NFS configuration questions + NFS /etc/fstab configuration issue with AMI issue
by Scott Jeschonek
Hi,
I’m setting up a ‘local’ Galaxy server in AWS and had a few questions that I can’t seem to answer.
1. Directory configuration in universe_wsgi.ini — I want to use an NFS from another server. The purpose would be to deposit results there. I may also want to point to another NFS server as a centralized reference / index file system. I tried changing the path for the Indices setting and restarted Galaxy, but CloudMan is showing the file system as “error”. Basically I am trying to wrap my head around the steps to re-pointing to NFS mounts (is it just change the paths in universe_wsgi.ini then restart everything?)
2. CloudMan AMI and fstab — I’m using the latest AMI Cloudman instance and it seems to have an issue with NFS configurations in the fstab. I am not quite sure what is going on, the entry is correct. I’m able to manually mount the filesystems as well so the paths are correct. Is there something specific I need to change on that image?
Thanks in advance for any assistance!
Scott Jeschonek
Avere Systems
6 years, 10 months
History not updated after upload from custom data source
by Jonathan Laperle
Hi,
I am trying to add a custom data source to my local galaxy following approximatly the methodology described here:
https://wiki.galaxyproject.org/Admin/Internals/DataSources?action=show&re... <https://wiki.galaxyproject.org/Admin/Internals/DataSources?action=show&re...>
The way I went about it is :
1. Galaxy displays my website in the middle frame with a GET containing an URL and a tool_id.
2. The user selects parameters and presses a button which sends a POST request at the URL obtained at point 1. This request contains the URL to download the file and the tool_id
3. Galaxy does a GET request to the given URL and downloads the file.
For the xml file it is mostly copy-paste from the UCSC main tool except that it ends with a get rather than a post.
The communication seems to work, in fact I can see that the data is properly written to a dataset_XXX.dat file at database/files/000/ just like UCSC. Unfortunately, despite not detecting any error there seems to be an issue as the history is never updated to reflect the fact that a file was added.
By comparing the terminal output of UCSC main and my custom data source tool I noticed that the difference was the following line which is not present when I run my tool:
127.0.0.1 - - [24/Jan/2015:19:17:30 -0400] "GET /api/histories/24d84bcf64116fe7/contents HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_1) AppleWebKit/600.2.5 (KHTML, like Gecko) Version/8.0.2 Safari/600.2.5”
This occurs right after:
galaxy.jobs.handler DEBUG 2015-01-24 19:17:30,330 (110) Dispatching to local runner
The request to the history API seems to never occur with my custom tool but I cannot figure out why.
Thank you for your help.
6 years, 10 months
Adding a new web-service or perhaps a "webapp" to Galaxy
by Lukasse, Pieter
Hi,
In one of my tools I generate a HTML report which I would like to enhance with some ajax functionality. I would like the possibility to do some backend computations based on the ajax requests.
My question is: is there an easy way to add a new web-service to my Galaxy server? The web-service implementation would be in python. Ideally I would like to be able to ship this python file together with my tool via tool shed (and when installing from toolshed, the necessary configurations are applied to the server to enable this python code as a local web-service on the respective Galaxy server).
Thanks!
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur
http://www.pri.wur.nl<http://www.pri.wur.nl/>
6 years, 10 months
show stopper for my galaxy installation
by Fernandez Edgar
Hello gents,
I started this new thread because I have a showstopper for my installation of galaxy.
Here's my situation:
1. I have a galaxy server that has internet access.
2. My galaxy server is also my torque server and my only torque submit node.
3. I have three torque compute nodes that DOESN'T have internet access.
Now, I've tried uploading a file (larger than 2Gb) via and URL and it fails.
However, I've added my galaxy server as a compute node and re-tried to upload the same file and I made sure the job will run on that machine and it works.
Now, my compute nodes are in a network that is completely protected from the outside world.
So no internet access.
What are my option in this case?
Cordialement / Regards,
Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
* Bur. : 1-514-343-6111 poste 16568
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-218
6 years, 10 months
Manually installing rsem_datatypes package from toolshed
by Ryan G
I'm trying to manually install rsem_datatypes package into my local Galaxy
install. I can't use the Toolshed for various reasons.
Anyway, I downloaded the package using
hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes
I see two files:
1) datatypes_conf.xml, and
2) rsem.py
I copied the <datatype extension ...> lines into my
config/datatypes_conf.xml file.
I also copied rsem.py to lib/galaxy/datatypes/.
When I restart Galaxy, it doesn't seem that Galaxy knows how to handle rsem
datatypes, as I get this error:
galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing
datatype module galaxy.datatypes.rsem: 'module' object has no attribute
'rsem'
Traceback (most recent call last):
File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line
210, in load_datatypes
module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'rsem'
galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing
datatype module galaxy.datatypes.rsem: 'module' object has no attribute
'rsem'
Traceback (most recent call last):
File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line
210, in load_datatypes
module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'rsem'
galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing
datatype module galaxy.datatypes.rsem: 'module' object has no attribute
'rsem'
Traceback (most recent call last):
File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line
210, in load_datatypes
module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'rsem'
I'm obviously missing something but not sure what. I suspect maybe the
rsem.py file is not in the right place?
Ryan
6 years, 10 months
Local Galaxy + Google Drive ?
by Nicholas Kline
Hello and Happy New Year,
Back in September 2014, Google announced unlimited storage for users
of Google Drive for Education:
"Unlimited storage: No more worrying about how much space you have
left or about which user needs more gigabytes. Drive for Education
supports individual files up to 5TB in size and will be available in
coming weeks."
source: http://googleforeducation.blogspot.com/2014/09/announcing-drive-for-educa...
Pardon me if I missed a discussion about this, but I was wondering if
there are any plans to include a feature in Galaxy that would allow it
to use Google Drive for storage instead of the local disk?
Thanks :)
6 years, 10 months
galaxy and torque - resource allocation
by Fernandez Edgar
Hello gents,
Hope everyone had a great holiday break!
Wish you guys all the best for 2015!
I have a couple of questions about how resources (CPU and memory) is allocated when you have a galaxy and torque installation.
So I've setup torque with some default and maximum amount of CPU and memory allocations.
However, I have some worries when it comes to application (like tophat for example).
By default, it takes half the CPU of a server unless specified otherwise.
How is the CPU allocation is specified to application like tophat through galaxy?
Also, how does galaxy react if a job needs more memory than the limit set by torque?
Any information would help me a lot!
My sincere salutations to you all!!!
Cordialement / Regards,
Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
* Bur. : 1-514-343-6111 poste 16568
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-218
6 years, 10 months
dataset collections
by Jorrit Boekel
Hi all,
I’m toying around a little in galaxy-dist with the dataset collections feature. Since I know this is work in progress, I was wondering about some things I haven’t really found online.
It seems to work really well to run a tool on a list of datasets, and a new job is run for each list item. But when I want to reduce to a smaller amount of list items, I understand I need to write some sort of merge tool myself, dependent on the data (all proteomics data here currently). This works well for reducing a dataset to a single file, but I am not sure about how to reduce to a new smaller collection. In the tool I’m writing, I let the user choose the size of the collection.
Is there some way to tell galaxy dynamically how many outputs to expect AND put them in a collection? Something like:
<outputs>
<output type=“data_collection” amount_of_files=“3”/>
</outputs>
Where 3 is set by the user in a param also.
Also, when running with two or more lists as input, is there some sort of correlation between the lists? It seems like it takes the files in dataset no order, so just checking.
By the way, thanks very much John and everyone else involved in collections for doing and pushing this stuff. If there are smaller issues I can help with, I’d be thrilled. Can’t stress enough how much this feature means for galaxy adoption in our lab and possibly field.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
6 years, 10 months
Setting a file download link in Galaxy help
by XiaoTao Jiang
Dear all
I have installed Galaxy in local and I want to set a file download link in
galaxy help. I want the user to download a small data-set from the help
with a link. However, the general HTML download syntax does not take
effect, look the figure I set.
Anyone knows how to set the download link?
[image: 内嵌图片 1]
Thanks for all your attention.
Regards
Jimmy
--
Department of Engineering
The University of HongKong
6 years, 10 months
