Hi Joachim,
At AgResearch we are using ZFS for our HPC storage, which is used by our
internal Galaxy instance. Currently we are running on FreeNAS (FreeBSD
derivative), but we are in transition to ZFS on Linux. We export the
filesystem over NFS (10Gb Ethernet), but not the database (PostgreSQ
Hi Vipin and Rui,
please have at the toolshed and test toolshed before developing
wrappers. For deseq2 there are already wrappers that are trying to solve
your issues and it would be nice if you could join that effort. Help
testing and contributing to it.
Ross has a cool wrapper of edgeR, DESeq2
We have migrated bowtie tool wrapper from dist to tool-shed using migration
script # 7 with install_dependencies option. We removed our locally installed
bowtie binaries so that install_dependencies option would work fine. I think an
earlier release would skip dependency installation if they we
Cool, I got a tweet about this tool from @GalaxyProject[1].
To further explain what I'm trying to accomplish here, as I realized
not everybody might know what using "Multiple Output Files" and
specifically "Number of Output datasets cannot be determined until
tool run"[2] entails.
The current Bar
There is currently no simple way to circumvent this behavior. If you want to
modify the code, take a look at display_data() in data.py -- you'll want to
bump up the max_peek_size (line 351 in -central) above 10 MB for HTML datasets.
Good luck,
J.
On Sep 9, 2013, at 6:16 AM, Gromobir wrote:
> H
I am having trouble getting a toolshed tool to be dispatched to the destination
I list in the job_conf.xml file.
My job_conf.xml file looks like this:
... stuff
Hello Rui,
We have DESeq2 wrapper in our oqtans package and you will find this at
https://github.com/ratschlab/oqtans_tools/tree/master/DESeq2
I am currently creating the associated tool_dependency.xml file for dumping
the package in galaxy toolshed. otherwise it requires some manual effort to
in
Hello,
I was wondering if there is any possibility to access user data from a galaxy
user using plugins such as OmniAuth. Of course the user would first have to
permit access for the web service using tools such as OmniAuth. If OAuth is not
yet available, it would be a nice feature to add.
B
Hi All,
we are making a wrapper for deseq2, and there is a step where
control/experimental conditions
need to be determined. For example, it would be a column like the following
in the input file
Type
CTC
CTC
LM
LM
PT
PT
and we want the select list to contain
CTC
LM
PT
In other words, we want
Dear all,
I have succeffully installed the local instance of Galaxy, that uses the
postgeSQL database, and it worked fine. After several monthes of uses, it
appeared the neccessety to reinstall the whole Galaxy. For this, I have
completely removed the old instance, and hg clone the new one to the
Hi Jennifer,
That's true. Completely forgot about this option which it is more
convenient than downloading and re-importing. I still think I need the
Multiple Output Files route cause I really want to automate the full
processing of the data using the API.
Thanks for pointing it out,
Carlos
On
Hi,
I've just updated my galaxy-central version and I can't use the tool shed
installer via admin user any more. When I click 'Install to Galaxy' it
throws and 500 error.
Could you please verify that? I tried the URL from tool_shed_url in the
browser and it also doesn't open.
Thanks,
Adhemar
1
Hi Joachim,
Something that may help with benchmarking: At the July 2012 GalaxyAdmins
meetup, Anne Black-Ziegelbein talked about how they evaluated filesystem
options. She also included benchmarking scripts and data. See
http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2012_07_09
> optimize performance? The purpose is to share the database over NFS to the
> Galaxy VM.
Are you moving the PostgreSQL/MySQL database over to ZFS or the actual
storage of your datasets over to ZFS? I am assuming the latter.
Remember, ZFS is just a file system, you still need a protocol, like
NFS,
Hi John,
Some news on the debugging yet?
I managed to deploy blend4j in my local maven installation, so now I
can test the client.setChunkedEncodingSize(CHUNKED_ENCODING_SIZE);
line on my setting.
Unfortunately with ChunkedEncoding enabled, it seems that the file is
not (recognized by || sent to
Galaxy Tearm,
I use "Select" in "Filter and Sort" to sort my sam file in my local Galaxy.But
I got "no peek " under "Matching pattern: ^@" ,while I got the same sam file
under "NOT Matching pattern: ^@" .Actually,I can got the correct results in
Galaxy main,I don't know what happened to my loca
Dear Administrator,
My apologies for using more than one account in Galaxy Main Server.
I am a master student. I present my thesis this month.
Please, re-enable my accounts for a week to give me time to download the
data I need. I have no time to redo all my experiments.
I'm sorry for the incon
Hi all,
I am performing some tests to move my galaxy database to ZFS. Does
anybody have experience with ZFS on linux, and some
recommendations/experiences to optimize performance? The purpose is to
share the database over NFS to the Galaxy VM.
Thanks,
Joachim.
--
Joachim Jacob
Contact deta
Okay.
So 'binary' and 'python-module' module are currently just treated
differently from 'package' in this context because they are kind of
not in use? But isn't it then a good idea to also include these type
tags into the dependency management system by generally changing this
line to:
On Tue, Sep 10, 2013 at 9:16 AM, Hans-philipp Brachvogel
wrote:
> Hey Dave,
>
> thanks for the reply! Guess I wrote too much and explained badly what I
> meant. I had already tested the Managed Tool Dependencies, but my problem
> was that those only work for xyz
>
> They do not handle type="pytho
Hello all,
There's a post-doc opening in the Makova Lab at Penn State. See below.
Dave C
Are you interested in genomics and do you have skills in Bioinformatics,
Computational Biology and Statistics? The Makova lab in the Department of
Biology at The Pennsylvania State University is looking to
Hey Dave,
thanks for the reply! Guess I wrote too much and explained badly what
I meant. I had already tested the Managed Tool Dependencies, but my
problem was that those only work for type="package">xyz
They do not handle type="python-module", which is what I am looking for (beacuse of our
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