Hello Galaxy People!
(it's been a while since I've last been here... a pleasure to be back).
I intend to publish a small command-line utility, which will also be available
through Galaxy Toolshed.
It'll be a small application note, so not a lot of space for many citations.
The relevant
Hello Carrie,
Ganote, Carrie L wrote, On 03/27/2013 01:22 PM:
I am trying to upgrade our instance to the newest dist but I get the
following in stderr when I attempt to run Bowtie or BWA:
PREFIX/subs/galaxy_31.sh: command substitution: line 7: syntax error near
unexpected token `('
Hello Joachim,
Joachim Jacob | VIB | wrote, On 03/26/2013 10:01 AM:
abrt was filling the root directory indeed. So disabled it.
I have done some exporting tests, and the behaviour is not consistent.
1. *size*: in general, it worked out for smaller datasets, and usually
crashed on
Hello Joachim,
Couple of things to check:
On Mar 25, 2013, at 10:01 AM, Joachim Jacob | VIB | wrote:
Hi,
About the exporting of history, which fails:
1. the preparation seems to work fine: meaning: choosing 'Export this
history' in the History menu leads to a URL that reports initially
Hello Ted!
Peter Cock wrote, On 03/25/2013 01:51 PM:
On Mon, Mar 25, 2013 at 5:41 PM, Ted Goldstein tedgoldst...@gmail.com wrote:
Hi
Does anyone have any experience or advice about running
two servers on the same database?
My advice is don't do it.
I'll second Peter's advice, don't ever
Couple of clarifications for the script, which aren't obvious:
Assaf Gordon wrote, On 03/25/2013 02:03 PM:
To facilitate that, we use the following script, that can quickly copy the
data from our production server to our development server.
Once it's run, the databases contain the same
Hello Dan,
Couple of lessons we learned from setting up similar workshop-galaxies:
Dan Sullivan wrote, On 09/17/2012 01:04 PM:
Hi, Galaxy Developers,
Is anybody out there managing a Galaxy environment that was designed and or
has been tested to support 35 concurrent users? The reason why
Hello Philip,
Philip Mabon wrote, On 08/29/2012 10:08 AM:
Looks like I forgot to reset that value. So making progress... I can install
freebayes successfully (the front end timeout but it worked)
However, samtools fails with the following message in web worker log:
[localhost] local: sed
(Moving to Galaxy-dev, seems more appropriate).
John Jones wrote, On 08/23/2012 05:29 PM:
His original question was about getting Galaxy to recognise LDAP
authentication and personal storage space rather than shared storage space as
is usual with Galaxy.
Licensing only came into it
Hello Russell,
Smithies, Russell wrote, On 07/17/2012 05:41 PM:
It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
Anyone else struck this and found a solution?
Our apache config looks like this:
Location /
AuthName Galaxy
NTLMAuth on
Hello Jesse,
Dam, Jesse van wrote, On 06/19/2012 01:27 PM:
I found a solution, it seemed that I made a stupid mistake somewhere. But the
following solution will work to preserve the original text in the edit field.
Add the following to your parameter
[...]
Then I use the following code
Hello,
Great work with the Galaxy on the Cloud - it's the first time I've used it and
it looks very impressive (and I'm not a big cloud fan :) ).
Once I got it working it was very nice, but before it worked I encountered two
issues (not sure if those were voodoo or not) that could be perhaps
Hello Sarah,
Sarah Maman wrote, On 01/19/2012 10:49 AM:
I'm talking to Open LDAP. I have changed
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
to
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
But I always have the same message /(Access to Galaxy is denied
Galaxy is configured
Hello,
It seems this issue (rpy) pops up every now and then:
Has anyone managed to get rpy-1.0.3 working properly with R-13.1 (including
loading packages) ?
After compiling R-2.13.1 from source, and recompiling rpy-1.0.3, I get the
following error when trying to load an R module through rpy:
Hello,
With the recent upgrade to CASAVA 1.8, Illumina's FASTQ files now contain both
filtered and non-filtered reads (i.e. high and low quality reads, what used to
be called reads that passed filtering).
Here's a program (+galaxy wrapper) that can filter those FASTQ files, preparing
them for
Your rewrite rules are not taking affect (as evident by the fact that apache
is looking for a folder named galaxy in your document root folder
(/usr/local/apache/htdocs/).
First thing to try is to take the RewriteRules statements outside the
location block.
Then, enable mod_rewrite logging
Hi Colin,
colin molter wrote, On 08/05/2011 01:54 PM:
Is there a way to directly move/copy data from your galaxy history to a given
location in the filesystem of the same galaxy server?
Said differently, there is a nice way to import data from the server to
galaxy, is it possible to do the
As a follow-up for SGE + TMP variables,
I've also encountered problems with settings TEMP,TMP and TMPDIR variables.
Tried setting ~/.sge_request and changing the Galaxy environment variables
before starting python - nothing worked -
TMPDIR and TMP were always set to /tmp/all.q.X by SGE .
Hello,
Question for galaxy maintainers: have you encountered situations where BWA jobs
run 'forever' (for days) ?
A little digging shows that it's the bwa sampe step, and SEQanswers thread
mention it's somewhat common:
http://seqanswers.com/forums/showthread.php?t=11652
Chris Fields wrote, On 07/29/2011 12:35 PM:
On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:
Question for galaxy maintainers: have you encountered situations where BWA
jobs run 'forever' (for days) ?
...
I'm wondering if this is common enough to justify adding -A to the
wrapper
Hello Peter and all,
Peter Cock wrote, On 07/28/2011 05:08 PM:
It concerns me that you're doing this for both fastqillumina format
(good) and fastqsolexa (bad). Treating the later as fastqillumina
would give negative scores and probably cause trouble. Unless BWA
copes but if so it is a poor
Hi John,
John Chilton wrote, On 07/22/2011 11:40 AM:
We have Galaxy behind an apache proxy, and apache is taking care of
the authentication. If I want to enable exporting workflows and
histories to other galaxy instances do I just need to disable the
authentication checks for locations
Hi,
I've noticed a ticket on the wiki for per-user tool permissions:
https://bitbucket.org/galaxy/galaxy-central/issue/269/use-galaxy-security-to-restrict-tool
If anyone is interested, the following patch implements such thing (but
requires manual code changes whenever the access needs to be
?
Best,
Jen Galaxy team
On 7/19/11 11:45 AM, Assaf Gordon wrote:
Hi all,
I got around to writing the report I always needed: how much time
each job actually runs and how much time it spends waiting in the
SGE queue.
The attached shell script produces the report, combining
information
Hi all,
I got around to writing the report I always needed: how much time each job
actually runs and how much time it spends waiting in the SGE queue.
The attached shell script produces the report, combining information from SGE's
QACCT with the galaxy job/dataset information.
The output
Hi Greg (again),
This patch adds messages for the purge histories step:
1. A message is printed when processing a new history (so that the user can
tell to which history the following dataset/hda messages belong).
2. in info_only mode, a message is printed about each deleted history
3. in
Hi Greg,
Another small patch for cleanup_datasets.py, that makes the output messages
slightly more informative.
The changes are:
1. If a dataset is skipped (because it's shared/cloned and was already
process), no message is printed at all.
2. If a dataset can not be deleted because it is
Hello John,
I'm not an apache expert, but I can try to help with some info.
your question involves two different issues, which are not dependent on one
another.
First, can one setup apache authentication that will affect both Galaxy and
other things on your server ?
The answer is yes.
Hi all,
Jeremy Goecks wrote, On 06/07/2011 01:25 PM:
If you modify the Cufflinks/compare/diff wrappers to be compatible
with 1.0.2/3, please either put them in the toolshed or send them to
me and I'll incorporate them into the Galaxy code base.
We are actually working on customized
Hi,
It seems the cuffcompare XML wrapper expects a file named cc_output to
contain the transcript accuracy report.
I guess it worked with versions 0.9.3 and 1.0.1, but at least in version 1.0.2,
this file is now named cc_output.stats, and the transcript accuracy file is
empty.
so the XML
Hi,
In cuffdiff_wrapper.xml, there are three outputs associated with CDS:
data format=tabular name=cds_exp_fpkm_tracking label=${tool.name} on
${on_string}: CDS Expression FPKM Tracking/
data format=tabular name=cds_fpkm_tracking label=${tool.name} on
${on_string}: CDS FPKM tracking/
data
(moved to galaxy-dev)
Nate Coraor wrote, On 06/02/2011 01:31 PM:
Peter Cock wrote:
On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor n...@bx.psu.edu wrote:
pbs.py then knows to translate 'resource type=cores8/resource' to
'-l nodes=1:ppn=8'.
Your tool can access that value a bunch, like
Just FYI,
With the recent version of cufflinks (at least 1.0.2), the developers added a
'feature' of automatic version check.
While the idea is nice, the implications are not:
cufflinks,cuffcompare and cuffdiff will connect to host
cufflinks.cbcb.umd.edu every time you run them.
I'm sure the
I would also recommend getting the latest XML wrappers from here:
http://hannonlab.cshl.edu/fastx_toolkit/download.html
Or at least changing zcat to cat in your XML files, as zcat on Mac-OS
behaves differently than linux's (and that is the source of your error message).
Nate Coraor wrote,
Hi Leandro,
Leandro Hermida wrote, On 04/29/2011 06:17 AM:
But I have one complication I guess. My tool is already running a Python
code file to dynamically create a drop-down menu using the dynamic_options
attribute a la:
param type=select dynamic_options=my_options()
...
code
Leandro Hermida wrote, On 04/28/2011 08:55 AM:
Hi galaxy developers,
Just want to double-check, there is no way to import some kind of galaxy tool
context info into python code you are running for a tool?
Nothing is impossible... just depends on how messy you want to get :)
for me, the
Question:
The recent galaxy-central revision ( 2b057869b72f ) doesn't work on my
computer, saying DistributionNotFound: cython=0.12.1.
Example:
$ hg clone http://bitbucket.org/galaxy/galaxy-central/
galaxy_hidden_dataset_test
$ cd galaxy_hidden_dataset_test
$ hg id
2b057869b72f tip
$ sh
it :)
http://cython.org/#download
From: galaxy-dev-boun...@lists.bx.psu.edu
[galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Assaf Gordon
[gor...@cshl.edu]
Sent: 28 April 2011 20:52
To: galaxy-...@bx.psu.edu
Subject: [galaxy-dev] problem running latest
Hi Peter,
Peter Cock wrote, On 04/21/2011 11:00 AM:
Is there any built in way to control the Unix priority level (e.g.
nice or ionice)
used to run tasks? I don't see anything on here, but perhaps I'm looking
in the wrong place:
Peter Cock wrote, On 04/21/2011 12:59 PM:
On Thu, Apr 21, 2011 at 5:43 PM, Assaf Gordon gor...@cshl.edu wrote:
Hi Peter,
Peter Cock wrote, On 04/21/2011 11:00 AM:
Is there any built in way to control the Unix priority level (e.g.
nice or ionice) used to run tasks? I don't see anything
Thanks for the quick answer,
Jeremy Goecks wrote, On 04/11/2011 12:50 PM:
Assuming cuffcompare generates a TMAP and REFMAP file for each
input file, does this mean the wrapper tool retrieves only the
first and second input files' TMAP and REFMAP files ?
Yes, this is the way it works
Couple of voodoo things to try:
1. Manually clean the cache of your web browser
2. Restart your apache/nginx
Depending on your last update revision, it's possible that some of your
javascripts were updated by the latest pull, but your webbrowser maintains a
cached older version.
Those are the
, apache, and cleared my cache. Still didn't
help. I'd be happy to share the URL of my instance via private email if
it'll help.
On 4/11/11 3:05 PM, Assaf Gordon wrote:
Couple of voodoo things to try:
1. Manually clean the cache of your web browser
2. Restart your apache/nginx
Depending
:13 PM, Assaf Gordon wrote:
It doesn't give the modification date of the dataset (also: what exactly is
modification ? all datasets in Galaxy are immutable).
It seems that the modification date is affected by any modification to the
history.
Just note that changing the history name affects
Assaf Gordon wrote, On 04/08/2011 10:07 AM:
Processes:
The servers processes that you should plan for are:
1 galaxy process for job-runner
2 or 3 galaxy processes for web-fronts
1 process of postgres
1 process of apache
optionally 1 process of galaxy-reports
you'll also want to leave
the error message
was not so informative at all, to a point a traceback was needed...
-gordon
On Apr 7, 2011, at 1:05 AM, Assaf Gordon wrote:
Just another example why python's misleadingly simple idioms are
quite dangerous in production code (couldn't help myself from
teasing about
Until a better solution comes along, this tiny patch makes the temp files
world-readable:
http://cancan.cshl.edu/labmembers/gordon/files/apache_xsendfile_temp_files.patch
Assaf Gordon wrote, On 04/05/2011 11:14 AM:
Hello,
I've encountered a strange combination of factors that results
/samtools/sam_to_bam.py, line 150,
in __main__
if len( open( tmp_aligns_file_name ).read() ) == 0:
MemoryError
Error extracting alignments from
(/home/galaxy/galaxy-dist/database/files/000/dataset_785.dat),
(galaxy_env)[galaxy@vail pbs]$
On 4/6/11 7:29 PM, Assaf Gordon wrote:
Ryan,
Since we're
/labmembers/gordon/files/cshl_sam_to_bam.tar.bz2
/shameless plug
On 04/07/2011 01:05 AM, Assaf Gordon wrote:
Just another example why python's misleadingly simple idioms are quite
dangerous in production code (couldn't help myself from teasing about
python... sorry about that).
Seems like line 150
Hello,
I've encountered a strange combination of factors that results in file access
problems.
Perhaps I'm doing something wrong - any advice will be appreciated.
I'm using Apache + XSendFile.
when viewing a strict BED file, everything works, because the actual dataset
filename is passed on
Daniel,
Note that this (and similar) password solutions in Galaxy is not secure in any
real way (especially if you're dealing with patient data or HIPPA):
The password (hidden or visible in a text field) is still transmitted in
clear-text over the network (unless you're using HTTPS/SSL).
If
More bug fixes, and a paired-end TopHat tool.
Available here:
http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_2011_04_04.tar.bz2
See the interface here:
http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1
Comments are very welcomed,
Cufflinks is next,
-gordon
Assaf
Hi,
Couple of things that can be slightly improved in the SAM-to-BAM tool:
1. Reference list is not informative (it's the technical way to say: list of
chromosomes and their sizes based on a FASTA file). Users do not generally
know what reference list is.
2. The Locally Cached option is not
Tiny bug:
When viewing a file inside a tarball, the content-type is forced to
text/plain.
Works for most files, but not with image files (example: the Sequence Logo
tool has a jpg image in the tarball, the browser will display it as text/plain
with binary characters).
This is done in
anton wrote, On 04/01/2011 09:02 PM:
We are getting multiple requests for this but did not have the
bandwidth to do it. So if you are planning to implement - share
through the toolshed and we will roll it to main.
To start, this patch adds SRA binary type with sniffing and upload support:
Hi all,
It's been a long while since I had to install a fresh production galaxy server,
and I can offer some tips or requests for minor improvements (but to give
credit were it's due - installation is much smoother now, and DRMAA works great
with SGE out of the box).
These are just minor
Hi Peter,
Peter Cock wrote, On 03/29/2011 05:39 AM:
2. the tools accepts FASTA, FASTQ in both Sanger and Illumina
format (no more need for grooming). Illumina is the default for
newly uploaded FASTQ files.
I think that's a bad idea - use Sanger FASTQ as the default to be
consistent with
Hi Dan,
Daniel Blankenberg wrote, On 03/29/2011 10:55 AM:
When files are added to Galaxy, the datatype can be directly set to
any of the fastq variants (e.g. fastqillumina), which removes the
requirement of grooming (but should only be done when users know what
they are doing).
I'm not using
Dan and Peter,
Peter Cock wrote, On 03/29/2011 12:08 PM:
Why not do the Illumina to Sanger conversion as part of your
pipeline that gets the data into Galaxy (and mark the files as
fastqsanger)? As Glen said, with a C tool that isn't really so slow.
That future proofs you for the pending
Hello Sebastian,
We are doing similar clean-ups as you've requested (except the automated email
notification, which will be implemented soon).
We would like to see how much space is used by an individual user and
evenutally be able to remove them after some time of inactivity (180
days?),
Hi Nick,
If you're running your own local instance, then nothing is impossible - it's
just a bit ugly...
Nate Coraor wrote, On 02/21/2011 12:36 PM:
[...] many tools that operate on these files produces multiple,
uncompressed large files which quickly eat up the disk allocation.
[...] With no
Hi,
Trying to upgrade DB schema ('sh manage_db.sh upgrade') from 67 to 68 fails
with the following message:
===
sqlalchemy.exc.ProgrammingError: (ProgrammingError) syntax error at or near
RENAME
LINE 1: ALTER SEQUENCE sequencer_id_seq RENAME TO external_service_i...
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