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 sentenc
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
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 data
Hello Ted!
Peter Cock wrote, On 03/25/2013 01:51 PM:
> On Mon, Mar 25, 2013 at 5:41 PM, Ted Goldstein 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 do that :)
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
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 w
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
(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 be
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:
>
>
> AuthName "Galaxy"
> NTLMAuth on
> NTLMAuth
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 followi
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 do
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 conf
Lucinda Lawson wrote, On 11/03/11 17:51:
> [...] but when we ran Reverse-Compliment, we got the following error:
>
> fastx_reverse_complement: writing quality scores failed: File too large
>
> gzip: stdout: Broken pipe
>
You are very likely using a 32-bit executable version of
"fastx_reverse_co
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 fo
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 t
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
"" block.
Then, enable mod_rewrite logging wit
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 .
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 c
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
http://seqanswers.com/
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
Hi,
The attached patch enables the BWA wrapper to work with Illumina-1.3+ FASTQ
files without Grooming (which goes well with the name of the tool: "Map with
BWA for Illumina" ).
Actually,
Changing the XML and the python code, testing the tool and mapping to the mouse
genome all together took l
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 "/h
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 cha
n"
section in the toolshed ?
>
> 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 spen
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 conta
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 "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 shared
Hi,
I've encountered a strange error when trying to view a failed job/dataset.
I'm using the latest stable revision ( june 23rd, 720455407d1c ).
A user executed a job and it failed (bad parameters, so no problem here).
The program (bowtie) failed, returned information in STDERR.
The "peek" field
Hello Sergei,
I'm experimenting with the clean-up scripts myself, so perhaps I can offer some
information (the galaxy team is welcomed to correct me and/or explain better).
1. If you look at the output of your query, you'll notice that the "purged"
field is 0 for all datasets (I assume 0 is "f
Hi,
I'm trying to use the built-in cleanup scripts (instead of my own), came across
a possible bug:
1. When running "delete_datasets.sh", the "info_only" flag is ignored.
This is evident by running it twice with "-i" and getting different results
(the second time - no datasets are deleted).
2.
Hello Ross and Galaxy team,
May I suggest this small patch, that enables WebLogo to plot either Entropy
bits (the current default) or just nucleotides probabilities ?
It uses the standard "-U" parameter of "weblogo3".
-gordon
# HG changeset patch
# User A. Gordon
# Date 1309468091 14400
# Nod
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.
Examp
Hi,
Sorry for complaining or sounding ungrateful,
but before you push the new "Delete and remove datasets from disk" to
galaxy-dist, can you make it optional (with enable/disable in
universe_wsgi.ini) ?
Or at the very least, add a big warning and a confirmation message box before
actually dele
Hi,
I recently needed to generate the dataset's hashed-id from a reporting script
outside galaxy (a script that reads Galaxy database directly).
Here's how to generate the hashed-id from perl and postgres, hope it would save
you some time if you ever need it.
(The python code to do the same is
Hi,
with the new ToolShed inplace, and support for cloning/pulling tools directly:
What's the recommend way to organize the repositories ?
For example, I want to use Peter's Venn tool:
hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/venn_list
If I clone, I get the following folder hierarchy
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 ve
Hi,
In "cuffdiff_wrapper.xml", there are three outputs associated with CDS:
Based on the naming convention of the other outputs (and the output files from
cuffdiff),
I think the label of the first one should be renamed to "CDS Expression" only
(assuming the relevant input file "cds_exp.dif
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 X
date-check option for for Cuffcompare; I haven't checked
> to see if Cuffcompare actually contacts cufflinks.cbcb.umd.edu before running
> or not.
>
> *galaxy-central changeset 5638:1ab3dfb5d929 disables the update check for
> Cuffdiff.
>
> Best,
> J.
>
>
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
(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 wrote:
>>>
>>> pbs.py then knows to translate '8' to
>>> '-l nodes=1:ppn=8'.
>>>
>>> Your tool can access that value a bunch, like $__resources__.cores.
>>>
>>> The
Hello,
There's a small bug when entering a double-quote character in a dataset name:
The double-quote confuses some later-on processing (templates and
Display-Application XML), resulting in some problems.
Example:
This history has one BAM dataset with a name of:
Hello "world"
http://main.g2.b
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 wro
>
> Thanks!
>
> Jen
> Galaxy team
>
> On 3/30/11 3:12 PM, Assaf Gordon wrote:
>> 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
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:
>
>
> ...
>
>
> In this function my_options I would need the t
> Looks like 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.e
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 run
Hi,
There's a small bug with the "hide dataset" button in the workflow editor -
once any dataset is marked as "output" (by clicking on the star icon), there's
no way to show all the datasets, even if the user manually un-checked every
star icon for every workflow step.
meaning:
If I have a wor
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
Peter Cock wrote, On 04/21/2011 12:59 PM:
> On Thu, Apr 21, 2011 at 5:43 PM, Assaf Gordon 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
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:
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebA
;
> On Apr 11, 2011, at 7:13 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 modif
Hi,
Kudos on the new "View Details" button implementation, both visually nice and
less intrusive tooltips.
However, you know me - I can't just give praise without complaining...
1. The "View Details" tooltip (the actual tooltip) is not using JQuery, so the
yellow (browser native) tooltip is sh
s,
-gordon
Ryan Golhar wrote, On 04/11/2011 03:13 PM:
> I restarted the galaxy daemon, 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 w
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 t
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 wor
Hello,
I'm trying to write my own wrappers for Cufflinks,Cuffcompare,Cuffdiff,
learning mostly by looking at the existing tools.
I have a question regarding the multiple input/output implementation in
CuffCompare:
In CuffCompare, the XML can accept multiple input files (with a ), and
the sect
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-repor
Hello Ryan,
Ryan Golhar wrote, On 04/07/2011 05:40 PM:
> Hi all - So, I been asked to provide specs for a production Galaxy
> system to support approximately 20-30 users. Most of these users
> are new to bioinformatics and very new to NGS. I'm targeting a user
> base that will use a light to mo
an just
> "successfully" output an empty file.
>
Depends on your definition of "informative" - in this case 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 wrot
/gordon/files/cshl_sam_to_bam.tar.bz2
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 in "sam_to_b
170)
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/tools/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),
(galax
Ryan,
Since we're shooting in the dark here, best to try and understand what's the
exception.
Add the following line to the beginning of "sam_to_bam.py":
import traceback
and add the following line to "sam_to_bam.py" line 156 (before the call to
"stop_err"):
traceback.print_exc()
Hopefully
Hi,
A small bug:
When clicking "re-run" to view a tool form, and the tool has embedded images,
the URL of the images is not working.
When viewing a tool that has embedded images, the relative URL is
"./static/images/histogram2.png".
The tool's URL comes from:
"http://main.g2.bx.psu.edu/tool
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 t
Hello Ryan,
I'm in the exact same situation with my bowtie/tophat tools,
going back and forth between outputing a SAM, sorted SAM, BAM or sorted BAM,
and I'm still not sure what's the best method.
Storage wise - you're correct, just saving the sorted BAM is the best (even
more with the fact the
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 to
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
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 you
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 sup
Hi all,
Does any one have (or galaxy team: are you planning to develop) tools for
NCBI's SRA binary container format ?
For starters, a wrapper for the "fastq-dump" program that converts a lite-sra
back to fastq ?
Just trying to avoid re-inverting a wheel,
-gordon
_
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 "./lib
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 i
Hello all,
After 7 enjoyable hours of cheetah debugging ...
for those (like me) who are not well versed in python or cheetah templates,
here are couple of debugging tips that can help.
=1= RTFM.
It's here:
http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html
=2= printi
+1
Nate Coraor wrote, On 03/31/2011 12:34 PM:
> Ryan Golhar wrote:
>>
>> Nate - Is there a way to get the pbs job scripts to still get saved
>> with debugging turned off?
>
> Not without modifying the call to cleanup() in the job runner
> (lib/galaxy/jobs/__init__.py). It'd be a simple change,
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 annoy
Still very much work-in-progress, but I'd like to hear any comments or ideas
that you might have.
No need to install, just visit here to see TopHat's interface:
http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_se1
Main differences from the existing TopHat tool:
1. Far fewer visible o
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 I
Ryan Golhar wrote, On 03/29/2011 12:26 PM:
>> Note about multithreaded bowtie:
>> currently the tools use 10 threads (hard-coded in the XML files) - easily
>> changeable.
>
> If possible, have the user indicate as a parameter how many threads they wish
> to use.
>
This will never happen, at le
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 us
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
Hello all,
We're developing alternative bowtie tools that more closely suit our needs, are
we're happy to share (and get comments).
The main differences are:
1. separate tools for paired-end and single-end
2. the tools accepts FASTA, FASTQ in both Sanger and Illumina format (no more
need for gr
refer no delay.
>
> On Mar 17, 2010, at 3:49 PM, Kanwei Li wrote:
>
>> I think a delay would be good and maybe a lighter background
>>
>> On Wed, Mar 17, 2010 at 3:35 PM, Assaf Gordon wrote:
>>> Hi,
>>>
>>> I was wondering if there's
Hello all,
Greg Von Kuster wrote, On 03/14/2011 11:09 AM:
> Sebastian and Assaf,
>
> For the above, determining whether a dataset is shared is currently
> available, but what is your definition of a "published dataset"?
>
We use the following query to see if a dataset is shared between more t
Sebastian J. Schultheiss wrote, On 03/14/2011 10:31 AM:
> Is there a way to completely delete a user and their data at the same
> time? We would like to keep published pages and shared data though.
>
Do you really want to delete all the user's records from the database ? I think
the database size
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.
>> [...] Wi
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...
On 01/25/2011 10:25 AM, Hans-Rudolf Hotz wrote:
On Jan 25, 2011, at 3:40 PM, Hans-Rudolf Hotz wrote:
[...]
Once again be careful with what you are doing, and don't blame me if you
create a mess ;)
-1-
PgAdmin ( http://www.pgadmin.org/ ) is a GUI application to manage Postgres
databases - it m
Slightly off-topic, but for a new Galaxy installation -
What would you recommend for a free (FOSS) Grid/Cluster management product ?
SGE is not free any more (Oracle Grid Engine is "90-days evaluation, binaries
only" free, starting 6.2u6).
Ease of administration is top-priority, more than sophis
92 matches
Mail list logo
