Hello Jianpeng,
The output files from TopHat are described on the TopHat tool form:
--- quote ---
Outputs
Tophat produces two output files:
junctions -- A UCSC BED track of junctions reported by TopHat. Each
junction consists of two connected BED blocks, where each block is as
long as
Picking up on this thread, I said:
As per the title, I'm trying to setup a toolshed for our local use. After
creating a repo, I try to upload the initial file only to get:
TypeError: array item must be char
Which seems to happen repeatedly, i.e. it's not a passing error.
And Greg
Hi everyone,
I as wondering if there was a way to get the history name of an input
dataset within a tool (i.e. in the cheetah between the command tags),
is there?
Thanks,
L-A
___
Please keep all replies on the list by using reply all
in
Ok, after a lot of testing and searching in the libs, I found the solution:
$inputdataset.dataset.history.name
Le 18/04/2012 10:22, Louise-Amélie Schmitt a écrit :
Hi everyone,
I as wondering if there was a way to get the history name of an input
dataset within a tool (i.e. in the cheetah
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
Hello Paul,
I apologize for somehow missing the first line of your paster log, which in
fact shows the upload step. Since you've tried uploading various files with no
success, the problem is likely to be caused by something specific to your
environment - possibly the version of the mercurial
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,
Hi,
Is it possible to pass the parameters of an input dataset?
For example: the user selects a dataset of the history. I want to pass
to my wrapperscript the input parameters of that dataset (the
information you see when clicking the small 'i' on a dataset in the
history).
Regards,
Joachim
Hi Frank,
This should be resolved as of changeset 7057:08fbfeaaf3e1. Thanks!
-Dannon
On Mar 27, 2012, at 4:37 AM, Frank Sørensen wrote:
Hi Dannon,
Unfortunately our server is (still) behind a firewall, so I can't share
anything, but I hope you can reproduce the error from the following
Hi Danny,
For moving workflows from one instance to another you'll want to click on
Download or Export in the workflow context menu and use the URL for
Importing to Another Galaxy. It looks something like this: (note the
for_direct_import, that's how you'll know you have the right link
I’m good with everything except the output dir. I can’t figure out how to
pass that directory information from Galaxy to the RUM_runner.pl in such a
way that Galaxy will be able to subsequently capture the data. Does anybody
have any advice, or can someone point me towards an existing
Thanks.
I have set up Mercurial to fetch updates from galaxy-dist, and it seems
that my version of galaxy is up to date.
- Should I pull from galaxy-central to get this update (7057:08fbfeaaf3e1)?
- If so, could you please tell me how I do that?
- Do you know how I permanently change
On Apr 18, 2012, at 8:44 AM, Frank Sørensen wrote:
- Should I pull from galaxy-central to get this update (7057:08fbfeaaf3e1)?
- If so, could you please tell me how I do that?
Sure, you can pull from galaxy-central by issuing a manual pull with source
from your galaxy-dist directory:
hg
Dear all,
We have our own galaxy instance and the idea is to have trackster enabled for
users to be able to visualize NGS mapping. We were able to configure trackster
in our instance and the visualization works fine.
We have two questions regarding trackster:
1) We can't display genomic
On Mar 26, 2012, at 12:18 PM, Shantanu Pavgi wrote:
{{{
TimeoutError: QueuePool limit of size 40 overflow 50 reached, connection
timed out, timeout 30
}}}
These limits are not reached for regular (non-workflow) galaxy jobs. Any help
on optimum values for these settings or performance
Hi Ross,
Thank you for your reply.
It still did not work.
I think SGE knows the path of samtools. Here is a test case I added to Galaxy,
and it creates the index for fasta file. I pasted the samtools faidx wrapper
and xml files below:
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$
--- 12年4月18日，周三, JIE CHEN jiechenable1...@gmail.com 写道：
发件人: JIE CHEN jiechenable1...@gmail.com
主题: Re: [galaxy-dev] Fetch taxonomic representation DOESN'T WORK
收件人: galaxy-dev@lists.bx.psu.edu
日期: 2012年4月18日,周三,上午5:36
On Tue, Apr 17, 2012 at 1:00 PM, JIE CHEN jiechenable1...@gmail.com
Hi, Cai - sorry to hear it's still not working right.
You've compiled/installed samtools using the --prefix configure option
and tested that all the samtools based Galaxy wrappers work if you use
the local job runner? That means that both the appropriate lib and bin
directories are on the Galaxy
Hi Ross,
I did not compile samtools using the --prefix. The samtools I used comes with
Galaxy AMI image, and I copied it to the same path on my EC2. How to compile
samtools using --prefix? I just typed 'make', and there is not a configuration
file. In the cloudman version of Galaxy (it is
Hi, Cai.
Apologies but I had not noticed any reference to the cloud
distribution before - that changes everything - I was talking about a
normal cluster/SGE install - you should definitely not need to do
anything at all to the AMI - maybe someone with cloudman experience
can be more helpful than I
Hi Ross,
I have a cloudman version of Galaxy working well. What I am doing now is trying
to install Galaxy on starcluster, which is a SGE cluster. I should followed the
install method for the normal cluster/SGE install, not for the cloud.
Thank you for your quick reply.
Have a nice day.
Cai
Hi Naharajan,
My best guess is that you've found some bugs. Fortunately, they are likely
fixed in galaxy-central and will soon be available in galaxy-dist (we're
planning an update in the next couple days). Once galaxy-dist is updated,
please try updating your Galaxy instance and seeing if
% sh manage_db.sh downgrade 92
% sh manage_db.sh upgrade
The downgrade to 92 and upgrade created job.params.
This is progress. You should be able to run jobs again, yes?
Unfortunately, we are still getting errors about duplicate key values. The
debug output when I try to export a history
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.
On Wed, Apr 18, 2012 at 3:20 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Wed, Apr 18, 2012 at 10:53 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi
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,
Hello,
I am trying to connect an EC2 instance to an EBS volume.
I have attached the EBS volume to the EC2 instance (running Galaxy). I now
need to mount the EBS volume to the EC2 instance. To do this I will use
Putty to make the connection. But first I have to convert the private key
from .pem
I have installed local galaxy and am using it to run some programs. The
output files in the history seems to be stored in the directory
.../galaxy-dist/database/files/000/, there are files dataset_100.dat,
dataset_120.dat etc. My question is that: If I run a program, is there a
way to check which
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. Right now,
mira can run successfully in the command line prompt. However when i
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 Mo,
On Wed, Apr 18, 2012 at 4:53 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote:
Hello,
I am new to cloud computing and am trying to use the Galaxy cloudman
service through Amazon to analyse NGS data. I have a couple of questions
regarding data transfer:
If I am running an EC2 instance,
The version I installed is : mira_3.4.0_prod_linux-gnu_x86_64_static
On Wed, Apr 18, 2012 at 3:31 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
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.
Mo,
I just tested one of my amazon keys with PuTTYgen and the default settings and
it worked. Can you verify the contents of the .pem file you're using for me?
On windows I'd open it in http://notepad-plus-plus.org/ or a similar utility to
see it correctly.
The file should look something
Hi,
I have ran Cuffdiff and got output files: transcript differential expression
testing, gene differential expression testing. Could you please tell me how to
get the significant differential expression gene and transcript ?
Thanks,
This e-mail message
Of course. I deleted lots of times. But be careful if some of the files are
important. Once you deleted them, all the files will disappear from the
user's history(or when you open them, you will run into errors). You should
know the files you are deleting.
On Wed, Apr 18, 2012 at 8:40 PM, diana
This would work for both .dat and tmp files? I was thinking about deleting
them manually but the idea of them being connected to a database was
bothering me. Other than minor errors, will there be no other serious
repercussions?
Thanks for the reply!
DM
On Thu, Apr 19, 2012 at 1:34 PM, JIE CHEN
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