show urls in csv (in eye mode)
by Hagai Cohen
Hi,
I have a tool which outputs a csv file with links.
When I press the eye icon - I would like these links to be shown as links
in the browser.
It is possible?
Thanks,
Hagai
6 years, 11 months
Updating help text for a tool shed repository
by Lance Parsons
I recently updated the htseq-count tool in the Galaxy toolshed to
version 0.3. This version has some functional changes and thus the tool
version was incremented. I installed this new version of the tool in my
local Galaxy instance.
However, I realized later that I missed updating one part of the help
text. Today I fixed that text (but left the tool version the same),
tarred up the file, and uploaded it to the toolshed. I then attempted
to "Get Updates" from my local Galaxy instances for that tool got the
following error:
URL:
http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revisi...
File
'/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
return self.app( environ, start_response )
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py',
line 160 in __call__
body = method( trans, **kwargs )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py',
line 206 in decorator
return func( self, trans, *args, **kwargs )
File
'/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 1677 in update_to_changeset_revision
update_repository( repo, latest_ctx_rev )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py',
line 1428 in update_repository
rev=ctx_rev )
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py',
line 5661 in update
rev = scmutil.revsingle(repo, rev, rev).rev()
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
line 515 in revsingle
l = revrange(repo, [revspec])
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
line 588 in revrange
for r in m(repo, range(len(repo))):
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 1414 in mfunc
return getset(repo, subset, tree)
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 156 in getset
return methods[x[0]](repo, subset, *x[1:])
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 171 in symbolset
return stringset(repo, subset, x)
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 161 in stringset
x = repo[x].rev()
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py',
line 235 in __getitem__
return context.changectx(self, changeid)
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py',
line 103 in __init__
_("unknown revision '%s'") % changeid)
RepoLookupError: unknown revision '11'
I believe this is because the revision I have installed (10) is not
longer considered a valid revision by the toolshed (I presume since it
is an older revision of with the same tool version).
Any help would be appreciated. Thanks.
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
6 years, 11 months
Please help with fastx broken pipe
by Jorge Sepulveda
Hi,
Fresh new installation of galaxy on a MacPro 12 core Mountain Lion
Trying to run fastx_quality_stats:
galaxy.jobs.manager DEBUG 2013-01-16 16:03:49,646 (7) Job assigned to handler 'main'
galaxy.jobs DEBUG 2013-01-16 16:03:54,759 (7) Working directory for job is: /Users/JS/galaxy-dist/database/job_working_directory/000/7
galaxy.jobs.handler DEBUG 2013-01-16 16:03:54,759 dispatching job 7 to local runner
galaxy.jobs.handler INFO 2013-01-16 16:03:54,854 (7) Job dispatched
galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:54,919 Local runner: starting job 7
galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,198 executing: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat'
galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,396 execution finished: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat'
galaxy.jobs DEBUG 2013-01-16 16:03:55,440 Tool did not define exit code or stdio handling; checking stderr for success
galaxy.jobs DEBUG 2013-01-16 16:03:55,496 setting dataset state to ERROR
galaxy.tools DEBUG 2013-01-16 16:03:55,618 Error opening galaxy.json file: [Errno 2] No such file or directory: '/Users/JS/galaxy-dist/database/job_working_directory/000/7/galaxy.json'
galaxy.jobs DEBUG 2013-01-16 16:03:55,679 job 7 ended
127.0.0.1 - - [16/Jan/2013:16:03:59 -0400] "GET /history HTTP/1.1" 200 - "http://127.0.0.1:8080/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17"
Galaxy reports the following error:
/bin/sh: fastx_quality_stats: command not found
cat: stdout: Broken pipe
When run on the cmd line, it runs fine:
$ cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_6.dat'
$ more /Users/JS/galaxy-dist/database/files/000/dataset_6.dat
column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count
1 912999 7 46 31022469 33.98 32 35 37 5 25 44 153534 361457 322516 75492 0 912999
2 912999 3 46 29744797 32.58 31 34 36 5 24 43 316245 255564 197711 143479 0 912999
Jorge Sepulveda, MD, PhD
Associate Director for Laboratory Medicine,
Medical Director of Laboratory Informatics,
Columbia University Medical Center
Associate Professor,
Department of Pathology & Cell Biology
Columbia University College of Physicians and Surgeons
PH1590B
622 W 168 St
New York, NY 10032
Cell: (917) 862-6050
Office: 212-305-6360
E-mail:jls2282@columbia.edu
6 years, 11 months
Composite datatype output for Cuffdiff
by Jim Johnson
Checking to see if there is any interest in including a parameter option to select outputs for cuffdiff,
potentially including a composite output and a cummeRbund sqlite database.
Issues:
cuffdiff produces 21 output files, which is a little unwieldy in a galaxy history.
cummeRbund generates its database when given a cuffdiff output directory, but manually hooking up 21 outputs to the cummerbund_wrapper is a pain.
I've put demo code in the testtoolshed under the name repository name cummerbund
http://jjohnson@testtoolshed.g2.bx.psu.edu/repos/jjohnson/cummerbund
This includes new datatypes defined in datatypes_conf.xml and implemented in cuffdata.py:
<!-- html composite dataset with cuffdiff outputs in the extra files path -->
<datatype extension="cuffdata" type="galaxy.datatypes.cuffdata:CuffDiffData"/>
<!-- cummeRbund SQLite database -->
<datatype extension="cuffdatadb" type="galaxy.datatypes.cuffdata:CuffDataDB"/>
The cuffdiff wrapper has a multiple select parameter to choose which output files to put in the history.
In addition to the 21 cuffdiff outputs, the wrapper can also generate:
cuffdata - which is a composite HTML output with links to the 21 cuffdiff outputs
cuffdatadb - which is the cummeRbund SQLite database
I also added utility tools:
cuffdata_datasets - which will take files from the composite cuffdata and copy them as datasets into the history
cuffdata_cummerbund - which generates the cummeRbund cuffdatadb from the composite cuffdata
I updated the cummerbund_wrapper:
with tryCatch so that a R error on a plot won't exit the Rscript
to include a small image of each plot on the html page
added plots for : dispersion, scatter matrix, MDS, and PCA
Thanks,
JJ
6 years, 11 months
Bug in handling user job limits
by Lance Parsons
I submitted a trello "ticket" [(https://trello.com/c/6vxkqdjT) regarding
this, but wanted to make sure I brought it to someone's attention (it's
causing me some queue issues with my instance of galaxy).
When registered_user_job_limit and anonymous_user_job_limit are set in
universe.wsgi jobs cannot be run, instead the following error occurs:
galaxy.jobs.handler ERROR 2012-12-04 12:44:51,869 failure running job 22396
Traceback (most recent call last):
File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
line 183, in __monitor_step
job_state = self.__check_if_ready_to_run( job )
File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
line 253, in __check_if_ready_to_run
state = self.__check_user_jobs( job )
File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
line 274, in __check_user_jobs
if not self.user_job_count:
AttributeError: 'JobHandlerQueue' object has no attribute 'user_job_count'
Commenting out the lines for registered_user_job_limit and
anonymous_user_job_limit in universe.wsgi allows job to be queue one again.
It looks like this is due to the fact that
`self.__clear_user_job_count()` on line 159 of `handler.py` is only
called when jobs are tracked in the database. If jobs are not tracked in
the database (as in my case), the error occurs. Perhaps the fix would be
to simply move the call outside the `if` block.
It appears this was broken in the 2012-11-13 revision (73e05bc).
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
6 years, 11 months
macs error for chipseq data
by Jennifer Jackson
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so
that he or or one of the developers more experienced with
troubleshooting cloud issues can help. My guess is that there is a path
problem (covered in the first wiki link) but by no means is that the
only possibility.
Thanks!
Jen
Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
>
> Hi Jen,
>
> Sorry that I missed some part of your email. It is not for local
> galaxy install. I am using the cloudman from aws and it seemed to have
> everything for having the input files and reference genome chose. The
> job was shown on the right panel and then the error message coming out.
>
> It seems to me that MACS was installed.... What is the issue?
>
> Thank you very much,
>
> Kathryn
>
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
>
> Hi Jennifer,
>
> Thanks for the information on MACS tools.
>
> Yes, I forgot to mention that I used bowtie mapped files as the input.
>
> Thank you very much,
>
> Kathryn
>
> **
>
> *From:*Jennifer Jackson [mailto:jen@bx.psu.edu]
> *Sent:* Friday, January 11, 2013 3:48 AM
> *To:* Sun, Wenping [USA]
> *Cc:* galaxy-user(a)bx.psu.edu
> *Subject:* [External] Re: [galaxy-user] macs error for chipseq data
>
> Hello Kathryn,
>
> This is occurring on your local Galaxy install? Have you installed the
> actual MACS tool and set up the proper configuration paths? Details
> for how to do this are in these wikis:
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
>
> Apart from that, I should let you know that prior to running MACS,
> groomed fastq datasets first need to be mapped. An example can be
> found in our Using Galaxy paper, protocol #3. Links to the paper and
> supplemental materials (including a screencast walk-through) are
> available here:
> https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
>
> If you need more help with your local install, directing questions to
> the galaxy-dev(a)bx.psu.edu <mailto:galaxy-dev@bx.psu.edu> mailing list
> would be best,
>
> Thanks!
>
> Jen
> Galaxy team
>
> On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
>
> Dear galaxy users,
>
> I've encountered the error while running macs on galaxy for
> chipseq data. I used fastq groomed files as input and had the
> following error
>
> An error occurred running this job: //bin/sh: macs: not found/
>
> //
>
> Anybody can kindly provide some hints?
>
> Thanks,
>
> Kathryn
>
>
>
>
> ___________________________________________________________
>
> 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/
>
>
>
> --
> Jennifer Hillman-Jackson
> Galaxy Support and Training
> http://galaxyproject.org
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
6 years, 11 months
Tabular file metadata - columns names
by Peter
Hi all,
I'd like to know more about Galaxy's column metadata for tabular files.
In the workflow editor under "Edit Step Actions" you can pick "Assign
Columns", and then give column numbers for five predefined cases:
Chrom, Start, End, Strand, Name.
Do these "named columns" get shown anywhere in the Galaxy UI?
For example, in a column select parameter widget?
Is it possible to assign these columns in a tool's wrapper XML file?
>From http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
I'm aware of the metadata_source attribute to *copy* the meta data
from the input file, but that isn't always relevant. Can I somehow
specify that my tool has tabular output where column 1 is "Name"?
Is it possible to introduce additional column types? e.g. "evalue" or
"Description".
Thanks,
Peter
6 years, 11 months
environment variables and paths for toolshed tools
by David Hoover
Are there any environment variables that are honored by toolshed installed tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or $GALAXY_HOME, then uploaded it the test toolshed, then installed it automatically. Neither of these resolved to what I expected. I don't want to hard-code the path in the xml tool file, but rather have a default location for other executables and jar files. How should this best be done?
David Hoover
Helix Systems Staff
6 years, 12 months
changing datasets file_path storage location
by Shantanu Pavgi (Campus)
We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed?
--
Thanks,
Shantanu
6 years, 12 months
