Re: [galaxy-user] Need your helps about Galaxy

[Lei Yan]

Thanks Jen and James so much.

Now it looks like I have fixed the problem about tophat_indexes_color,
because "Tophat for SOLiD" tool is running in my account (still running,
but not finished yet). Here is a summary:

   - The hg19 index files for colorspace have been there, so I don’t need
   to build or download.

/mnt/galaxyIndices/genomes/Hsapiens/hg19/bowtie_color/hg19

   - Change the tool_data_table_conf.xml file, add this:

< 
< value, dbkey, name, path
< 
< 
/mnt/galaxy/galaxy-app/tool_data_table_conf.xml

   - Yes, both Bowtie and Tophat use the same indexes.


   - bowtie_indexes and tophat_indexes use this loc file:

/mnt/galaxyIndices/galaxy/tool-data/bowtie_indices.loc

   - bowtie_indexes_color and tophat_indexes_color use this loc file:

/mnt/galaxyIndices/galaxy/tool-data/bowtie_indices_color.loc

Hope this can help somebody.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


On Wed, Oct 16, 2013 at 3:21 PM, Jennifer Jackson  wrote:

>  Hi Lei,
>
> You can download all at once or in two parts (for slower connections):
>
>
>
> iGenomes has been pretty good about using the exact same build as released
> by the source with no changes for the GTF files, but I do not know about
> the indexes - so do a test run once in place. Just to let you know,
> creating these may be easier than downloading, is just a single line
> command and you have a server to run this on, but the choice is yours.
>
> Jen
> Galaxy team
>
>
>
> On 10/16/13 1:11 PM, Lei Yan wrote:
>
>  Hi James,
>
>  I found this: http://bowtie-bio.sourceforge.net/manual.shtml
> There are some Pre-built indexes in the right side of this page.
> If I just need an hg19 index for colorspace, which index file can work for
> us?
> Thanks again.
>
>
>  Lei Yan
> Center for Integrative and Translational Genomics
> The University of Tennessee Health Science Center
>
>
> On Wed, Oct 16, 2013 at 2:54 PM, Lei Yan  wrote:
>
>>  Hi Jen and James,
>>
>>  Thanks for your info.
>> Yes, we are already running a cloud instance (
>> http://galaxyclass.genenetwork.org/).
>> So if I can build the index for colorspace, then how to configure it?
>> And I didn’t find the “tophat_indexes_color” record in the Admin - “View
>> data tables registry”. Please see attachment.
>>
>>
>>  Lei Yan
>> Center for Integrative and Translational Genomics
>> The University of Tennessee Health Science Center
>>
>>
>>   On Wed, Oct 16, 2013 at 2:35 PM, James Taylor wrote:
>>
>>> They are already running a local instance.
>>>
>>> I didn't realize that bowtie required a different index for colorspace
>>> alignment. So Lei, you will have to build the index using bowtie-build
>>> -C.
>>>
>>> --
>>> James Taylor, Associate Professor, Biology/CS, Emory University
>>>
>>>
>>>  On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson 
>>> wrote:
>>> > Hello Lei,
>>> >
>>> > If genomes are not listed, that means that they are not indexed for
>>> use with
>>> > the tool. The test server is primarily for demonstration or test use
>>> > besides, and there could be other unexpected issues even if genomes are
>>> > listed (we really do test here). Also, the quotas are very small
>>> (10G). If
>>> > you want to use this tool, a local, cloud, or slipstream Galaxy is
>>> > recommended. Full choices with details are listed here:
>>> > http://wiki.galaxyproject.org/BigPicture/Choices
>>> > http://usegalaxy.org/toolshed
>>> >
>>> > Help for setup is here, with the galaxy-...@bx.psu.edu mailing list
>>> > available for further support. Tools will need to be installed, and
>>> indexes
>>> > created. You can rsync the genome, but most genomes will not have loc
>>> file
>>> > entries and indexes for SOLiD already created - see the Tophat manual
>>> for
>>> > the command to create these:
>>> >
>>> http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
>>> > http://wiki.galaxyproject.org/Admin/Data%20Integration
>>> > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
>>> >
>>> > Hopefully this helps!
>>> >
>>> > Jen
>>> > Galaxy team
>>> >
>>> >
>>> > On 10/16/13 11:57 AM, Lei Yan wrote:
>>> >>
>>> >> Hi all,
>>> >>
>>> >> We are trying to use “Tophat for SOLiD”.
>>> >> But this tool (Tophat for SOLiD) does not seem to be linked to the
>>> >> reference genomes that are installed. I can see those genomes on the
>>> Tophat
>>> >> for illumina tool and the other tools that require a reference genome.
>>> >> Please see attachments.
>>> >> Does anybody have any ideas for this? Thanks a lot.
>>> >>
>>> >>
>>> >> Lei Yan
>>> >> Center for Integrative and Translational Genomics
>>> >> The University of Tennessee Health Science Center
>>> >
>>> >
>>> > --
>>> > Jennifer Hillman-Jackson
>>> > http://galaxyproject.org
>>> >
>>>
>>
>>
>
> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
<>___
The

Re: [galaxy-user] Need your helps about Galaxy

[Larry Reiter]

On 10/16/13 5:49 PM, Lei Yan wrote:


Hope this can help somebody.

Me too!  I'll try it ASAP.

LTR

--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page 
Reiter Citation Index 


Tooth Study 
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Re: [galaxy-user] Need your helps about Galaxy

[Jennifer Jackson]

Lei Yan,

I am very glad that this worked out! It looks like you have already 
helped at least one other user and I am sure others to come!


We were discussing this internally while you were working. Updates to 
the ready-loaded data on cloud instances will be getting a make-over in 
the near term (this has been in planning for a while). Ease of data 
install for locals is included in the larger project goals. Technical 
implementation details are being sorted out to ensure the most robust 
solution, but data services that meet our project's three core goals of 
"accessible, reproducible, and transparent" are without question the 
central design criteria for success.


Thank you again! We very much value the patience, tenacity, and time you 
took to not only see this through for yourself, but to post your 
experience & methods back to the list so clearly to share with others. 
Our community, most definitely including you, are so important. We are 
all "Galaxy team" :)


Jen
Galaxy team


Hope this can help somebody.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center



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

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Re: [galaxy-user] Need your helps about Galaxy

[Jennifer Jackson]

Hello Lei,

If genomes are not listed, that means that they are not indexed for use 
with the tool. The test server is primarily for demonstration or test 
use besides, and there could be other unexpected issues even if genomes 
are listed (we really do test here). Also, the quotas are very small 
(10G). If you want to use this tool, a local, cloud, or slipstream 
Galaxy is recommended. Full choices with details are listed here:

http://wiki.galaxyproject.org/BigPicture/Choices
http://usegalaxy.org/toolshed

Help for setup is here, with the galaxy-...@bx.psu.edu mailing list 
available for further support. Tools will need to be installed, and 
indexes created. You can rsync the genome, but most genomes will not 
have loc file entries and indexes for SOLiD already created - see the 
Tophat manual for the command to create these:

http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
http://wiki.galaxyproject.org/Admin/Data%20Integration
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Hopefully this helps!

Jen
Galaxy team

On 10/16/13 11:57 AM, Lei Yan wrote:

Hi all,

We are trying to use “Tophat for SOLiD”.
But this tool (Tophat for SOLiD) does not seem to be linked to the 
reference genomes that are installed. I can see those genomes on the 
Tophat for illumina tool and the other tools that require a reference 
genome. Please see attachments.

Does anybody have any ideas for this? Thanks a lot.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


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

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Re: [galaxy-user] Need your helps about Galaxy

[Lei Yan]

Dear Dannon,

Since the log files are quite large, so I put them onto a server.
Now you can get them from here:
http://tyche.uthsc.edu/ftp/user/leiyan/20131009_galaxylog/

Thanks again.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


On Wed, Oct 9, 2013 at 4:29 PM, Dannon Baker  wrote:

> Ahh, ok, so you're hitting a bug from a previous release, sorry about
> that.  If you're able, updating cloudman itself will fix that (among other
> small issues).
>
> That file is also in /mnt/cm as 'paster.log' if you can SSH in to get it.
>
>
> On Wed, Oct 9, 2013 at 5:18 PM, Lei Yan  wrote:
>
>> Dear Dannon,
>>
>> When I click the four “Log” links for Galaxy, PostgreSQL, SGE, and Galaxy
>> Reports on the Admin Console interface, all of they throw exceptions.
>> Please see attachments.
>> There is another way I can get the log files?
>> Thanks.
>>
>>
>> Lei Yan
>> Center for Integrative and Translational Genomics
>> The University of Tennessee Health Science Center
>>
>>
>> On Wed, Oct 9, 2013 at 4:04 PM, Dannon Baker wrote:
>>
>>> Can you send me the more detailed full cloudman log from the admin
>>> interface (it may be quite large).  This will help me see what may have
>>> happened.
>>>
>>>
>>> On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan  wrote:
>>>
 Hi all,

 I found some very strange problems on our cloud Galaxy (
 http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.

- It shows galaxy and galaxyIndices have errors in CloudMan Admin
Console.
- This Galaxy had 3 nodes before, but right now only one node is
there.
- Galaxy front end still can be opened, but I don’t know it really
works as before or not.

 I attached some screenshot and log files.
 Does anybody have any ideas for this? Thanks a lot.


 Lei Yan
 Center for Integrative and Translational Genomics
 The University of Tennessee Health Science Center

>>>
>>>
>>
>
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Re: [galaxy-user] Need your helps about Galaxy

[Larry Reiter]

If you read the message, you will see that I can upload files as well.  
LOTS OF FILES.  I'm just wondering if the reason you are having CloudMan 
problems is that I have uploaded over 100Gb of data today.


LTR

On 10/9/13 3:05 PM, Lei Yan wrote:
I tried, and I can upload files with URL on 
http://galaxyclass.genenetwork.org/.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


On Wed, Oct 9, 2013 at 2:59 PM, Larry Reiter > wrote:


I've been uploading the .csfasta files and .qual files for my
run.  LOTS of data.  Could that be doing this?

LTR


On 10/9/13 2:56 PM, Lei Yan wrote:

Hi all,

I found some very strange problems on our cloud Galaxy
(http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.

  * It shows galaxy and galaxyIndices have errors in CloudMan
Admin Console.
  * This Galaxy had 3 nodes before, but right now only one node
is there.
  * Galaxy front end still can be opened, but I don’t know it
really works as before or not.

I attached some screenshot and log files.
Does anybody have any ideas for this? Thanks a lot.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center



-- 
Lawrence T. Reiter, Ph.D.

Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635  (Office)
901-448-7440  (FAX)
901-448-7443  (Lab)
e-mail: lrei...@uthsc.edu 

Reiter Faculty Page

Reiter Citation Index

Tooth Study 





--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page 
Reiter Citation Index 


Tooth Study 
___
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Re: [galaxy-user] Need your helps about Galaxy

[Lei Yan]

I don't think this is the reason.

Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


On Wed, Oct 9, 2013 at 3:07 PM, Larry Reiter  wrote:

>  If you read the message, you will see that I can upload files as well.
> LOTS OF FILES.  I'm just wondering if the reason you are having CloudMan
> problems is that I have uploaded over 100Gb of data today.
>
> LTR
>
>
> On 10/9/13 3:05 PM, Lei Yan wrote:
>
> I tried, and I can upload files with URL on
> http://galaxyclass.genenetwork.org/.
>
>  Lei Yan
> Center for Integrative and Translational Genomics
> The University of Tennessee Health Science Center
>
>
> On Wed, Oct 9, 2013 at 2:59 PM, Larry Reiter  wrote:
>
>>  I've been uploading the .csfasta files and .qual files for my run.
>> LOTS of data.  Could that be doing this?
>>
>> LTR
>>
>>
>> On 10/9/13 2:56 PM, Lei Yan wrote:
>>
>>  Hi all,
>>
>>  I found some very strange problems on our cloud Galaxy (
>> http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.
>>
>>- It shows galaxy and galaxyIndices have errors in CloudMan Admin
>>Console.
>> - This Galaxy had 3 nodes before, but right now only one node is
>>there.
>> - Galaxy front end still can be opened, but I don’t know it really
>>works as before or not.
>>
>>  I attached some screenshot and log files.
>> Does anybody have any ideas for this? Thanks a lot.
>>
>>
>>  Lei Yan
>> Center for Integrative and Translational Genomics
>> The University of Tennessee Health Science Center
>>
>>
>>
>>  --
>> Lawrence T. Reiter, Ph.D.
>> Associate Professor, Department of Neurology
>> 855 Monroe Ave., Link 415
>> Memphis, TN 38163
>>
>> 901-448-2635 (Office)
>> 901-448-7440 (FAX)
>> 901-448-7443 (Lab)
>> e-mail: lrei...@uthsc.edu
>>
>> Reiter Faculty Page
>> Reiter Citation 
>> Index
>> Tooth Study 
>>
>
>
>
> --
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
>
> 901-448-2635 (Office)
> 901-448-7440 (FAX)
> 901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
>
> Reiter Faculty Page
> Reiter Citation 
> Index
> Tooth Study 
>
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Re: [galaxy-user] Need your helps about Galaxy

[Larry Reiter]

I've been uploading the .csfasta files and .qual files for my run.  LOTS 
of data.  Could that be doing this?


LTR

On 10/9/13 2:56 PM, Lei Yan wrote:

Hi all,

I found some very strange problems on our cloud Galaxy 
(http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.


  * It shows galaxy and galaxyIndices have errors in CloudMan Admin
Console.
  * This Galaxy had 3 nodes before, but right now only one node is there.
  * Galaxy front end still can be opened, but I don't know it really
works as before or not.

I attached some screenshot and log files.
Does anybody have any ideas for this? Thanks a lot.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center



--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page 
Reiter Citation Index 


Tooth Study 
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Re: [galaxy-user] Need your helps about Galaxy

[Lei Yan]

I tried, and I can upload files with URL on
http://galaxyclass.genenetwork.org/.

Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


On Wed, Oct 9, 2013 at 2:59 PM, Larry Reiter  wrote:

>  I've been uploading the .csfasta files and .qual files for my run.  LOTS
> of data.  Could that be doing this?
>
> LTR
>
>
> On 10/9/13 2:56 PM, Lei Yan wrote:
>
>  Hi all,
>
>  I found some very strange problems on our cloud Galaxy (
> http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.
>
>- It shows galaxy and galaxyIndices have errors in CloudMan Admin
>Console.
> - This Galaxy had 3 nodes before, but right now only one node is
>there.
> - Galaxy front end still can be opened, but I don’t know it really
>works as before or not.
>
>  I attached some screenshot and log files.
> Does anybody have any ideas for this? Thanks a lot.
>
>
>  Lei Yan
> Center for Integrative and Translational Genomics
> The University of Tennessee Health Science Center
>
>
>
> --
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
>
> 901-448-2635 (Office)
> 901-448-7440 (FAX)
> 901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
>
> Reiter Faculty Page
> Reiter Citation 
> Index
> Tooth Study 
>
___
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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Ahh, ok, so you're hitting a bug from a previous release, sorry about that.
 If you're able, updating cloudman itself will fix that (among other small
issues).

That file is also in /mnt/cm as 'paster.log' if you can SSH in to get it.


On Wed, Oct 9, 2013 at 5:18 PM, Lei Yan  wrote:

> Dear Dannon,
>
> When I click the four “Log” links for Galaxy, PostgreSQL, SGE, and Galaxy
> Reports on the Admin Console interface, all of they throw exceptions.
> Please see attachments.
> There is another way I can get the log files?
> Thanks.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> The University of Tennessee Health Science Center
>
>
> On Wed, Oct 9, 2013 at 4:04 PM, Dannon Baker wrote:
>
>> Can you send me the more detailed full cloudman log from the admin
>> interface (it may be quite large).  This will help me see what may have
>> happened.
>>
>>
>> On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan  wrote:
>>
>>> Hi all,
>>>
>>> I found some very strange problems on our cloud Galaxy (
>>> http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.
>>>
>>>- It shows galaxy and galaxyIndices have errors in CloudMan Admin
>>>Console.
>>>- This Galaxy had 3 nodes before, but right now only one node is
>>>there.
>>>- Galaxy front end still can be opened, but I don’t know it really
>>>works as before or not.
>>>
>>> I attached some screenshot and log files.
>>> Does anybody have any ideas for this? Thanks a lot.
>>>
>>>
>>> Lei Yan
>>> Center for Integrative and Translational Genomics
>>> The University of Tennessee Health Science Center
>>>
>>
>>
>
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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Can you send me the more detailed full cloudman log from the admin
interface (it may be quite large).  This will help me see what may have
happened.


On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan  wrote:

> Hi all,
>
> I found some very strange problems on our cloud Galaxy (
> http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.
>
>- It shows galaxy and galaxyIndices have errors in CloudMan Admin
>Console.
>- This Galaxy had 3 nodes before, but right now only one node is there.
>- Galaxy front end still can be opened, but I don’t know it really
>works as before or not.
>
> I attached some screenshot and log files.
> Does anybody have any ideas for this? Thanks a lot.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> The University of Tennessee Health Science Center
>
___
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Re: [galaxy-user] Need your helps about Galaxy

[Lei Yan]

Hi all,

Larry got another problem on our cloud Galaxy (
http://galaxyclass.genenetwork.org/).
He cannot execute some commands successfully:
/opt/sge/default/spool/execd/ip-10-184-11-27/job_scripts/152: line 13:
wigToBigWig: command not found
/opt/sge/default/spool/execd/ip-10-152-136-219/job_scripts/72: line 13:
bedtools: command not found
/opt/sge/default/spool/execd/ip-10-152-136-219/job_scripts/72: line 13:
bedGraphToBigWig: command not found

I tried to fix it, but still no ideas so far. I checked something on the
master and on all the nodes, everything looks right for me. Please see an
attached file.

Does anybody have any ideas for this? Thanks a lot.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center
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Re: [galaxy-user] Need your helps about Galaxy

[Lei Yan]

Hi all,

I think I have fixed this bug, and Galaxy GUI can execute MACS successfully
on my cloud Galaxy.
I did the following changes to fix it:

   - It looks like the latest version of cloud Galaxy uses MACS 1.3, so I
   changed the default:

default -> /mnt/galaxy/tools/macs/1.3.7.1/

   - There are two path mistakes in the MACS environment variable file
   (/mnt/galaxy/tools/macs/1.3.7.1/env.sh), and "galaxyTools" should be
   "galaxy":

< PATH=/mnt/galaxy/tools/macs/1.3.7.1/bin:$PATH
< PYTHONPATH=/mnt/galaxy/tools/macs/
1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
> PATH=/mnt/galaxyTools/tools/macs/1.3.7.1/bin:$PATH
> PYTHONPATH=/mnt/galaxyTools/tools/macs/
1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH


Maybe this can help somebody.


Lei Yan
Center for Integrative and Translational Genomics
UTHSC


On Tue, Sep 24, 2013 at 2:55 PM, Lei Yan  wrote:

> Hi all,
>
> http://galaxyclass.genenetwork.org/
> This cloud Galaxy was built by Cloud Galaxy Launch (
> https://main.g2.bx.psu.edu/cloudlaunch) yesterday.
> I found two problems about MACS on it:
>
>- When I execute MACS on Galaxy GUI, I got a “not found” error. Please
>see attachment (error1.png).
>- If I login the Galaxy server by ssh, I found it looks like MACS was
>already installed on it, please see attachment (error2.png). But if I run
>MACS in a terminal, I got another error. Please see attachment 
> (error3.png).
>
> Anybody has any idea for this? Thanks a lot.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> UTHSC
>
>
> On Tue, Sep 24, 2013 at 2:24 PM, Jennifer Jackson  wrote:
>
>>  Hi Lawrence,
>>
>> What version of MACS are you running? The Galaxy wrapper in galaxy-dist
>> supports v1.3. I am 99% certain that the latest Cloudman image is the same,
>> but Dannon can correct me. The two Tool Shed repos for MACS support v1.4
>> and v2.0.10. Making sure that the wrapper & binary are a match might be the
>> first place to check - these can get easily confused, especially when
>> binaries install with un-versioned symbolic links by default.
>>
>> If you are re-running a workflow/job that came from the public Main
>> server, and running galaxy-dist/central, then you want to use the v1.3
>> binary, unless purposefully upgrading both wrapper & binary. The workflow
>> reproducibility tracking will alert you about a change in tool versions and
>> permit you to select updated tools upon execution (once tool is configured)
>> if from the *same exact wrapper/tool*, but not if a *different
>> wrapper/tool/repo* - so will likely take a workflow edit to change out
>> the tool in this case if upgrading to newer MACS version.
>>
>> I noticed that the tool form README link for the MACS v2.0.10 wrapper is
>> incorrect, copy link & add an ".rst" to find doc. Fairly certain these are
>> expected to be ".txt" - I'll ask our team if this is a Tool Shed or repo
>> input issue if extension different.
>>
>> Full help for installing tools from the Tool Shed is here:
>>
>> http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
>>
>> And current wrapper/binary versions in galaxy-dist/central are listed
>> here:
>> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
>> With help for managing those dependencies here:
>> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>>
>> Hopefully this helps,
>>
>> Jen
>> Galaxy team
>>
>>
>> On 9/24/13 9:41 AM, Reiter, Larry T wrote:
>>
>> Thanks, James. I worked it out by downloading my data files and workflow. 
>> For some reason MACS still doesn't work. Any ideas?
>>
>> Lawrence T Reiter, PhD
>> UTHSC, Memphis, TN
>>
>>
>>  --
>> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>>
>>
>
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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Sorry for not being able to take a look at this sooner, thanks for figuring
it out and posting back!  This one must have fallen through the cracks when
we updated all the paths with the last Cloudman release, I'll make a note
to fix it with our next minor update.

-Dannon


On Thu, Sep 26, 2013 at 12:05 PM, Lei Yan  wrote:

> Hi all,
>
> I think I have fixed this bug, and Galaxy GUI can execute MACS
> successfully on my cloud Galaxy.
> I did the following changes to fix it:
>
>- It looks like the latest version of cloud Galaxy uses MACS 1.3, so I
>changed the default:
>
> default -> /mnt/galaxy/tools/macs/1.3.7.1/
>
>- There are two path mistakes in the MACS environment variable file
>(/mnt/galaxy/tools/macs/1.3.7.1/env.sh), and "galaxyTools" should be
>"galaxy":
>
> < PATH=/mnt/galaxy/tools/macs/1.3.7.1/bin:$PATH
> < PYTHONPATH=/mnt/galaxy/tools/macs/
> 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
> > PATH=/mnt/galaxyTools/tools/macs/1.3.7.1/bin:$PATH
> > PYTHONPATH=/mnt/galaxyTools/tools/macs/
> 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
>
>
> Maybe this can help somebody.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> UTHSC
>
>
> On Tue, Sep 24, 2013 at 2:55 PM, Lei Yan  wrote:
>
>> Hi all,
>>
>> http://galaxyclass.genenetwork.org/
>> This cloud Galaxy was built by Cloud Galaxy Launch (
>> https://main.g2.bx.psu.edu/cloudlaunch) yesterday.
>> I found two problems about MACS on it:
>>
>>- When I execute MACS on Galaxy GUI, I got a “not found” error.
>>Please see attachment (error1.png).
>>- If I login the Galaxy server by ssh, I found it looks like MACS was
>>already installed on it, please see attachment (error2.png). But if I run
>>MACS in a terminal, I got another error. Please see attachment 
>> (error3.png).
>>
>> Anybody has any idea for this? Thanks a lot.
>>
>>
>> Lei Yan
>> Center for Integrative and Translational Genomics
>> UTHSC
>>
>>
>> On Tue, Sep 24, 2013 at 2:24 PM, Jennifer Jackson  wrote:
>>
>>>  Hi Lawrence,
>>>
>>> What version of MACS are you running? The Galaxy wrapper in galaxy-dist
>>> supports v1.3. I am 99% certain that the latest Cloudman image is the same,
>>> but Dannon can correct me. The two Tool Shed repos for MACS support v1.4
>>> and v2.0.10. Making sure that the wrapper & binary are a match might be the
>>> first place to check - these can get easily confused, especially when
>>> binaries install with un-versioned symbolic links by default.
>>>
>>> If you are re-running a workflow/job that came from the public Main
>>> server, and running galaxy-dist/central, then you want to use the v1.3
>>> binary, unless purposefully upgrading both wrapper & binary. The workflow
>>> reproducibility tracking will alert you about a change in tool versions and
>>> permit you to select updated tools upon execution (once tool is configured)
>>> if from the *same exact wrapper/tool*, but not if a *different
>>> wrapper/tool/repo* - so will likely take a workflow edit to change out
>>> the tool in this case if upgrading to newer MACS version.
>>>
>>> I noticed that the tool form README link for the MACS v2.0.10 wrapper is
>>> incorrect, copy link & add an ".rst" to find doc. Fairly certain these are
>>> expected to be ".txt" - I'll ask our team if this is a Tool Shed or repo
>>> input issue if extension different.
>>>
>>> Full help for installing tools from the Tool Shed is here:
>>>
>>> http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
>>>
>>> And current wrapper/binary versions in galaxy-dist/central are listed
>>> here:
>>> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
>>> With help for managing those dependencies here:
>>> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>>>
>>> Hopefully this helps,
>>>
>>> Jen
>>> Galaxy team
>>>
>>>
>>> On 9/24/13 9:41 AM, Reiter, Larry T wrote:
>>>
>>> Thanks, James. I worked it out by downloading my data files and workflow. 
>>> For some reason MACS still doesn't work. Any ideas?
>>>
>>> Lawrence T Reiter, PhD
>>> UTHSC, Memphis, TN
>>>
>>>
>>>  --
>>> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>>>
>>>
>>
>
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Re: [galaxy-user] Need your helps about Galaxy

[Jennifer Jackson]

Hi Lawrence,

What version of MACS are you running? The Galaxy wrapper in galaxy-dist 
supports v1.3. I am 99% certain that the latest Cloudman image is the 
same, but Dannon can correct me. The two Tool Shed repos for MACS 
support v1.4 and v2.0.10. Making sure that the wrapper & binary are a 
match might be the first place to check - these can get easily confused, 
especially when binaries install with un-versioned symbolic links by 
default.


If you are re-running a workflow/job that came from the public Main 
server, and running galaxy-dist/central, then you want to use the v1.3 
binary, unless purposefully upgrading both wrapper & binary. The 
workflow reproducibility tracking will alert you about a change in tool 
versions and permit you to select updated tools upon execution (once 
tool is configured) if from the /same exact wrapper/tool/, but not if a 
/different wrapper/tool/repo/ - so will likely take a workflow edit to 
change out the tool in this case if upgrading to newer MACS version.


I noticed that the tool form README link for the MACS v2.0.10 wrapper is 
incorrect, copy link & add an ".rst" to find doc. Fairly certain these 
are expected to be ".txt" - I'll ask our team if this is a Tool Shed or 
repo input issue if extension different.


Full help for installing tools from the Tool Shed is here:
http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance

And current wrapper/binary versions in galaxy-dist/central are listed here:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
With help for managing those dependencies here:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

Hopefully this helps,

Jen
Galaxy team

On 9/24/13 9:41 AM, Reiter, Larry T wrote:

Thanks, James. I worked it out by downloading my data files and workflow. For 
some reason MACS still doesn't work. Any ideas?

Lawrence T Reiter, PhD
UTHSC, Memphis, TN


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

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Re: [galaxy-user] Need your helps about Galaxy

[Reiter, Larry T]

Thanks, James. I worked it out by downloading my data files and workflow. For 
some reason MACS still doesn't work. Any ideas?

Lawrence T Reiter, PhD
UTHSC, Memphis, TN

On Sep 24, 2013, at 11:32 AM, "James Taylor"  wrote:

> As I said before, there is no easy way to do this. You just need to
> dump the old database and load into the new database. I would suggest
> making a copy of the old database with a current version of Galaxy.
> The migration scripts will then bring it up to date so you will have
> identical schemas. You should then be able to dump and load easily
> enough, you will just need to move the dump file between servers.
> 
> --
> James Taylor, Associate Professor, Biology/CS, Emory University
> 
> 
> On Mon, Sep 23, 2013 at 3:36 PM, Lei Yan  wrote:
>> Dear Dannon,
>> 
>> I built a new cloud Galaxy instance today.
>> Would you please tell me how to transfer given accounts from an old Galaxy
>> to this new one?
>> This is old Galaxy: http://galaxylocal.genenetwork.org:8080/
>> This is new Galaxy: http://galaxyclass.genenetwork.org/
>> Thanks a lot.
>> 
>> 
>> Lei Yan
>> Center for Integrative and Translational Genomics
>> UTHSC
>> 
>> ___
>> 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/
>> 
>> To search Galaxy mailing lists use the unified search at:
>> 
>>  http://galaxyproject.org/search/mailinglists/

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Re: [galaxy-user] Need your helps about Galaxy

[James Taylor]

As I said before, there is no easy way to do this. You just need to
dump the old database and load into the new database. I would suggest
making a copy of the old database with a current version of Galaxy.
The migration scripts will then bring it up to date so you will have
identical schemas. You should then be able to dump and load easily
enough, you will just need to move the dump file between servers.

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


On Mon, Sep 23, 2013 at 3:36 PM, Lei Yan  wrote:
> Dear Dannon,
>
> I built a new cloud Galaxy instance today.
> Would you please tell me how to transfer given accounts from an old Galaxy
> to this new one?
> This is old Galaxy: http://galaxylocal.genenetwork.org:8080/
> This is new Galaxy: http://galaxyclass.genenetwork.org/
> Thanks a lot.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> UTHSC
>
> ___
> 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/
>
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>
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[galaxy-user] Need your helps about Galaxy

[Lei Yan]

Dear Dannon,

I built a new cloud Galaxy instance today.
Would you please tell me how to transfer given accounts from an old Galaxy
to this new one?
This is old Galaxy: http://galaxylocal.genenetwork.org:8080/
This is new Galaxy: http://galaxyclass.genenetwork.org/
Thanks a lot.


Lei Yan
Center for Integrative and Translational Genomics
UTHSC
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