On Thu, Jun 14, 2012 at 6:15 PM, Dannon Baker dannonba...@me.com wrote:
On Jun 14, 2012, at 12:48 PM, Peter Cock wrote:
In a separate example with 33 sub-tasks, there were two of these
inversions, while in yet another example with 33 sub-tasks there was
a trio submitted out of order. This non
On Fri, Jun 8, 2012 at 9:15 AM, Nicholas Robinson
nicholas.robin...@nofima.no wrote:
Hi,
1. INPUT
I am trying to make a simple tool that sends a command to run crimap without
a wrapper ie.
.
command
crimap $param_file $option gt;$output1
/command
..
However,
On Fri, Jun 8, 2012 at 2:38 PM, Raj Ayyampalayam ra...@uga.edu wrote:
Hello,
I am interested in this local upload file tool. Can you please send the
files to me as well.
Thanks.
-Raj
This seems a potentially very useful tool, so putting it on the Galaxy Tool
Shed seems like a better idea
Dear all,
Does Galaxy have any mechanisms to set the priority of jobs
submitted to the cluster? Specifically I am interested in SGE
via DRMAA, but this is a general issue. If there is some existing
code, I might be able to use it for the following situation:
The specific motivation is for
On Thu, May 31, 2012 at 12:53 AM, Anthonius deBoer thondeb...@me.com wrote:
Hi,
I often find my self having to battle with other users of the cluster, even
for the one-off jobs that someone runs interactively...
We have setup Fast/short queues and Long queues...
Is there a way for a tool to
On Fri, Jun 1, 2012 at 6:25 PM, Michael Reich
micha...@broadinstitute.org wrote:
Dear Galaxy developer community,
Galaxy tool developers attending ISMB are encouraged to sign up for the
Bioinformatics Interoperability SIG to be held on Friday, June 13. The SIG
will include presentations on
On Tue, May 1, 2012 at 3:46 PM, Dannon Baker dannonba...@me.com wrote:
On Tue, May 1, 2012 at 3:10 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On May 1, 2012, at 10:03 AM, Dannon Baker dannonba...@me.com wrote:
On May 1, 2012, at 9:51 AM, Peter Cock wrote:
I'm a little confused about
On Fri, May 25, 2012 at 4:54 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Edward,
It has taken me a while but I'm how trying to use HMMER3, and do so
from within Galaxy.
I've realised that the per sequence and per domain tables from hmmscan
and hmmsearch (via the --tblout
Hi,
Could someone take a look at the Tool Shed server please?
I'm getting this for http://toolshed.g2.bx.psu.edu/
502 Bad Gateway
nginx/1.1.4
Thanks,
Peter
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On Fri, May 25, 2012 at 12:03 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
The tool shed should be functional now. Thanks for reporting this!
Greg
It was working again when I got your email, but while I was out to
lunch it has gone back to Error 502 Bad Gateway :(
Peter
On Fri, May 25, 2012 at 4:54 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
I ran into some similar problems wrapping other tools giving table based
output, and used a wrapper script to make them into tab separated tables
for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT4 (semi-colons
On Thu, May 24, 2012 at 1:54 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Julie wrote:
Thank you Jeremy,
you answered partially. I would like insert a command, to launch my script,
in the script or in the xml files of my tools to force it to change the
extension
of output files. But it
On Thu, May 24, 2012 at 3:27 PM, julie dubois dubju...@gmail.com wrote:
Ok I've tried to add my script perl in the command line with semi-colon.
It's work
But this script sets in entry the variable $wigoutput of my file xml. But
when I show it, it's not what I want; It's just the value : 1 .
On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl di...@immunbio.mpg.de wrote:
Thanks Peter! It's very likely that I have the exact same problem, because I
also have CentOS and needed to compile Python.
In that case make sure you've done this:
sudo yum install openssl openssl-dev
and then repeat
On Thu, May 17, 2012 at 12:13 PM, Peter van Heusden p...@sanbi.ac.za wrote:
Hi there
I'm trying to wrap Bioperl's bp_genbank2gff script. This script, by
default, produces an output file named the same as the basename of the
input file, with .gff added. So e.g.
bp_genbank2gff data.gbk
Hello all,
What is the current status in Galaxy for supporting compressed files?
We've talked about this before, for example in addition to FASTQ,
many of us have expressed a wish to work with gzipped FASTQ.
I understand that some have customized their local Galaxy
installations to use gzipped
On Mon, May 14, 2012 at 10:22 PM, Jean-Christophe Ducom
jcdu...@scripps.edu wrote:
All-
Is there a way to change the upload default directory structure
(/database/files) to organize files per user_id instead?
something along the following lines
~galaxy-dist/database/files/postgresql_user_id0
On Mon, May 14, 2012 at 9:03 PM, Claudia Gottstein
gottst...@cnsi.ucsb.edu wrote:
Hi,
I would like to understand which parameters, ideally which algorithm go into
the scores one obtains from the quality statistics out of fastQ illumina
data.
What is this score composed of? And how come that
On 12-05-03 9:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hello all,
Currently the Galaxy experimental task splitting code allows splitting
into N chunks, e.g. 8 parts, ...
Or, into chunks of at most size N (units dependent on the file type, e.g.
lines in a tabular file or number
On Friday, May 4, 2012, Michael Moore wrote:
I have a long string of steps dying on the last step because GNUPLOT sends
a warning to the log which galaxy faithfully records 11 faithful times in
my history files. The 10 other files have downloadable content, and in
fact, outside of galaxy the
Hi all,
Is it possible for a Galaxy Admin to browse any user's history?
Sadly the Admin page on the wiki is still rather lean:
http://wiki.g2.bx.psu.edu/Admin/Interface
For instance, I've monitored a large Galaxy job on our cluster, and now
that it has finished I'd like to see the results (in
On Thu, May 3, 2012 at 11:40 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
On 05/03/2012 12:10 PM, Peter Cock wrote:
Hi all,
Is it possible for a Galaxy Admin to browse any user's history?
Sadly the Admin page on the wiki is still rather lean:
http://wiki.g2.bx.psu.edu/Admin/Interface
On Tue, May 1, 2012 at 3:46 PM, Dannon Baker dannonba...@me.com wrote:
I'll take care of it. Thanks for reminding me about the TODO!
On a related point, I've noticed sometimes one child job from a split task
can fail, yet the rest of the child jobs continue to run on the cluster wasting
CPU
On Thu, May 3, 2012 at 3:54 PM, Dannon Baker dannonba...@me.com wrote:
On a related point, I've noticed sometimes one child job from a split task
can fail, yet the rest of the child jobs continue to run on the cluster
wasting
CPU time. As soon as one child job dies (assuming there are no
Hello all,
Currently the Galaxy experimental task splitting code allows splitting into
N chunks, e.g. 8 parts, with:
parallelism method=multi split_mode=number_of_parts split_size=8 ... /
Or, into chunks of at most size N (units dependent on the file type, e.g. lines
in a tabular file or number
On Wed, May 2, 2012 at 7:18 PM, Anne Pajon anne.pa...@cancer.org.uk wrote:
Hi,
I am struggling at integrating galaxy with our cluster. I am currently
running galaxy on a separate server machine from our LSF cluster.
The DRMAA library has been installed on the cluster and I've
re-installed
On Wed, May 2, 2012 at 9:58 PM, Anne Pajon anne.pa...@cancer.org.uk wrote:
Hi Peter,
Thanks for the clarification, it is really helpful.
Would you mind sharing what needs to be done in
term of configuration and instalation to transform
the galaxy server into a submitting job to the cluster?
Hello all,
I'm curious if there is any way to manipulate the Galaxy job
queuing in order to be 'fairer' to multiple simultaneous users.
My impression is that Galaxy uses a simple FIFO queue itself,
with for cluster jobs offloaded to the cluster queue immediately.
In our case, I'm looking at
Hi all,
We're running our Galaxy with an SGE cluster, using the DRMAA
support in Galaxy, and job splitting. I've noticed if the user cancels
a job (that was running or queued on the cluster) while the job is
shows as deleted in Galaxy, looking at the queue on the cluster
with qstat shows it
On Thu, Apr 26, 2012 at 10:40 PM, Edward Kirton eskir...@lbl.gov wrote:
your suggestion for blastdbn and blastdbp sounds fine.
it's okay if a few of our users need to edit the metadata of the dbs in
their history. thanks for asking and doing this.
Great.
Perhaps you can throw some light on
Hello all,
The shell script scripts/cleanup_datasets/update_metadata.sh tries to
call non-existent file scripts/get_python.sh
What is this intended to do?
Thanks,
Peter
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Hi Edward,
I've started work on this in earnest now. I see you only defined one
new datatype, blastdb, which worked for nucleotide databases.
I want to handle protein databases too, so I think two datatypes
makes sense - which I am currently calling blastdbn and blastdbp.
That won't be
Hello all,
I'm looking at 'basic' composite datatypes in Galaxy, based on how
Edward did BLAST databases in his BLAST+ fork on the toolshed.
I've extended his work to handle both protein and nucleotide databases,
and have got this working for tools to create a database (i.e. wrapped
makeblastdb)
On Fri, Mar 16, 2012 at 11:00 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 10, 2012, at 6:47 AM, Peter Cock wrote:
Hello all,
I've noticed we have about a dozen stalled upload jobs on our server
from several users
On Tue, Apr 24, 2012 at 10:03 AM, Ciara Ledero lede...@gmail.com wrote:
Hi there,
I know Galaxy already has a SAM-to-BAM converter, but part of my
exercise/task is to incorporate a script that uses samtools' view command. I
get this error:
[samopen] SAM header is present: 66338 sequences.
On Mon, Apr 23, 2012 at 7:08 PM, Nate Coraor n...@bx.psu.edu wrote:
Not quite shortly, but it's been committed as 476ce0b78713. Sorry for the
wait.
--nate
Thanks Nate - that did the trick :)
Peter
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On Fri, Apr 20, 2012 at 2:17 AM, Brad Chapman chapm...@50mail.com wrote:
Lance and Peter;
Peter, thanks for noticing the problem and duplicate tools. Lance, I'm
happy to merge these so there are not two different versions out there.
I prefer your use for genomeCoverageBed over my custom
On Fri, Apr 20, 2012 at 4:12 PM, Brad Chapman chapm...@50mail.com wrote:
Peter and Lance;
I've made the update to Brad's script from the Tool Shed (attached),
switching to using genomeCoverageBed and bedGraphToBigWig
(based on the approach used in Lance's script), although in doing so
I
On Thu, Apr 19, 2012 at 12:40 AM, JIE CHEN jiechenable1...@gmail.com wrote:
The version I installed is : mira_3.4.0_prod_linux-gnu_x86_64_static
OK, good.
The other key question I asked was did you get anything in the MIRA
log file (it should be in your history with text data even though it
Hi Brad Lance,
I've been using Brad's bam_to_bigwig tool in Galaxy but realized
today (with a new dataset using a splice-aware mapper) that it
doesn't seem to be ignoring CIGAR N operators where a read is
split over an intron. Looking over Brad's Python script which
calculates the coverage to
On Thu, Apr 19, 2012 at 1:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Brad Lance,
I've been using Brad's bam_to_bigwig tool in Galaxy but realized
today (with a new dataset using a splice-aware mapper) that it
doesn't seem to be ignoring CIGAR N operators where a read is
split
On Thu, Apr 19, 2012 at 2:32 PM, Greg Von Kuster g...@bx.psu.edu wrote:
The tool shed forces unique repository names per user account, allowing for
uniqueness with that combination. All tools uploaded into a tool shed
repository are assigned a unique id called a guid, which is unique for all
On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor n...@bx.psu.edu wrote:
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running
galaxy-dist when using the task splitting functionality? I'm using the
latest code from the default
On Thu, Apr 19, 2012 at 6:35 PM, JIE CHEN jiechenable1...@gmail.com wrote:
Hi Peter,
Thank you for your patience. I checked the error message in the history.
They all give exactly the same error-- the one i gave in the first thread.
Are you saying this is the entire contents of the MIRA log
On Thu, Apr 19, 2012 at 7:13 PM, JIE CHEN jiechenable1...@gmail.com wrote:
Hi Peter,
Here is the full log:
Excellent :)
The good news is MIRA seems to be installed and running
fine - it just didn't like your test data, and I understand why:
...
Sanger will load 1 reads.
Longest Sanger:
Hi Edward,
We're now running BLAST+ searches on our local Galaxy via our cluster,
and some of the cluster nodes have relatively small amounts of RAM.
This means I've become more aware of limitations in the NCBI BLAST+
tools' support for using a subject FASTA file (instead of making a local
BLAST
On Wed, Apr 18, 2012 at 10:53 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Edward,
We're now running BLAST+ searches on our local Galaxy via our cluster,
and some of the cluster nodes have relatively small amounts of RAM.
This means I've become more aware of limitations in the NCBI
Dear all,
I've looked over the wiki and as far as I can see, 'when' tags used inside
'conditional' tags only work on another input variable's values.
I would like to be able to do is a conditional based on the file format
of an input file. For instance, a tool might take XML or tabular files,
On Wed, Apr 18, 2012 at 6:10 PM, Edward Kirton eskir...@lbl.gov wrote:
sounds great, thanks peter. i granted you access to my toolshed repo, but
perhaps we want only one tool in the toolshed when all done.
Thanks - but given the tools currently live in the main repository
with Galaxy itself,
On Wed, Apr 18, 2012 at 11:21 PM, JIE CHEN jiechenable1...@gmail.com wrote:
Dear all,
I just installed Mira-Assembler via Galaxy tool sheds. As expected, it
downloaded the wrappers into the shed-tools directory. Then I downloaded
and installed Mira binaries on the system and add it to $PATH.
Hi all,
Does anyone know what might have introduced this problem running
galaxy-dist when using the task splitting functionality? I'm using the
latest code from the default branch, changeset: 7027:f6e790d94282
galaxy.jobs.manager DEBUG 2012-04-17 13:55:03,610 (4) Job assigned to
handler 'main'
On Mon, Apr 16, 2012 at 8:12 AM, Frank Sørensen frank.soren...@ki.au.dk wrote:
Hi dev-list,
I have noticed, that when I clone a workflow, the new workflow apparently
inherits all tags from all my workflows or something similar. The result is
that when ever I clone a workflow the number of
On Fri, Apr 13, 2012 at 1:00 AM, Aaron Gallagher agall...@fhcrc.org wrote:
Hi again,
I'm trying to set up a workflow for Galaxy (6799:40f1816d6857), but I can't
seem to find a way to make a workflow that invokes another workflow. It seems
like this wouldn't be unreasonable, since workflows
On Wed, Apr 4, 2012 at 12:30 PM, Praveen Raj Somarajan
pravee...@ocimumbio.com wrote:
Hello All,
Is there a way to set auto delete some datafiles at the end of workflow
run? I'm asking this because it is sometimes useful to delete some outputs
(say intermediate files, .logs, etc), for
On Tue, Apr 3, 2012 at 1:57 AM, Xu, Jianpeng jianpeng...@emory.edu wrote:
Hi,
I have installed our local galaxy. I have a question for Fastq Groomer:
Is it an interior tool within Galaxy ? I mean you already incorporate it
into Galaxy? Or, you incorporate an external tool into Galaxy ? Do
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked to make this kind of documentation
more visible
On Tue, Apr 3, 2012 at 7:25 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Invalid tools are now displayed in the Preview tools and inspect metadata
by tool version section - here is the list for the hmmer repository.
Lovely - that will help with the existing tools which are not all
fully
On Mon, Apr 2, 2012 at 2:00 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote:
Hi Greg,
I made a tool for Galaxy which produces a normal XML output file and next to
that it also produces a HTML report with some quick summarized details for
the user.
I could solve this by using 2 output files,
On Fri, Mar 23, 2012 at 10:45 PM, Luciano Cosme cosme.sim...@gmail.com wrote:
Howdy,
Thanks Jen, I will try it tomorrow.
I installed Blast2Go from the Toolshed in my local instance of Galaxy and
when I try to run it I get the following error:
Index file named 'blast2go.loc' is
On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang yangl...@isu.edu wrote:
Hi, all,
Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am
wondering if there is an update on megablast web interface and wrapper in
Galaxy?
Yes, there are wrappers for the main tools from NCBI
On Thu, Mar 22, 2012 at 3:34 PM, Daniel Sobral
dsob...@igc.gulbenkian.pt wrote:
Hello,
For certain tools, like bwa or blast, there is a non-configurable number
of threads to use inside the tool xml.
This is inconvenient for certain cluster configurations, where what we
want is division of a
Hello all,
I was looking at Edward's updated HMMER wrapper on the toolshed,
http://toolshed.g2.bx.psu.edu/
There is a preview offered for the (simple) hmmpress.xml only, giving
the impression that Edward's repository isn't very useful.
Why isn't anything shown for the more complex hmmer.xml? If
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Here is the error produced by attempting to load the hmmr.xml tool config
into the tool shed. With regard to tool validity, the definition of a valid
tool in the tool shed has always been restricted to the tool
On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 10, 2012, at 6:47 AM, Peter Cock wrote:
Hello all,
I've noticed we have about a dozen stalled upload jobs on our server
from several users. e.g.
Job ID User Last Update Tool State Command Line
I have a guess:
In the history (right hand column) entry for your FASTQ file, click
on the pencil icon to edit the attributes. Try explicitly setting the
type of FASTQ, e.g. for Sanger FASTQ Galaxy uses the filetype
'fastqsanger'. This controls how the quality string is interpreted
(which is
On Mon, Mar 12, 2012 at 6:28 PM, John Major john.e.major...@gmail.com wrote:
A small warning re-the current cloud-Blast+ config.
To properly use the metagenomic tools, if you use the blast+ galaxy tool,
make sure to export in blast.XML, then you'll need a script to parse out the
readID and
On Thu, Mar 8, 2012 at 3:54 PM, Sivasangari NANDY nsi...@hotmail.com wrote:
Hi friends,
I've got a problem, i'm not able to add a tool in ttol_conf.xml. Actually i
can see one tool that i've added but when i put the second Galaxy doesn't
take it into account :
section name=My_tools
Hi all,
I just debugged a problem one of our users was having filtering BLAST
tabular output using the Filter tool (version 1.1.0), where it was
accepting 100% of the data.
He had entered the filter condition as: 'c8-c7=0.8*c23'
If you know how the tool works internally (essentially evaluating
On Tuesday, March 6, 2012, Edward Kirton eskir...@lbl.gov wrote:
i gave it a bad name previously and peter didn't find it in a
search at first, but i couldn't change the name, so i created
a new repository. i put a note in the old repo (hmmscan),
referring to the new repo (hmmer). that may
Hello all,
Are there (or were there) any known problems with Galaxy under
Microsoft Internet Explorer 9? One of our biologists is now having
problems with our local Galaxy server, probably after updating his
browser.
Specifically new history entries do not seem to automatically update
from
On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton eskir...@lbl.gov wrote:
hi, peter - i will fix the description and upload hmmsearch and infernal
today.
Great.
Assuming hmmscan and hmmsearch have (almost) the same command
line API, there is something to be said for presenting them as one tool
in
Hello all,
Has anyone done a wrapper for HMMER2 or HMMER3?
http://hmmer.janelia.org/software
I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so
we are likely to look into doing this ourselves - starting with hmmerscan.
Thanks,
Peter
On Saturday, February 25, 2012, Yingwei HU wrote:
Dear Peter,
Thank you for your response.
Yes. it is a custom binary file type. I attached the sample binary files.
humanK562C_d2.splib is the original one.
temp.splib is the uploaded and corrupted one.
For definition in Galaxy, I just
On Sat, Feb 25, 2012 at 9:40 AM, Yingwei HU husi...@gmail.com wrote:
Dear Peter,
I am sorry I do not know the version of my galaxy by using hg. I directly
downloaded the zip file from the address:
http://dist.g2.bx.psu.edu/galaxy-dist.tip.zip
That would be fine for a one-off test
On Fri, Feb 24, 2012 at 4:03 PM, Yingwei HU husi...@gmail.com wrote:
Dear all,
I found one of my binary files was corrupted after its uploading through
Get data'. I used editplus to check its hex code and found some 0D is
changed to 0A and also one byte is lost. May I ask how to solve this
On Wed, Feb 22, 2012 at 7:07 PM, dannonba...@me.com wrote:
Awesome, I'll take a look. And, if you're able to pull it together easily
enough, clean branches are always nice.
-Dannon
It is all on one new branch, but this covers FASTA splitting (ready),
splitting in the BLAST+ wrapper (ready
On Thu, Feb 16, 2012 at 9:02 PM, Peter wrote:
On Thu, Feb 16, 2012 at 6:42 PM, Chris wrote:
On Feb 16, 2012, at 12:24 PM, Peter wrote:
I also need to look at merging multiple BLAST XML outputs,
but this is looking promising.
Yep, that's definitely one where a simple concatenation
wouldn't
On Tue, Feb 21, 2012 at 5:49 PM, Borrone, James
james.w.borr...@okstate.edu wrote:
hello,
I am trying to use the FastX tools on the Main server to trim and manipulate
FASTQ files extracted directly from an sff file (again using the main galaxy
web server). In using Clip and the Reverse
On Sat, Feb 18, 2012 at 10:40 PM, Mikal Ustad mikal.e.us...@gmail.com wrote:
Hello,
I am part of a senior project group at Northern Arizona University. We are
interested in adapting Galaxy for a project related to building image
processing workflows. The existing system that we are working
On Mon, Feb 20, 2012 at 8:08 AM, Bram Slabbinck br...@psb.vib-ugent.be wrote:
Hi Dannon,
If I may further elaborate on this issue, I would like to mention that this
kind of functionality is also supported by the Sun Grid Engine in the form
of 'array jobs'. With this functionality you can
On Thu, Feb 16, 2012 at 9:02 PM, Peter wrote:
On Thu, Feb 16, 2012 at 6:42 PM, Chris wrote:
Cool! Seems like a perfectly fine start. I guess you could
grab the # of sequences from the dataset somehow (I'm
guessing that is set somehow upon import into Galaxy).
Yes, I should be able to get
On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker dannonba...@me.com wrote:
Main still runs these jobs in the standard non-split fashion, and as a
resource that is occasionally saturated (and thus doesn't necessarily have
extra resources to parallelize to) will probably continue doing so as long
On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker dannonba...@me.com wrote:
Good luck, let me know how it goes, and again - contributions are certainly
welcome :)
I think I found the first bug, method split in lib/galaxy/datatypes/sequence.py
for class Sequence assumes four lines per sequence. This
On Thu, Feb 16, 2012 at 10:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker dannonba...@me.com wrote:
Good luck, let me know how it goes, and again - contributions are certainly
welcome :)
I think I found the first bug, method split in
lib
On Thu, Feb 16, 2012 at 1:53 PM, Fields, Christopher J
cjfie...@illinois.edu wrote:
Makes sense from my perspective; splits have to be defined based on
data type. It could be as low-level as defining a simple iterator per
record, then a wrapper that allows a specific chunk-size. The split
Hi Dan,
I think I need a little more advice - what is the role of the script
scripts/extract_dataset_part.py and the JSON files created
when splitting FASTQ files in lib/galaxy/datatypes/sequence.py,
and then used by the class' process_split_file method?
Why is there no JSON file created by the
On Thu, Feb 16, 2012 at 4:28 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dan,
I think I need a little more advice - what is the role of the script
scripts/extract_dataset_part.py and the JSON files created
when splitting FASTQ files in lib/galaxy/datatypes/sequence.py,
and then used
Hi all,
The comments on this issue suggest that the Galaxy team is/were
working on splitting large jobs over multiple nodes/CPUs:
https://bitbucket.org/galaxy/galaxy-central/issue/79/split-large-jobs
Is there any relevant page on the wiki I should be aware of?
Specifically I am hoping for a
On Wed, Feb 15, 2012 at 5:08 PM, Dannon Baker dannonba...@me.com wrote:
It's definitely an experimental feature at this point, and there's no wiki,
but basic support for breaking jobs into tasks does exist. It needs a lot
more work and can go in a few different directions to make it better,
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu wrote:
Hello,
I was recently adjusting advanced parameters when running Tophat in Galaxy
and noticed that when advanced parameters are used, every field is converted
and submitted as command line parameter to the tool at
Hello all,
I've noticed we have about a dozen stalled upload jobs on our server
from several users. e.g.
Job ID UserLast Update ToolState Command LineJob Runner
PID/Cluster ID
235221 hours agoupload1 upload NoneNoneNone
...
2339
Hi all,
I've just updated our Galaxy to the current release 26920e20157f which
now includes quota support. This means I need to run
set_dataset_sizes.py in order to record the current usage, as
explained here:
http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas
However, I have run into a problem:
$
On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu wrote:
Hello,
I was recently adjusting advanced parameters when running Tophat in Galaxy
and noticed that when advanced parameters are used, every
On Thu, Feb 9, 2012 at 2:57 AM, Fields, Christopher J
cjfie...@illinois.edu wrote:
Forgot to add, but this also seems tied to the same problem
Ryan's describing. IIRC Galaxy also runs 'samtools sort' after
certain jobs, correct?
chris
This sounds like part of the BAM grooming (assuming
On Mon, Feb 6, 2012 at 6:17 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 6, 2012, at 1:05 PM, Nate Coraor wrote:
On Feb 3, 2012, at 7:30 AM, Peter Cock wrote:
On Fri, Feb 3, 2012 at 11:55 AM, Ryan Golhar
ngsbioinformat...@gmail.com wrote:
'qstat -f | grep jobname' will give you the full
On Thu, Feb 2, 2012 at 6:29 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 2, 2012, at 12:22 PM, Nate Coraor wrote:
Ahh, I see what's going on here. The drm out/err files are now
being written to the job working directory, which is cleaned up at
the end of the job wrapper's finish method,
Hello all,
We're not planning to try the new run cluster jobs as user
functionality (at least, not just yet), so for now all our SGE jobs
show on the cluster via qstat or any other monitoring tool as
belonging to the user galaxy.
Currently the jobs are submitted as shell scripts galaxy_NNN.sh
Hi all,
I'm trying to configure Galaxy to talk to our SGE cluster via DRMAA.
I've got jobs submitting, and can verify they are in the queue and then
run via qstat (from the cluster). However, something isn't right.
I'm testing with blastp using the following in universe_wsgi.ini
On Thu, Feb 2, 2012 at 1:54 PM, Langhorst, Brad langho...@neb.com wrote:
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...)
No sign of any SGE logs there - could be system configuration dependent,
but thanks.
Hi all,
I'm working on a test setup using an SGE cluster. During start of
run.sh up I see:
galaxy.jobs ERROR 2012-02-01 15:03:14,164 Job runner is not loadable:
galaxy.jobs.runners.drmma
Traceback (most recent call last):
File /data/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line
1187,
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