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" james@jamestaylor.org 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 leiyan2000@gmail.com 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

---

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

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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 jen@bx.psu.edu 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_unin...

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

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 leiyan2000@gmail.com 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 leiyan2000@gmail.com 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 jen@bx.psu.edu 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_unin...

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

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

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 lreiter@uthsc.edu 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: lreiter@uthsc.edu

Reiter Faculty Pagehttp://www.uthsc.edu/neuroscience/faculty/L_Reiter.php Reiter Citation Indexhttp://scholar.google.com/citations?user=-kaQJ14AAAAJ&hl=en Tooth Study http://tinyurl.com/88f688l

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 lreiter@uthsc.edu 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 lreiter@uthsc.edu 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: lreiter@uthsc.edu

Reiter Faculty Pagehttp://www.uthsc.edu/neuroscience/faculty/L_Reiter.php Reiter Citation Indexhttp://scholar.google.com/citations?user=-kaQJ14AAAAJ&hl=en Tooth Study http://tinyurl.com/88f688l

-- 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: lreiter@uthsc.edu

Reiter Faculty Pagehttp://www.uthsc.edu/neuroscience/faculty/L_Reiter.php Reiter Citation Indexhttp://scholar.google.com/citations?user=-kaQJ14AAAAJ&hl=en Tooth Study http://tinyurl.com/88f688l

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 dannon.baker@gmail.com 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 leiyan2000@gmail.com 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

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 dannon.baker@gmail.com 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 leiyan2000@gmail.com 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 dannon.baker@gmail.comwrote:

...

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 leiyan2000@gmail.com 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

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-dev@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_unin... 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