentioned on the ML but 
the solution was not given. Anyone could help please?

Thanks
Delong


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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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Re: [galaxy-user] Upload files to Galaxy via FTP

[Jennifer Jackson]

Hello Thanh,

First, you will want to be sure that you are following the protocols 
outlined on our wiki here. There are two screencasts that have a demo of 
the process.

http://wiki.galaxyproject.org/FTPUpload

And second, double check that you are using the correct Galaxy server 
name (main.g2.bx.psu.edu) and Galaxy credentials (same email and 
password that you use for your account on the public Main Galaxy instance).


If by chance you created your account new during a specific time frame 
in May, you may need to update your password, since a specific FTP login 
problem may be a factor. Please see this notice for the details and remedy:

http://wiki.galaxyproject.org/Main/Notices#May_29th_2013_FTP_login_resolution

Please let us know if you continue to have problems after reviewing this 
info,


Thanks!

Jen
Galaxy team

On 6/10/13 11:00 PM, Hoang, Thanh wrote:

Hi,
I have been trying to upload my RNA-seq data files (~20 Gb total) via 
FTP using my account in Galaxy. But I could not connect to the server. 
The following message showed up:

/"Error:Critical error/
/Error:Could not connect to server"/

Could you suggest any idea to overcome this problem?
Thank you so much
Thanh
/
/


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--
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Re: [galaxy-user] problem with custom database build

[Sun, Jiajie - ARS]

Hi Ann,
I think that you can change Browser, such as google.

jia

From: galaxy-user-boun...@lists.bx.psu.edu 
[mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Dannon Baker
Sent: Tuesday, June 11, 2013 11:11 AM
To: Ann Holtz-Morris, M.S.
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] problem with custom database build

Hi Ann,

My guess is that this is related to the issue you were having before.  I'm 
taking a look now.

-Dannon

On Mon, Jun 10, 2013 at 7:31 PM, Ann Holtz-Morris, M.S. 
mailto:aholtzmor...@chori.org>> wrote:
Hi,
I'm trying to create a new custom build . I keep getting GURU MEDITATION: 
#aa96a62c69784be49b7864f6ef42ddc6  I've been trying  1 or 2 times a day for the 
last 3 days. Thanks
Ann



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Re: [galaxy-user] problem with custom database build

[Dannon Baker]

Hi Ann,

My guess is that this is related to the issue you were having before.  I'm
taking a look now.

-Dannon


On Mon, Jun 10, 2013 at 7:31 PM, Ann Holtz-Morris, M.S. <
aholtzmor...@chori.org> wrote:

> Hi,
>
> I’m trying to create a new custom build . I keep getting *GURU
> MEDITATION: #aa96a62c69784be49b7864f6ef42ddc6  *I’ve been trying  1 or 2
> times a day for the last 3 days. Thanks
>
> Ann
>
> ** **
>
> ** **
>
> CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use 
> only of the named recipient, and may contain information that is confidential 
> or privileged. If you are not the intended recipient, you are hereby notified 
> that any disclosure, copying, distribution or use of the contents of this 
> message is strictly prohibited. If you have received this message in error or 
> are not the named recipient, please notify us immediately by contacting the 
> sender at the electronic mail address noted above, and delete and destroy all 
> copies of this message. Thank you.
>
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[galaxy-user] Upload files to Galaxy via FTP

[Hoang, Thanh]

Hi,
I have been trying to upload my RNA-seq data files (~20 Gb total) via FTP
using my account in Galaxy. But I could not connect to the server. The
following message showed up:
*"Error: Critical error*
*Error: Could not connect to server"*

Could you suggest any idea to overcome this problem?
Thank you so much
Thanh
*
*
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[galaxy-user] problem with custom database build

[Ann Holtz-Morris, M.S.]

Hi,

I'm trying to create a new custom build . I keep getting GURU MEDITATION: 
#aa96a62c69784be49b7864f6ef42ddc6  I've been trying  1 or 2 times a day for the 
last 3 days. Thanks

Ann





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Re: [galaxy-user] Tophat problem on a new local instance

[James Taylor]

Regarding (2), have you installed bowtie and tophat on your Mac Pro?
Galaxy does not currently automatically install all of the software
needed to run tools (we are working on this through the toolshed, but
at the moment it is a manual process).

Dependencies of various tools included in the distribution are here:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jun 11, 2013 at 9:20 AM, Elwood Linney  wrote:
> Hello, I will try this again without attachments and hope it gets on the
> list.
>
> I have installed a local instance of Galaxy as a one user in a Mac Pro
> desktop.  I got some valuable help from Dannon Baker regarding how to load
> large datasets into it.  However I noticed that the Upload file for this
> instance would only go up to the
>
> Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish
> assembly while where as the online version went up to the newer assembly
>
> zebrafish assembly   Jul. 2010 (Zv9/danRER7)
>
>
> While I could download newer reference genome in the program from UCSC Main
> table browser
> whenever the local instance offered alternatives for genomes it only went up
> the earlier version
> (Zv8/danRer6) (danRer6) .
>
> I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat,
>
> An error occurred with this dataset: Could not determine Tophat version
> /bin/sh: tophat: command not found Error indexing reference sequence
> /bin/sh: bowtie-build: command not found
>
> So minimally I have two problems that may or may not be related:
>
> 1)The Galaxy-dist that I just installed into a Mac pro does not have the
> latest zebrafish assembly
>
> 2) but more importantly when I try to process groomed datasets through
> Tophat and "Use a built-in genome" as reference it does not allow me an
> option for the reference genome AND if I try to use a reference genome from
> the UCSC download, it won't allow that.
>
> So right now I am stymied--any advice?
>
> Elwood Linney
> Duke University Medical Center
>
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[galaxy-user] Tophat problem on a new local instance

[Elwood Linney]

Hello, I will try this again without attachments and hope it gets on the
list.

I have installed a local instance of Galaxy as a one user in a Mac Pro
desktop.  I got some valuable help from Dannon Baker regarding how to load
large datasets into it.  However I noticed that the Upload file for this
instance would only go up to the

Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish
assembly while where as the online version went up to the newer assembly

zebrafish assembly   Jul. 2010 (Zv9/danRER7)


While I could download newer reference genome in the program from UCSC Main
table browser
whenever the local instance offered alternatives for genomes it only went
up the earlier version
(Zv8/danRer6) (danRer6) .

I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat,

An error occurred with this dataset: Could not determine Tophat version
/bin/sh: tophat: command not found Error indexing reference sequence
/bin/sh: bowtie-build: command not found

So minimally I have two problems that may or may not be related:

1)The Galaxy-dist that I just installed into a Mac pro does not have the
latest zebrafish assembly

2) but more importantly when I try to process groomed datasets through
Tophat and "Use a built-in genome" as reference it does not allow me an
option for the reference genome AND if I try to use a reference genome from
the UCSC download, it won't allow that.

So right now I am stymied--any advice?

Elwood Linney
Duke University Medical Center
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