Need Your Helps About Galaxy

Question: Need Your Helps About Galaxy

5.2 years ago by

Lei Yan • 130

Lei Yan • 130 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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modified 5.1 years ago • written 5.2 years ago by Lei Yan • 130

5.2 years ago by

James Taylor ♦ 470

United States

James Taylor ♦ 470 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

ADD COMMENT • link written 5.2 years ago by James Taylor ♦ 470

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

ADD REPLY • link written 5.2 years ago by Larry Reiter • 100

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

ADD REPLY • link written 5.2 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 5.2 years ago by Lei Yan • 130

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 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH Maybe this can help somebody. Lei Yan Center for Integrative and Translational Genomics UTHSC

ADD REPLY • link written 5.2 years ago by Lei Yan • 130

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

ADD REPLY • link written 5.2 years ago by Lei Yan • 130

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 dont 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

ADD REPLY • link written 5.1 years ago by Lei Yan • 130

I've been uploading the .csfasta files and .qual files for my run. LOTS of data. Could that be doing this? 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: lreiter@uthsc.edu Reiter Faculty Page <http: www.uthsc.edu="" neuroscience="" faculty="" l_reiter.php=""> Reiter Citation Index <http: scholar.google.com="" citations?user="-kaQJ14AAAAJ&hl=en"> Tooth Study <http: tinyurl.com="" 88f688l="">

ADD REPLY • link written 5.1 years ago by Larry Reiter • 100

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

ADD REPLY • link written 5.1 years ago by Lei Yan • 130

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 -- 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 Page <http: www.uthsc.edu="" neuroscience="" faculty="" l_reiter.php=""> Reiter Citation Index <http: scholar.google.com="" citations?user="-kaQJ14AAAAJ&hl=en"> Tooth Study <http: tinyurl.com="" 88f688l="">

ADD REPLY • link written 5.1 years ago by Larry Reiter • 100

I don't think this is the reason. Lei Yan Center for Integrative and Translational Genomics The University of Tennessee Health Science Center

ADD REPLY • link written 5.1 years ago by Lei Yan • 130

5.2 years ago by

Dannon Baker • 270

United States

Dannon Baker • 270 wrote:

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

ADD COMMENT • link written 5.2 years ago by Dannon Baker • 270

5.1 years ago by

Dannon Baker • 270

United States

Dannon Baker • 270 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.

ADD COMMENT • link written 5.1 years ago by Dannon Baker • 270

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

ADD REPLY • link written 5.1 years ago by Lei Yan • 130

5.1 years ago by

Dannon Baker • 270

United States

Dannon Baker • 270 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.

ADD COMMENT • link written 5.1 years ago by Dannon Baker • 270

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

ADD REPLY • link written 5.1 years ago by Lei Yan • 130

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

ADD REPLY • link written 5.1 years ago by Lei Yan • 130

5.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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-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_an d_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 -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.1 years ago by Jennifer Hillman Jackson ♦ 25k

5.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

ADD COMMENT • link written 5.1 years ago by Jennifer Hillman Jackson ♦ 25k

5.1 years ago by

Lei Yan • 130

Lei Yan • 130 wrote:

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 dont need to build or download. /mnt/galaxyIndices/genomes/Hsapiens/hg19/bowtie_color/hg19 - Change the tool_data_table_conf.xml file, add this: < < <columns>value, dbkey, name, path</columns> < <file path="/mnt/galaxyIndices/galaxy/tool-data/bowtie_indices_color.loc"/> <

/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

ADD COMMENT • link written 5.1 years ago by Lei Yan • 130

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: lreiter@uthsc.edu Reiter Faculty Page <http: www.uthsc.edu="" neuroscience="" faculty="" l_reiter.php=""> Reiter Citation Index <http: scholar.google.com="" citations?user="-kaQJ14AAAAJ&hl=en"> Tooth Study <http: tinyurl.com="" 88f688l="">

ADD REPLY • link written 5.1 years ago by Larry Reiter • 100

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