Re: [galaxy-dev] Several jobs stalled in the queue: Job runner assigned but no external ID recorded

Hi guys, My list of the stalled jobs is getting longer and longer. Is there a fix of this? Cheers, Derrick On Sat, Jun 15, 2013 at 3:36 PM, Derrick Lin wrote: > Hi guys, > > I have several jobs have been stuck in the queue for long time, I checked > the handler log and found t

[galaxy-dev] Several jobs stalled in the queue: Job runner assigned but no external ID recorded

Hi guys, I have several jobs have been stuck in the queue for long time, I checked the handler log and found the following message: Job runner assigned but no external ID recorded, adding to the job handler queue Is there a way that I can clean these orphan jobs out of the queue? Cheers, Derric

Re: [galaxy-dev] Error when upgrading the database to version 110

char long. Any one can confirm if the Galaxy will be OK without these indexes? Or it effectively means no MySQL support in the new Galaxy release? Regards, Derrick On Mon, Mar 4, 2013 at 10:13 AM, Derrick Lin wrote: > HI Hans, > > Yours happened when upgrading from 108 - 109 (which

Re: [galaxy-dev] Error when upgrading the database to version 110

26 14:04:55,821 > Creating repository_repository_**dependency_association table failed: > (OperationalError) (1050, "Table > 'repository_repository_**dependency_association' > already exists") u'\nCREATE TABLE > repository_repository_**dependency_associati

[galaxy-dev] Error when upgrading the database to version 110

Hi guys, I was given the following error when upgrading the database from 109 to 110: 0109_add_repository_dependency_tables DEBUG 2013-03-01 15:14:15,554 Creating repository_repository_dependency_association table failed: (OperationalError) (1059, "Identifier name 'ix_repository_repository_depend

Re: [galaxy-dev] Merge internal head to release_2012.02.08

local changes when executed with the '-C' > > option, otherwise it'll try to merge. > > > > If you're concerned about persisting local changes, it's probably a > > good idea to go ahead and commit them to your local repository or at > > least create

[galaxy-dev] Merge internal head to release_2012.02.08

Hi guys, We have checked in few internal changesets to our galaxy. Normally we did hg pull then hg merge for upgrading. With the 8 Feb release, it advice that we must do hg update release_2013.02.08 if we want to upgrade from stable branch. My understanding for hg update is, it will overwrite al

Re: [galaxy-dev] changing datasets file_path storage location

ssues from this. At the time Nate just advised > not to have any jobs running at the time (and stop Galaxy of > course). > http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-February/008383.html > > Peter > > > On Thursday, February 14, 2013, Derrick Lin wrote: > >>

Re: [galaxy-dev] changing datasets file_path storage location

Hi Shantanu, We are facing the same situation that migrating galaxy dataset to a new location is needed. I am wondering if you have done it successfully? Would be nice if you can share your experience with us. Cheers, D On Fri, Nov 30, 2012 at 9:21 AM, Shantanu Pavgi (Campus) wrote: > > We are

Re: [galaxy-dev] Job handler : crash

Hi, I had the similar issue a while ago, and it's fixed in https://bitbucket.org/galaxy/galaxy-central/commits/c015b82b3944f967e2c859d5552c00e3e38a2da0 Hope this help D On Wed, Jan 30, 2013 at 9:39 AM, Christophe Caron < christophe.ca...@sb-roscoff.fr> wrote: > Hello, > > We run Galaxy (2013 J

Re: [galaxy-dev] Job handler keeps crashing

: > > > >> I have seen this same issue exactly. Python just dies without any > errors in the log. Using the latest galaxy-dist > >> > >> Sent from my iPhone > >> > >> On Jan 20, 2013, at 8:35 PM, Derrick Lin wrote: > >> > >>>

Re: [galaxy-dev] Job handler keeps crashing

xy-dist > > > > Sent from my iPhone > > > > On Jan 20, 2013, at 8:35 PM, Derrick Lin wrote: > > > >> Update to the 11 Jan 2013 dist does not help with this issue. :( > >> > >> I checked the database and have the look at the job entrie

Re: [galaxy-dev] deleted_new kills handlers

Hi Ido, I just found you post, and I think we are having the similar issue as your. (I posted it in the mailing yesterday, you can find it for the detail of my problem). I am wondering if you are able to fix your problem? Cheers, Derrick On Tue, Dec 11, 2012 at 12:13 AM, Ido Tamir wrote: >

Re: [galaxy-dev] Job handler keeps crashing

t;deleted". I think if I manually change the job state from "deleted_new" to "deleted" in the db, the handler0 will become fine. I am just concerned about how these jobs were created (like assigned to a handler but marked as "deleted_new"). Cheers, D On Mon, Jan 21, 2

Re: [galaxy-dev] Job handler keeps crashing

e. D On Fri, Jan 18, 2013 at 4:03 PM, Derrick Lin wrote: > Hi guys, > > We have updated our galaxy to 20 Dec 2012 release. Recently we found that > some submitted jobs could not start (stay gray forever). > > We found that it was caused by the job manager sent jobs to a handler

[galaxy-dev] Job handler keeps crashing

Hi guys, We have updated our galaxy to 20 Dec 2012 release. Recently we found that some submitted jobs could not start (stay gray forever). We found that it was caused by the job manager sent jobs to a handler (handler0) whose python process crashed and died. >From the handler log we found the l

Re: [galaxy-dev] How to make toolshed tool to create dummy env.sh

Hi Greg, I am wondering the similar thing. If I understand Kevin's post correctly, I think the question really is: if the automated tools build is the requirement for creating the shed tool version specific env.sh automatically during the shed tool installation. Take BWA on the Tool Shed as an ex

Re: [galaxy-dev] A new tool_data_table_conf.xml created under tool-data directory

Fantastic! Thanks for all the details Greg. Cheers, Derrick On Fri, Nov 9, 2012 at 10:55 PM, Greg Von Kuster wrote: > Hi Derrick, > > On Nov 9, 2012, at 12:56 AM, Derrick Lin wrote: > > For issue 1), so I think it's safe to remove the > tool-data/tool_data_table

Re: [galaxy-dev] A new tool_data_table_conf.xml created under tool-data directory

ately both of these fixes have not made it into the Galaxy release > that is currently planned for this week, so they will be available in the > release currently scheduled for 2 weeks from now. > > Thanks very much for reporting both of these issues, and sorry for the > inconvenience th

Re: [galaxy-dev] A new tool_data_table_conf.xml created under tool-data directory

nately both of these fixes have not made it into the Galaxy release > that is currently planned for this week, so they will be available in the > release currently scheduled for 2 weeks from now. > > Thanks very much for reporting both of these issues, and sorry for the > inconvenience t

Re: [galaxy-dev] A new tool_data_table_conf.xml created under tool-data directory

8, 2012 at 10:20 AM, Derrick Lin wrote: > Hi guys, > > After installing the BWA from the Tools Shed, I find there is a > new tool_data_table_conf.xml got created under tool-data directory. The > file contains the entries of BWA's loc files. > > I believe the installed BW

[galaxy-dev] A new tool_data_table_conf.xml created under tool-data directory

Hi guys, After installing the BWA from the Tools Shed, I find there is a new tool_data_table_conf.xml got created under tool-data directory. The file contains the entries of BWA's loc files. I believe the installed BWA still relies on the tool_data_table_conf.xml under galaxy root dir. Anyone can

Re: [galaxy-dev] download dataset from the proxy-ed Galaxy failed with broken link

On Tue, Oct 30, 2012 at 4:03 PM, Ross wrote: > Doesn't make sense that you can wget directly from the paste process > if you have security properly configured! > That's what you can do with the main Galaxy site. Not sure if that's intentional though. You can try wget --no-check-certificate http

Re: [galaxy-dev] download dataset from the proxy-ed Galaxy failed with broken link

2012 at 3:32 PM, Ross wrote: > That url requires a login from here - have you tried supplying it - eg > curl -i -u > > On Tue, Oct 30, 2012 at 3:27 PM, Derrick Lin wrote: > > If I downloaded with curl -i, the page it returned was: > > > > pwbcad@gamma01:tmp$ cur

Re: [galaxy-dev] download dataset from the proxy-ed Galaxy failed with broken link

nked Found Found The resource was found at /root?dataset_id=dc097fa4e7ad53f6&filename=None; you should be redirected automatically. WSGI Server Don't know why the apache returned 302 only when access via wget or curl. Derrick On Sat, Oct 27, 2012 at 7:44 AM, Derri

[galaxy-dev] Apache static contents compression caused corrupted history export tar.gz file

Hi guys, Just found that history export file created on our galaxy always corrupted. We spotted that enabling the Apache Compression (on Galaxy wiki) is the cause. SetOutputFilter DEFLATESetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-varySetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)

[galaxy-dev] download dataset from the proxy-ed Galaxy failed with broken link

Hi guys, On our Galaxy is proxy-ed via Apache according to the wiki guide, the normal download dataset via browser is working fine. However, when I tried download from command line via wget or curl -O (I copied the dataset URL by right clicking the floppy disk icon). And here is the wget output:

Re: [galaxy-dev] The migrated BWA installed but missing dependencies

at 2:43 PM, Derrick Lin wrote: > Thanks Greg, > > Indeed, I tried to be smart and removed the entries from tool conf xml > before running the script. :) > > About the missing dependencies, I still couldn't make it happy. I have > added: > > $GALAXY_ROOT/tool_depende

Re: [galaxy-dev] The migrated BWA installed but missing dependencies

this approach will work fine. > > Greg Von Kuster > > On Oct 8, 2012, at 11:44 PM, Derrick Lin wrote: > > Can I actually just skip executing the migration script, and just install > BWA from the tool shed like I did for other shed tools?? Should be fine I > guess? >

Re: [galaxy-dev] The migrated BWA installed but missing dependencies

Can I actually just skip executing the migration script, and just install BWA from the tool shed like I did for other shed tools?? Should be fine I guess? Derrick On Tue, Oct 9, 2012 at 11:49 AM, Derrick Lin wrote: > Hi Greg, > > I did another test on a fresh installed galaxy Oct 5 r

Re: [galaxy-dev] The migrated BWA installed but missing dependencies

edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2 > "> > toolshed.g2.bx.psu.edu > bwa_wrappers > devteam > > ffa8aaa14f7c > > toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2 > > 1.0.

[galaxy-dev] The migrated BWA installed but missing dependencies

Hi guys, I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via the migration script. However, I couldn't find any entry has been added in migrated_tools_conf.xml (thus the BWA tools are not display in the tool panel). I check in the admin "Installed tool shed repositories" sec

Re: [galaxy-dev] migrated BWA installed but missing dependencies

Hi Bjorn, I saw that printed message but I decided not to append install_dependencies flag to the command because we have had BWA binary in the galaxy running environment. I don't think the use of install_dependencies is compulsory? Derrick On Mon, Oct 8, 2012 at 5:14 PM, Björn Grüning < bjoern

[galaxy-dev] migrated BWA installed but missing dependencies

Hi guys, I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via the migration script. However, I couldn't find any entry has been added in migrated_tools_conf.xml (thus the BWA tools are not display in the tool panel). I check in the admin "Installed tool shed repositories" sec

Re: [galaxy-dev] Galaxy workflow editor cannot be loaded due to some JS files received 404 not found

Hi Jeremy, We found the cause, there are some corrupted file under database/compiled_templates, we clean up that folder and allow Galaxy to recompile everything. Now it's working. Cheers, Derrick On Wed, Oct 3, 2012 at 11:33 AM, Jeremy Goecks wrote: > > We are using Sep 7 release of galaxy-dis

[galaxy-dev] Galaxy workflow editor cannot be loaded due to some JS files received 404 not found

Hi guys, We just discovered this issue on our new production galaxy. When trying to open the workflow editor, the page just stuck in the loading bar. I opened the JavaScript debug console of the web browser, I found; GET http://pwbcglxprod:8081/galaxy/static/scripts/jquery.js?v=1348871183404 (Not

Re: [galaxy-dev] Galaxy workflow editor cannot be loaded due to some JS files received 404 not found

with either galaxy-dist or galaxy-central. > > Thanks, > J. > > On Oct 2, 2012, at 1:45 AM, Derrick Lin wrote: > > Hi guys, > > We just discovered this issue on our new production galaxy. When trying to > open the workflow editor, the page just stuck in the loading bar. I

[galaxy-dev] Galaxy workflow editor cannot be loaded due to some JS files received 404 not found

Hi guys, We just discovered this issue on our new production galaxy. When trying to open the workflow editor, the page just stuck in the loading bar. I opened the JavaScript debug console of the web browser, I found; GET http://pwbcglxprod:8081/galaxy/static/scripts/jquery.js?v=1348871183404 (Not

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

ng > galaxy-dist/scripts/cleanup_datasets/pgcleanup.py > > --nate > > On Sep 13, 2012, at 11:55 PM, Derrick Lin wrote: > > > Thanks Jeremy, > > > > I am sure it's trivial for us to do a manual clean up > > > > Cheers, > > D > > > > On

Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

replace the path. Regards, Derrick On Thu, Sep 13, 2012 at 10:43 PM, Nate Coraor wrote: > On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote: > > > Hi guys, > > > > Just a quick question about the total size of the genome indexes just > made available via rsync server? >

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

history > export files soon. > > Best, > J. > > On Sep 13, 2012, at 10:37 PM, Derrick Lin wrote: > > > hi guys, > > > > I have been trying to clean up some old histories and datasets on our > local galaxy. I have spotted one very old dataset file with big s

[galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

hi guys, I have been trying to clean up some old histories and datasets on our local galaxy. I have spotted one very old dataset file with big size didn't get removed no matter what. I went to check the reports webapp, that dataset isn't on the largest unpurged data files list (despite it has big

Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

Thanks Nate, D On Thu, Sep 13, 2012 at 10:43 PM, Nate Coraor wrote: > On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote: > > > Hi guys, > > > > Just a quick question about the total size of the genome indexes just > made available via rsync server? > > > Hi De

[galaxy-dev] Size of the genome indexes repos in Galaxy Main

Hi guys, Just a quick question about the total size of the genome indexes just made available via rsync server? Cheers, Derrick ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions t

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

regenerate indexes, if the local ones > had somehow become corrupted. > >--Dave B. > > > On 9/11/12 02:03:45.000, Derrick Lin wrote: > >> Dave, >> >> I upgraded the galaxy to Sep 7 release. The KeyError error has gone as >> expected. >> >>

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

> The KeyError error you mentioned in your previous should be fixed in the > latest -dist and -central revisions. > >--Dave B. > > > On 9/9/12 21:20:44.000, Derrick Lin wrote: > >> Hi guys, >> >> I found that the problematic loc files were created by Cl

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

; --Dave B. > > > On 9/9/12 21:20:44.000, Derrick Lin wrote: > >> Hi guys, >> >> I found that the problematic loc files were created by CloudBioLinux and >> point to the reference indexes downloaded by CloudBioLinux script. I >> suspect that Manage Local

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

Manager' object has no attribute 'deferred_job_queue' Anyone can give some hints about what was going on? Regards, Derrick On Fri, Sep 7, 2012 at 4:26 PM, Derrick Lin wrote: > Hi guys, > > I enabled the tool with enable_beta_job_managers = True, server runs > fine.

[galaxy-dev] Manage local data admin tool failed with dbkey KeyError

Hi guys, I enabled the tool with enable_beta_job_managers = True, server runs fine. But after I clicked on Manage local data, it gave the following error: URL: http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data [^ ] F

Re: [galaxy-dev] galaxy database has two tables missing

ar.. Just saw the news brief, will that be possible that these two tables are added as part of the Tool Shed and Admin Genome Indexing update?? Regards, D On Thu, Jul 26, 2012 at 12:18 PM, Derrick Lin wrote: > Hi guys, > > Recently we have discovered there is a bug in the data

[galaxy-dev] galaxy database has two tables missing

Hi guys, Recently we have discovered there is a bug in the database dump utility. And we had used the same utility to migrate the galaxy mysql database once. That resulted the on the current galaxy database, two tables are missing: genome_index_tool_data tool_dependency I am wondering if there

Re: [galaxy-dev] Using $NSLOTS in tools to control thread number

Hi, Just add some info about this, I have attempted to do so on SGE cluster. I found that $NSLOTS works only for MPI jobs as it's part of the MPI integration in SGE. Other non MPI jobs won't work. For example: python parallel_groomer.py input output $NSLOTS, $NSLOTS won't be replaced by the SGE

Re: [galaxy-dev] Set job_working_directory to a cluster compute node /tmp

fast > space. Once the job completes, the outputs will be moved back to the > larger, slower pool configured for file_path. > > --nate > > On Jun 19, 2012, at 8:08 AM, Derrick Lin wrote: > > > Another relevant question, my institute has configured a NFS volume that > b

Re: [galaxy-dev] Set job_working_directory to a cluster compute node /tmp

er to there is impossible. Any recommendation for the galaxy to have a good use of the SSD? Thanks Derrick On Tue, Jun 19, 2012 at 9:55 PM, Derrick Lin wrote: > I think my question has been answered: > > > http://gmod.827538.n3.nabble.com/NFS-Cluster-and-working-directories-questio

Re: [galaxy-dev] Set job_working_directory to a cluster compute node /tmp

I think my question has been answered: http://gmod.827538.n3.nabble.com/NFS-Cluster-and-working-directories-questions-td3784165.html Hopefully can see the enhancements in the near future. Cheers. Derrick On Tue, Jun 19, 2012 at 5:01 PM, Derrick Lin wrote: > Hi guys, > > I have

[galaxy-dev] Set job_working_directory to a cluster compute node /tmp

Hi guys, I have deploy a galaxy on a cluster (so I installed it on a NFS share that it's accessible by all cluster compute nodes). Everything is running fine. Now I am looking for a way such that every job dispatched to a compute node uses that node's local /tmp as working directory. I know gala

Re: [galaxy-dev] Meme gives me UnicodeDecodeError. Is this an error from parsing the OUTPUT?

Okay, it turned out to be my execution hosts on the cluster didn't have the required packages installed. I then install libxslt-devel and ImageMagick<http://www.imagemagick.org/>-devel, everything now works as expected. Hope this help, Derrick On Wed, Jun 6, 2012 at 10:03 AM, Derrick

Re: [galaxy-dev] Meme gives me UnicodeDecodeError. Is this an error from parsing the OUTPUT?

/job_working_directory/000/973/dataset_2527_files/meme.html': No such file or directory Seems to me, the meme was ran but return its help page and didn't return any result. Still investigating why. Derrick On Wed, Jun 6, 2012 at 9:47 AM, Derrick Lin wrote: > Hi, > > I am hitting t

Re: [galaxy-dev] Meme gives me UnicodeDecodeError. Is this an error from parsing the OUTPUT?

Hi, I am hitting the same issue. meme itself runs fine on commandline. I suspected the html or xml generated by meme contains non-ascii, thus galaxy throw this error. Have you been able to fix that? MEME is not on the public galaxy server either.. Regards, Derrick On Thu, May 31, 2012 at 4:37

Re: [galaxy-dev] Task Manager: This Galaxy instance is not the job manager.

Hi guys, I just configured our galaxy to utilize multiple instance and having exact issue. Couldn't see any error from the log thought. Regards, Derrick On Fri, May 25, 2012 at 12:14 AM, Sarah Diehl wrote: > ** > Hi all, > > I have a similar, maybe related problem. I'm running a configuration

[galaxy-dev] Implement scaling and load balancing galaxy on a 8-core host with cluster backend

Hi guys, Today my institute ran a galaxy training with about 20 people. We didn't implement multiple instances for galaxy python. When everyone started submitting jobs, the thread pool filled up very quickly, soon after the galaxy threw worker queue full error then became unresponsive. It had to b

[galaxy-dev] file download returns empty file or webpage fails with ERR_CONNECTION_CLOSED

Hi guys, I have setup a test galaxy and configured Apache as proxy. It's been running fine when I did all testing on my machine with Chrome. Recently, I let some of my colleagues to try it out, then they experience some file download issues. On one machine, both FireFox and IE8 downloaded empty

Re: [galaxy-dev] Running Galaxy on Rocks Cluster

on your galaxy VM (I guess it's Centos 5 host)? Cheers, Derrick On Fri, Feb 3, 2012 at 7:09 AM, Shantanu Pavgi wrote: > > On Feb 1, 2012, at 9:13 PM, Derrick LIN wrote: > > > Hi guys, > > > > Is there anyone has actually setup galaxy on a Rocks based clust

[galaxy-dev] Running Galaxy on Rocks Cluster

Hi guys, Is there anyone has actually setup galaxy on a Rocks based cluster? I know that galaxy should be hosted on a submission host so that it can submit jobs to the cluster. Rocks provides preconfigured DRM such as SGE, so I start thinking if galaxy host should be deployed and managed by Rock

Re: [galaxy-dev] Setup galaxy to run on SGE cluster

e the node Galaxy runs on an exec > host. > > Ryan > > On Mon, Jan 9, 2012 at 8:45 PM, Derrick LIN wrote: > >> Hi guys, >> >> I am trying to configure our test galaxy to run on our SGE cluster >> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. >

[galaxy-dev] Setup galaxy to run on SGE cluster

Hi guys, I am trying to configure our test galaxy to run on our SGE cluster http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. This is my first time to come across to drmaa, so a bit confused. I installed teh galaxy on a NFS location where can be accessed clsuter-wide. I have configured

Re: [galaxy-dev] Galaxy Proxy by an External Apache Server

n 6, 2012 at 1:08 PM, Carlos Borroto wrote: > On Thu, Jan 5, 2012 at 8:51 PM, Derrick LIN wrote: > > Hi Carlos, > > > > You are right! I put the same config to site-available and now it works! > > > > Will do more testing/configuring base on that. > > > &

Re: [galaxy-dev] Galaxy Proxy by an External Apache Server

Hi Carlos, You are right! I put the same config to site-available and now it works! Will do more testing/configuring base on that. Do you know why the location of the settings cause this issue? Thanks Derrick On Fri, Jan 6, 2012 at 12:42 PM, Carlos Borroto wrote: > > I'm not sure this will so

[galaxy-dev] Fwd: Galaxy Proxy by an External Apache Server

Hi guys, Thanks for the helps. I used http://publicnet.org/galaxy for visiting the site, so it's my typo. On Fri, Jan 6, 2012 at 3:49 AM, Carlos Borroto wrote: > > The fact your apache server is looking in /var/www/galaxy means the > 'RewriteRule' is not working. Did you check if modwrite is act

[galaxy-dev] Galaxy Proxy by an External Apache Server

Hi guys, I am trying to setup a new galaxy for my institute. The galaxy itself runs fine in our private network. Now I am trying to configure the proxy so that it can be accessed publicly. The official guide here http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy It seems to assume both gala