[galaxy-dev] PATH env variable for SGE jobs

2011-12-01 Thread Langhorst, Brad
I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the galaxy user's .bashrc export PATH=/mnt/ngswork/galaxy/sw/bin:$PATH When I echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job runner node

[galaxy-dev] unpacking zip files during upload

2011-12-20 Thread Langhorst, Brad
I'm working on unpacking a zip file into multiple datasets. I think this is the code path Upload.py UploadToolAction upload_common.py: get_uploaded_datesets new_upload new_history_upload or new_library_upload Then a job gets spooled Which calles add_file in data_source/upload.py And does the

Re: [galaxy-dev] manage_db.sh upgrade fails after fresh install of Galaxy

2012-01-03 Thread Langhorst, Brad
Iry: I've run this recently on postgres without any trouble. Maybe the managedb_sh script is working on a different database than galaxy_1, or maybe there is some leftover information in galaxy_1? brad On 1/3/12 6:59 AM, Iry Witham iry.wit...@jax.org wrote: Hi Nate, I do not create

Re: [galaxy-dev] galaxy command line

2012-01-04 Thread Langhorst, Brad
Usha: Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to. brad -- Brad Langhorst New England Biolabs langho...@neb.com From: Usha Reddy

Re: [galaxy-dev] galaxy command line

2012-01-04 Thread Langhorst, Brad
...@neb.com Cc: Usha Reddy usha.reddy...@gmail.commailto:usha.reddy...@gmail.com, galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] galaxy command line On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad langho

Re: [galaxy-dev] LDAP authentification

2012-01-19 Thread Langhorst, Brad
Hi Sarah: I don't know what kind of LDAP you're talking to... I'm talking to Active Directory and this configuration works in that situation. Order allow,deny allow from all AuthType Basic AuthName NEB Credentials AuthBasicProvider

[galaxy-dev] naming of history steps

2012-01-30 Thread Langhorst, Brad
I'm having a tough time keeping track of which data is which after analysis... I can do a bunch of work customizing each tool and each workflow, renaming results etc. But I think it might be a lot easier to manage if step names were based on the titles of the history items instead of data 2 or

Re: [galaxy-dev] naming of history steps

2012-02-01 Thread Langhorst, Brad
Hi Jeremy and Ross I agree that the current chaining mechanism would get very long after even a few steps. Ususally the most important information is the first and last step E.g. The TopHat run should be called TopHat on SOLiD 24A The alignment stats should be SAM/BAM Summary Metrics of Solid

Re: [galaxy-dev] Missing stdout and stderr files from SGE cluster

2012-02-02 Thread Langhorst, Brad
Peter: I have a working sge setup. Two ideas: 1 - look in the sge logs on the worker node (on my system they are in /var/spool...) 2 - maybe a permission problem? brad -- Brad Langhorst New England Biolabs langho...@neb.com On 2/2/12 8:50 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

Re: [galaxy-dev] Adding a new python tool

2012-02-07 Thread Langhorst, Brad
Sarah: I've had trouble before with invalid xml files (in your case test.xml) I don't see an obvious problem with your file, but I've never tried such a minimal file. Have a look at galaxy's log during startup to see if it tells you what it does not like about the file. Brad -- Brad Langhorst

Re: [galaxy-dev] history box odd behaviour

2012-02-13 Thread Langhorst, Brad
On Feb 13, 2012, at 11:22 AM, Bossers, Alex wrote: When I press the eye icon on the running blast history box it drops an error in the mid panel that the xml is not there yet (XML-parse error). But than the box changes to green while the blast is still running in the background (checked

Re: [galaxy-dev] Galaxy workflow data

2012-02-14 Thread Langhorst, Brad
Paul: I was about to suggest the same - great idea! ++ brad On Feb 14, 2012, at 11:08 AM, Dannon Baker wrote: Hi Paul, Thanks for this suggestion, it would definitely make sense to create a reference to the actual workflow inputs in the new history. I'll see what I can do! -Dannon

Re: [galaxy-dev] bacterial genomes missing?

2012-03-06 Thread Langhorst, Brad
PM, Langhorst, Brad wrote: It seems that the bacterial genomes that used to come from ucsc via update_ucsc.sh are now gone... Has anybody else observed this? Fixed it? Brad -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564

Re: [galaxy-dev] Looking where to edit web view

2012-03-20 Thread Langhorst, Brad
I like this idea very much but i think it might be better placed as a link in http://galaxy.neb.com/admin (maybe as a replacement for profile memory usage?) brad On Mar 20, 2012, at 8:53 PM, Dannon Baker wrote: Ed, The top bar is defined in templates/webapps/galaxy/base_panels.mako. To

Re: [galaxy-dev] directories as inputs/dataset file extensions

2012-04-04 Thread Langhorst, Brad
On Apr 4, 2012, at 11:11 AM, Langhorst, Brad wrote: I'm no authority... but given that nobody else has replied yet I'll give my opinion. I think I would approach the directory problem with a wrapper script that takes arguments for each of the components needed by the tool. The script

Re: [galaxy-dev] directories as inputs/dataset file extensions

2012-04-04 Thread Langhorst, Brad
On Apr 4, 2012, at 1:48 PM, Aaron Gallagher wrote: On Apr 4, 2012, at 8:11 AM, Langhorst, Brad wrote: I think I would approach the directory problem with a wrapper script that takes arguments for each of the components needed by the tool. The script could lay out the various files

Re: [galaxy-dev] directories as inputs/dataset file extensions

2012-04-04 Thread Langhorst, Brad
On Apr 4, 2012, at 2:44 PM, Aaron Gallagher wrote: On Apr 4, 2012, at 11:35 AM, Langhorst, Brad wrote: This is somewhat akin to the reference area galaxy uses to store reference sequences (and their various indices, formats, annotations etc). It might be possible to modify galaxy's

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-27 Thread Langhorst, Brad
I'm interested On Apr 27, 2012, at 3:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for

Re: [galaxy-dev] server error

2012-05-09 Thread Langhorst, Brad
Ashley: I think he was joking around. Essentially - to provide any help, people here need to know much more detail about what kind of server error occurred, and what input was provided so that the problem can be reproduced or a helpful suggestion can be made. This guide to asking good

Re: [galaxy-dev] How to upload local files in Galaxy

2012-06-07 Thread Langhorst, Brad
Mehmet: It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive. I found that confusing at first too. Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote: Hi Everyone, I am

Re: [galaxy-dev] Requests to display_application mistakenly routed to route

2012-06-22 Thread Langhorst, Brad
While I have not yet added IGV for display, I would like to and I would also like to add tablet so I'm interested in how this plays out. Hopefully someone more knowledgable will chime in. Meanwhile, I'll try to help. I think that the 302 redirect indicates that REMOTE_USER is not being set or

[galaxy-dev] error when accessing toolshed

2012-06-28 Thread Langhorst, Brad
When i try to install a tool from the main toolshed i see this error Not Found The resource could not be found. No route for /repository/Noneadmin_toolshed/install_repository I see in the archive that there was a problem but Greg fixed it..

Re: [galaxy-dev] error when accessing toolshed

2012-06-28 Thread Langhorst, Brad
defined (apache?) that are messing up your routes. Where does Noneadmin_toolshed come from? Greg Von Kuster On Jun 28, 2012, at 1:24 PM, Langhorst, Brad wrote: When i try to install a tool from the main toolshed i see this error Not Found The resource could not be found. No route for /repository

[galaxy-dev] tuple unpack error during tool install

2012-06-28 Thread Langhorst, Brad
I found the problem with my blocked cookies, now I encounter a new error. File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 291 in install_repository description, repository_clone_url, changeset_revision = repo_info_tuple ValueError: too many values to

Re: [galaxy-dev] tuple unpack error during tool install

2012-06-28 Thread Langhorst, Brad
, Langhorst, Brad wrote: I found the problem with my blocked cookies, now I encounter a new error. File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 291 in install_repository description, repository_clone_url, changeset_revision = repo_info_tuple

Re: [galaxy-dev] tuple unpack error during tool install

2012-06-28 Thread Langhorst, Brad
? That is required for using the main galaxy tool shed. Greg Von Kuster On Jun 28, 2012, at 2:16 PM, Langhorst, Brad wrote: I found the problem with my blocked cookies, now I encounter a new error. File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line

[galaxy-dev] conflicting migration files

2012-07-04 Thread Langhorst, Brad
When I merged brad chapmans code into galaxy-central two 0099 migration files are created. I got things working by moving the ngs lims one to 0104 , but now i think i'll be in for a problem when a new 104 is created... What's the right way to solve this? Brad -- Brad Langhorst

[galaxy-dev] is there a way too automatically select references based on the genome of the dataset?

2012-07-11 Thread Langhorst, Brad
I would like the reference list to be automatically selected based on the dbkey of the selected input... I think I've seen this, but I can'f seem to find an example. Anybody know? Should be some easy jquery i guess. Brad -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564

[galaxy-dev] getting picard tools working in a workflow with inferred index

2012-07-16 Thread Langhorst, Brad
The picard based tools nicely infer a reference sequence, and still allow the user to override. However, this inference does not work in a workflow, since that select list has no value. I'm trying to come up with a clean way for the workflow logic to read the input dataset dbkeys, but I'm not

Re: [galaxy-dev] Local instance is running way too slow!!!

2012-07-24 Thread Langhorst, Brad
galaxy just wraps existing tools... so it's probably not galaxy that is slow per se, but the fastqgroomer too. Each tool has its own performance characteristics. I don't use fastqgroomer, so I don't know how it can be expected to perform. Are you sure you need it? If you know that your

Re: [galaxy-dev] Fwd: Re: [galaxy-user] Linking to Compressed Data

2012-08-21 Thread Langhorst, Brad
This is not tool specific. Instead, galaxy automatically unzips as files are uploaded. beware: it only supports one data set per zipped file - so gzipped fastqs are find.. but a tarball of a bunch of fastqs is not. Brad On Aug 21, 2012, at 10:23 AM, Carlos Borroto carlos.borr...@gmail.com

[galaxy-dev] metaphlan + krona = ?

2012-08-22 Thread Langhorst, Brad
I have installed both krona and metphlan from the toolshed to my local insttance. both seem to work ok, but I don't seen an easy way to get the metaphlan output into a form that krona can accept. has anybody solved this problem already? Brad -- Brad Langhorst

[galaxy-dev] patch contribution (was Re: So I think I fixed a bug.)

2012-08-23 Thread Langhorst, Brad
Maybe I'm just doing it wrong… but I find it unusually difficult to put together a coherent pull request without doing a dedicated repo clone. maybe somebody who knows a good way to submit pull requests could populate this wiki page? http://wiki.g2.bx.psu.edu/Develop/Mercurial brad On Aug 23,

Re: [galaxy-dev] Problem of global env $PATH when using galaxy in daemon mode in ubuntu

2012-08-25 Thread Langhorst, Brad
I have added information to the galaxy user's .profile export TEMP=/mnt/ngswork/galaxy/tmp export PATH=/mnt/ngswork/galaxy/sw/bin:$PATH export PYTHONPATH=/mnt/ngswork/galaxy/sw/lib/python2.6/site-packages and added a .sgerequest # set up temp and path environment variables for jobs -v

Re: [galaxy-dev] Problem of global env $PATH when using galaxy in daemon mode in ubuntu

2012-08-25 Thread Langhorst, Brad
I have added information to the galaxy user's .profile export TEMP=/mnt/ngswork/galaxy/tmp export PATH=/mnt/ngswork/galaxy/sw/bin:$PATH export PYTHONPATH=/mnt/ngswork/galaxy/sw/lib/python2.6/site-packages and added a .sgerequest # set up temp and path environment variables for jobs -v

Re: [galaxy-dev] Re-starting Galaxy

2012-08-27 Thread Langhorst, Brad
Unless something has recently changed, you will need to set up a cluster to get jobs to persist across galaxy restarts. You can do this with just a single node acting as both queue master and job runner using sun grid engine (i think, I have not tried this myself) Brad On Aug 27, 2012, at

Re: [galaxy-dev] Why doesn't bowtie in galaxy accepting colorspace reads directly?

2012-09-15 Thread Langhorst, Brad
Raj: It does support colorspace files, but you have to convert them to fastq first. That sounds bad, but you don't have to convert to basespace to store the data in fastq, so there is no loss of data - just one extra step. https://main.g2.bx.psu.edu/tool_runner?tool_id=fastq_combiner Only

Re: [galaxy-dev] Why doesn't bowtie in galaxy accepting colorspacereads directly?

2012-09-17 Thread Langhorst, Brad
/manual.shtml#bowtie-options-q, the default)” Why should the system spend time in converting the files when the tool itself provide the capability of accepting the original formats. Pl share your thoughts. Raj From: Langhorst, Brad [mailto:langho...@neb.comhttp://neb.com] Sent: Saturday, September 15

[galaxy-dev] unhandled exception

2012-10-03 Thread Langhorst, Brad
(with galaxy-central from a few days ago) URL: http://galaxy/datasets/10385e16ab51958e/display/?preview=True File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File

[galaxy-dev] stack trace from a history problem

2012-10-05 Thread Langhorst, Brad
On one particular history, I see this. I am at 035583d94b11https://bitbucket.org/galaxy/galaxy-central/changeset/035583d94b11200276aed333a859b8e49b64429f I don't know why this happens on this history… I cloned it, then re-ran one step. I hope this stacktrace is helpful: Exception happened

[galaxy-dev] stack track on attempt to kill job from admin manage jobs page

2012-10-13 Thread Langhorst, Brad
Error - type 'exceptions.NameError': global name 'string' is not defined URL: http://galaxy.neb.com/admin/jobs File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File

Re: [galaxy-dev] piping two scripts in the same xml tool wrapper

2012-11-18 Thread Langhorst, Brad
I think you could write a bash wrapper script around your tool, or if it's very simple, just switch from command interperter=python to bash with command python plotter.py variables ; r_wrapper.sh $Rplotter using a semicolon to delineate the two commands. Brad On Nov 18, 2012, at 1:13 PM,

[galaxy-dev] format sensitive tools not working properly after upgrade

2012-11-20 Thread Langhorst, Brad
I performed an upgrade over the weekend. Since then, I've observed an odd behavior - bowtie2 will not list the new fastqsanger files in my history. It will work with files that had already been groomed before the upgrade. I also see that the groomer is not recognizing fastq files. The format

Re: [galaxy-dev] Direct access the fastq files stored in galaxy server local storage

2012-11-20 Thread Langhorst, Brad
I don't think this is possible. Galaxy is designed to import data files and track their relationships and disk usage internally. You can import lots of files at once though.. see: http://wiki.galaxyproject.org/Admin/Data%20Libraries/Uploading%20Library%20Files Brad On Nov 20, 2012, at 3:49

Re: [galaxy-dev] Multiple language in one tool

2012-11-20 Thread Langhorst, Brad
Hi Philippe: You can just wrap a bash script if you want to to that… or even write a simple pipeline in the xml wrapper with interpreter='bash' or no interpreter at all. I've done that sort of thing before with good results. brad On Nov 20, 2012, at 10:03 PM, Philipe Moncuquet

Re: [galaxy-dev] pass more information on a dataset merge

2012-12-03 Thread Langhorst, Brad
John Yeah! I'm glad you took the initiative to do this. It's one of the most requested features from local users here. I'll happily test this in our environment. Also - thanks for the github link - it's vastly superior to hg i think for the situation of merging pull requests. I can't figure

[galaxy-dev] segfault in libdrmaa - galaxy front end failure

2012-12-05 Thread Langhorst, Brad
Galaxy is failing due to a segfault in libdrmaa [9116874.391434] python[5211]: segfault at 0 ip 7fcb9fd8ae62 sp 7fcb9affe490 error 4 in libdrmaa.so.1.0[7fcb9fc29000+1b9000] I first started observing this in the last few weeks. After the first event I pulled in this changeset

Re: [galaxy-dev] 回复: 回复: 回复: Speed up the galaxy

2012-12-07 Thread Langhorst, Brad
You can just change the format of the data from fastq to fastqsanger if you're sure about the error format (use the pencil, then datatype tab) note: fastqsanger !=fastqcsanger Brad On Dec 7, 2012, at 3:20 AM, 泽 蔡 caizexi...@yahoo.com.cnmailto:caizexi...@yahoo.com.cn wrote: Hi Alex Now is an

Re: [galaxy-dev] Working with compressed files

2012-12-18 Thread Langhorst, Brad
Yes, it decompresses them during import. On Dec 18, 2012, at 1:28 PM, Fenglou Mao feng...@gmail.commailto:feng...@gmail.com wrote: Is Galaxy capable of working with compressed files such as *.fastq.gz? Thanks, Fenglou ___ Please keep

[galaxy-dev] backtrace when attempting to view a shared workflow

2013-01-02 Thread Langhorst, Brad
File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 202 in display_by_username_and_slug return self.display(trans, stored_workflow) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 218 in display

Re: [galaxy-dev] backtrace when attempting to view a shared workflow

2013-01-07 Thread Langhorst, Brad
I've recently updated to the december 20th revision of galaxy and still have a problem with a few workflows. You can find the backtraces below. based on these I'm starting to look in /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py - but any hints would be appreciated. thanks

Re: [galaxy-dev] backtrace when attempting to view a shared workflow

2013-01-07 Thread Langhorst, Brad
. Once you are able to apply these changes, would you mind letting us know if this resolves your broken workflows? Thanks for using Galaxy, Dan On Jan 7, 2013, at 9:11 AM, Langhorst, Brad wrote: I've recently updated to the december 20th revision of galaxy and still have a problem

[galaxy-dev] anybody seen 403s after a recent upgrade?

2013-01-07 Thread Langhorst, Brad
galaxy.web.framework WARNING 2013-01-07 22:06:30,044 User logged in as '(null)' externally, but has a cookie as 'langho...@neb.commailto:langho...@neb.com' invalidating session 10.254.254.86 - - [07/Jan/2013:22:06:30 -0400] GET /api/histories/4c8cd68e0b9ed4a7 HTTP/1.1 403 -

[galaxy-dev] missing eye icon on running jobs…

2013-01-09 Thread Langhorst, Brad
In some cases (e.g. mira) it's nice to be able to follow what's going on in the log file… Does anybody else miss being able to view files as they're running? brad -- Brad Langhorst langho...@neb.commailto:langho...@neb.com ___ Please

Re: [galaxy-dev] anybody seen 403s after a recent upgrade?

2013-01-09 Thread Langhorst, Brad
, 2013, at 10:43 PM, Langhorst, Brad wrote: galaxy.web.framework WARNING 2013-01-07 22:06:30,044 User logged in as '(null)' externally, but has a cookie as 'langho...@neb.com' invalidating session 10.254.254.86 - - [07/Jan/2013:22:06:30 -0400] GET /api/histories/4c8cd68e0b9ed4a7 HTTP/1.1 403

Re: [galaxy-dev] anybody seen 403s after a recent upgrade?

2013-01-09 Thread Langhorst, Brad
set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e I just cargo culted those in to begin with… I don't really know what they do. Brad On Jan 9, 2013, at 1:21 PM, Nate Coraor n...@bx.psu.edu wrote: On Jan 7, 2013, at 10:43 PM, Langhorst, Brad wrote: galaxy.web.framework WARNING 2013-01

Re: [galaxy-dev] History not updating automatically

2013-01-28 Thread Langhorst, Brad
Hi Sajoscha: I have exactly the same problem… it started about a month ago. Also with external ldap auth. I have not yet investigated in detail, since it's not crippling - just annoying. Brad On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de wrote: Hi list, I have a weird

Re: [galaxy-dev] where to announce transcript annotation file in local Galaxy install

2013-02-21 Thread Langhorst, Brad
Hi Maxim: I think you have to load your annotations into your history to do this. I keep ours in the shared data area and have users import and provide it as input to our workflows. Brad On Feb 21, 2013, at 6:53 AM, Maxim deeeperso...@googlemail.commailto:deeeperso...@googlemail.com wrote:

[galaxy-dev] access to api when using apache ldap auth

2013-02-27 Thread Langhorst, Brad
I need to access the api using an api key… Does anybody have a working apache configuration for that? A search at galaxyproject.org/searchhttp://galaxyproject.org/search didn't turn anything up. I tried this: but that causes the history to fail to update. Location / Order

[galaxy-dev] workflow parameters

2013-03-15 Thread Langhorst, Brad
Workflow parameters still seem to be broken for me. I'm seeing the same problem as Liisa Koski http://dev.list.galaxyproject.org/Can-t-specify-workflow-parameters-for-integer-values-td4658193.html (this message comes up when i edit a workflow with ${mininsert} set on a bowtie2 job) Problems

Re: [galaxy-dev] workflow parameters

2013-03-15 Thread Langhorst, Brad
/b9afd514145740b4d5999158d51bd7dc4a409a99 Thanks for using Galaxy, Dan On Mar 15, 2013, at 5:04 PM, Langhorst, Brad wrote: Workflow parameters still seem to be broken for me. I'm seeing the same problem as Liisa Koski http://dev.list.galaxyproject.org/Can-t-specify-workflow-parameters-for-integer-values-td4658193.html

[galaxy-dev] slow history panel?

2013-03-25 Thread Langhorst, Brad
Is it my imagination or has the history panel become much slower in the latest release? Maybe I have something misconfigured? Brad -- Brad Langhorst langho...@neb.commailto:langho...@neb.com ___ Please keep all replies on the list by

[galaxy-dev] alphabetically sorted references from admin tool - numerically sorted?

2013-03-27 Thread Langhorst, Brad
GATK really does not like alphabetically sorted references. http://gatkforums.broadinstitute.org/discussion/1204/what-input-files-does-the-gatk-accept Does it make sense to rearrange genomes to be sorted in [chr1,chr2, chr3,...] order instead of [chr1,chr10,chr11,...] order before indexing?

Re: [galaxy-dev] Bowtie2 and Tophat2 versions

2013-04-10 Thread Langhorst, Brad
We are using bowtie 2.1.0 in via a galaxy wrapper. Since there has been no change in the bowtie command line options used by the wrapper, there are no problems. Similar for Tophat. Brad On Apr 10, 2013, at 3:05 PM, Lance Parsons lpars...@princeton.edu wrote: I noticed that the latest

[galaxy-dev] traceback - local error?

2013-04-19 Thread Langhorst, Brad
172.17.130.203 - - [19/Apr/2013:10:31:20 -0400] GET /api/datasets/dd61915e24aa3fd0?hda_ldda=hdadata_type=converted_datasets_statechrom=chr1 HTTP/1.1 200 - http://galaxy.neb.com/visualization/trackster?dataset_id=b8edc02014d74addhda_ldda=hda; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_3)

Re: [galaxy-dev] 回复: 回复: 回复: Speed up the galaxy

2013-04-25 Thread Langhorst, Brad
, Dave On Fri, Dec 7, 2012 at 3:53 AM, Langhorst, Brad langho...@neb.commailto:langho...@neb.com wrote: You can just change the format of the data from fastq to fastqsanger if you're sure about the error format (use the pencil, then datatype tab) note: fastqsanger !=fastqcsanger Brad On Dec 7

Re: [galaxy-dev] 回复: 回复: 回复: Speed up the galaxy

2013-04-25 Thread Langhorst, Brad
in batch? Either via the bioblend or manually via the UI? Thanks, Dave On Fri, Dec 7, 2012 at 3:53 AM, Langhorst, Brad langho...@neb.commailto:langho...@neb.com wrote: You can just change the format of the data from fastq to fastqsanger if you're sure about the error format (use the pencil

[galaxy-dev] very long load times for some shared libraries...

2013-05-17 Thread Langhorst, Brad
All of a sudden, some larger libraries are taking a very long time to open. [cid:BB83AE73-EAE2-44B9-B294-918CDE8C18F4@neb.com] This one timed out… Anybody else seen this? Could this be a database issue? Didn't see any really long queries in the postgres log (and i log anything longer than

[galaxy-dev] igv integration

2014-02-04 Thread Langhorst, Brad
I’m having some trouble with igv integration… it works fine for hg19, but for other this influenza genome i just added, i’m seeing from IGV [cid:9C974C45-560B-46C3-AF75-CC794D0D1ACD@neb.com] Any idea what I’m doing wrong? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product

[galaxy-dev] contributing patches to toolshed repos...

2014-02-25 Thread Langhorst, Brad
What’s the right way to contribute additions to other people’s repos? I have extended the picard wrappers to support the rna-seq metrics and downsample sam tools, but I don’t want to start a new repo just for these. I have attached the output from hg outgoing -p in case that’s useful

Re: [galaxy-dev] contributing patches to toolshed repos...

2014-02-25 Thread Langhorst, Brad
Hi Bjorn: I don’t appear to have permission to create cards on the the galaxy-tool-shed board… I can create cards on the main board via http://galaxyproject.org/trello but I can’t find an analog for the toolshed board. Am I missing something? Brad -- Brad Langhorst, Ph.D. Applications and

[galaxy-dev] local toolshed with remote-user=true and require-user=falase

2014-02-25 Thread Langhorst, Brad
Has anyone set up a local toolshed with external authentication? Is this expected to work? I have external auth working, but tools cannot be installed (403 forbidden) unless I turn of authentication. If i turn on remote-auth, i have to configure the webserver to ask for credentials otherwise i

Re: [galaxy-dev] local toolshed with remote-user=true and require-user=falase

2014-02-26 Thread Langhorst, Brad
: Wednesday, February 26, 2014 9:01 AM To: Langhorst, Brad Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] local toolshed with remote-user=true and require-user=falase Hi Brad, If you're using HTTP Auth, that will be the case since HTTP Auth has no notion of sessions, the auth credentials

[galaxy-dev] latest stable data management interface

2014-02-26 Thread Langhorst, Brad
When i click on the manage local data link i only see this: [cid:1d03bde5-8e93-4335-b4e6-25a5904b5dfc] none of which is clickable. ?Am I doing something silly? What am i missing? Brad inline: pastedImage.png___ Please keep all

Re: [galaxy-dev] latest stable data management interface

2014-02-26 Thread Langhorst, Brad
From: Daniel Blankenberg d...@bx.psu.edu Sent: Wednesday, February 26, 2014 2:58 PM To: Langhorst, Brad Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] latest stable data management interface Hi Brad, Galaxy doesn't come with any Data Managers

[galaxy-dev] new data manager can't build bowtie or sam fasta, interface differences, how to fetch ncbi stuff

2014-03-06 Thread Langhorst, Brad
I’m slowly wrapping my head around the new data manager stuff… but I don’t think I quite have it yet. I was able to download hg19 using the reference genome tool I see where it puts downloaded files now - took me a while to figure that out. When I run the sam fa build tool it fails like this:

[galaxy-dev] nginx upload - traceback

2014-03-12 Thread Langhorst, Brad
I’ve been trying to get the nxinx upload stuff working… I think i have the nginx config is working properly (files are present in the right spot with correct ownership and have correct content), but I see a traceback in the log (see below). I don’t see anything in the mail list search about

[galaxy-dev] restarting multiple web workers

2014-04-01 Thread Langhorst, Brad
Hi, I’m using the multiple web server stuff described here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling that seems to address the responsiveness issues i see when many users are active. However, when i add a new tool - it does not alway show up (only for one of the workers

[galaxy-dev] krona to metaphlan patch

2014-04-07 Thread Langhorst, Brad
I’m running with these local additions to Dannon’s metaphlan repo. I think it would be better to add these to the current metaphlan repo than to release them standalone. metaphlan_to_krona.xml Description: metaphlan_to_krona.xml #!/usr/bin/env python #

[galaxy-dev] patches to bjorn's bismark wrapper

2014-04-07 Thread Langhorst, Brad
This patch updates bjorn’s bismark wrapper to work with latest bismark and allows methylation extraction from SAM or BAM files. It no longer sorts the BAM from bismark (to allow methylation extraction to work). bismark_patch.diff Description: bismark_patch.diff Comments/corrections

[galaxy-dev] backtrace from set_dataset_sizes.py

2014-05-13 Thread Langhorst, Brad
python scripts/set_dataset_sizes.py Loading Galaxy model... Processing 134520 datasets... Completed 0% Traceback (most recent call last): File scripts/set_dataset_sizes.py, line 43, in module dataset.set_total_size() File lib/galaxy/model/__init__.py, line 1257, in set_total_size if

Re: [galaxy-dev] Repository installation on multiple servers

2014-05-23 Thread Langhorst, Brad
I had the same concern, and heard that this is being worked on. Meanwhile I’m using a rolling restart method from pjbriggs https://github.com/pjbriggs/galaxy-admin-utils/ I’m pretty happy with this (desipite the 2 minute restart per worker) because users do not see any interruption during

Re: [galaxy-dev] Repository installation on multiple servers

2014-05-23 Thread Langhorst, Brad
Microbial Biodiversity Bioinformatics | Science Technology Branch Agriculture Agri-Food Canada iyad.kandal...@agr.gc.camailto:iyad.kandal...@agr.gc.ca | (613) 759-1228 -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Friday, May 23, 2014 9:08 AM To: Langhorst, Brad Cc

Re: [galaxy-dev] galaxy install nginx

2014-08-01 Thread Langhorst, Brad
The order is not very important… however I would install nginx and postgres at the same time, then galaxy. brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 1, 2014, at 10:10 AM, ngsf...@hygenomics.commailto:ngsf...@hygenomics.com wrote: dear sir:

[galaxy-dev] bx version conflict causes failure for some tools (e.g. subtract interval tool)

2014-08-01 Thread Langhorst, Brad
see: https://biostar.usegalaxy.org/p/8095/ I can work around the problem by adding a stdio block to these tools, how should the underlying problem be solved? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist

Re: [galaxy-dev] Serious start-up delay in next-stable

2014-08-05 Thread Langhorst, Brad
I’ve noticed that startup is very slow. It’s about 15 minutes for me to stop and restart my 4 daemons. It was much faster with galaxy on local storage. brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 5, 2014, at 2:41 PM, Björn Grüning

[galaxy-dev] bug?

2014-08-05 Thread Langhorst, Brad
I see this in my database server logs… SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id,

[galaxy-dev] job not starting on cluster

2014-08-05 Thread Langhorst, Brad
I’m not aware of any recent changes to the configuration of galaxy… It seems that jobs are not being distributed at the moment. I have 2 job handlers... It seems that when I restart them only a single job is queued, it has an error and then sticks on Cleaning up external metadata files”

Re: [galaxy-dev] bug?

2014-08-05 Thread Langhorst, Brad
through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request? -Dannon On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad langho...@neb.commailto:langho...@neb.com wrote: I see this in my database server logs

Re: [galaxy-dev] bug?

2014-08-09 Thread Langhorst, Brad
, Aug 5, 2014 at 5:53 PM, Langhorst, Brad langho...@neb.commailto:langho...@neb.com wrote: I tried to do some time correlation between galaxy logs and postgres logs… postgres 2014-08-01 17:15:15.643 EDT handler1.log galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681: Fatal error

Re: [galaxy-dev] rename output dataset in workflow - input dataset variable

2014-11-12 Thread Langhorst, Brad
For what it's worth (not much ;), I think the dataset naming is the single least intuitive part of the galaxy system for biologists. I think there's a proposal to fix this problem - and mainain the connection between input data set and derived data, but It doesn't seem to have gone anywhere