Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
by TerAvest, Emily
Hi Leandro,
I am also experiencing the same problem with the latest version of galaxy. I just attempted to connect our sequencer for the first time yesterday. I do not have an older version of galaxy to test and compare to see if it works in earlier versions. I am able to transfer data from the sequence to the import directory, however it is not moved to the data library. My data_transfer.log also has the same error.
"The server could not comply with the request since it is either malformed or otherwise incorrect."
Does anyone have a solution for this?
Thanks
Emily
------------------------------
Message: 17
Date: Wed, 28 Mar 2012 13:15:47 +0200
From: Leandro Hermida <softdev(a)leandrohermida.com>
To: Luobin Yang <yangluob(a)isu.edu>
Cc: Galaxy Dev <galaxy-dev(a)bx.psu.edu>
Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in
queue" forever
Message-ID:
<CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA(a)mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Galaxy Dev,
Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you <Location
/> ... </Location> container to not match URLs starting with /api. To
do this you have to change it to <LocationMatch "^/(?!api)"> ....
</LocationMatch>.
best,
leandro
On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang <yangluob(a)isu.edu> wrote:
> I've got the same problem and when I looked at the data_transfer.log, I saw
> the following message:
>
> 2012-03-01 15:12:27,338 - datatx_13870 -
> (u'9c17d84742cd2acb63d88b5bd41d968f',
> u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
> {'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
> 'new_status': 'Adding to data library'})
> 2012-03-01 15:12:27,342 - datatx_13870 - Error. <!DOCTYPE HTML PUBLIC
> "-//IETF//DTD HTML 2.0//EN">
> <html><head>
> <title>405 Method Not Allowed</title>
> </head><body>
> <h1>Method Not Allowed</h1>
> <p>The requested method PUT is not allowed for the URL
> /api/samples/2d9035b3fc152403.</p>
> <hr>
>
> Using Galaxy instead of Apache as the web server changed the sample status
> from "in queue" to complete but didn't add the downloaded files to the data
> library.
>
> Luobin
>
> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
> <softdev(a)leandrohermida.com> wrote:
>>
>> Dear Galaxy Dev,
>>
>> I've set up the Galaxy sample tracking system data transfer
>> functionality exactly as specified here
>> https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
>> attempt to transfer datasets it puts them into the queue and then
>> never seems to transfer anything.
>>
>> The galaxy_listener.log shows:
>>
>> 2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
>> {'config_file': 'universe_wsgi.ini', 'http_server_section':
>> 'server:main'}
>> 2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
>> 'rabbitmqctl_path':
>>
>> '/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
>> 'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
>> 'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
>> 'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
>> '5672'}
>> 2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
>> 127.0.0.1:5672
>> 2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
>> 2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
>> 2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
>>
>> "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py"
>> " <data_transfer>
>> <galaxy_host>rd-galaxydev.app.pmi</galaxy_host>
>> <api_key>69bbd1a9b18eda2a888e9963820d8ef0</api_key>
>> <data_host>chp723</data_host>
>> <data_user>galaxy</data_user>
>> <data_password>mypassword</data_password>
>> <request_id>12</request_id>
>> <sample_id>12</sample_id>
>> <library_id>15</library_id>
>> <folder_id>52</folder_id> ? ? ? ? ? ? ? ? ? ?<dataset>
>> ?<dataset_id>10</dataset_id>
>> <name>ttt_2.fastq.gz</name>
>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz</file>
>> ? ? ? ? ?</dataset><dataset>
>> <dataset_id>9</dataset_id>
>> <name>ttt_1.fastq.gz</name>
>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz</file>
>> ? ? ? ? ?</dataset> ? ? ? ? ? ? ? ?</data_transfer>"
>> "universe_wsgi.ini"
>>
>> The FASTQ files are for testing and aren't very big (7.6 MB), what
>> could be going wrong?
>>
>> regards,
>> Leandro
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. ?To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> ?http://lists.bx.psu.edu/
>
>
************
This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its
affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for
the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete
this email from your system and notify the sender immediately. If you are not the intended recipient, you should not
disclose, distribute, use or copy this email or take any action in reliance on its contents.
10 years, 6 months
Announcement: Galaxy Reference Data
by Nate Coraor
Hi all,
A frequent request we've had is to make the locally cached reference data used by the public Galaxy server (Main) available for download to local installations. To facilitate this, we've created an rsync server at datacache.g2.bx.psu.edu that serves the exact reference builds and associated indexes that we use on Galaxy Main.
Fetching and installing such data is currently a manual process, so Dave Bouvier has been working on an administrative UI in Galaxy for automatically fetching references and building indexes. Keep your eyes on the development news briefs for an announcement once this feature is ready.
--nate
10 years, 6 months
for question
by huafang sheng
Hi,
I am a master student in Southern Medical University of China.
Thank you so much for LEFse development,which is a very important tool in microbial community data analysis. And I have try it on line,just found it failled for these two datasets. Woud you help me to check what is happend?
Thank you for your appreciation and looking forward to hear from you soon.
Best Wishes,
Yours sincerely,
Ms. Hua-Fang Sheng
10 years, 6 months
index file
by Unknown
Hi galaxy team,
How can we make an index file for a presorted bam file using galaxy?
Thanks,
Deepthi
10 years, 6 months
annoying bug when deleting datasets
by David Hoover
I recently switched from galaxy-dist to galaxy-central as the source of my local install (version 7427:cb9272041d95). When I delete a dataset from a history, all the delete icons disappear from the datasets. They come back if I refresh the page. Has anyone else noticed this?
David Hoover
Helix Systems Staff
10 years, 6 months
help
by romain desprat
I am trying to work on 23 giga text file. My laptop being not powerful
enough I have split it in 10 files and made some modification on them. Now
I have made (linux and window) a double boot on my laptop and install
galaxy ( on the linux partition). Unfortunately, galaxy doesn t have enough
memory to work with this file.
My question is : is it because I did not allocate enough memory to
galaxy/linux partition when I did the double boot ( 5 giga f I recall
right ) or is it because galaxy over 2 giga anyway will not be able to
handle the situation.
Thanks any advices are welcome,
Romain
romain.desprat(a)einstein.yu.edu
10 years, 6 months
Help to run a C program
by Rodrigo Faccioli
Hi,
I'm newbie in Galaxy. In fact, this is my first post.
I'd like to create a web-interface to run a C program. It is necessary a
config file which is used as input to this program. Therefore, the values
of parameters are informed by user through this web-interface. Its output
is some files.
I searched in Galaxy wiki some examples or tutorials. However, I didn't
find anything that helped me. I'm confused in what I can do.
Could you help me showing where I can find specific materials?
Best regards,
--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structural Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-8739
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
Personal Blogg - http://rodrigofaccioli.blogspot.com/
10 years, 6 months
having a directory and all contents retained as the 'output'
by Brian Haas
Greetings,
I have a process that is going to generate dozens of output files,
each of which I want to retain as a data repository that will be
leveraged by other downstream tools. I could just point the
downstream tool at the directory, and it'll know what to look for,
rather than to have to list each output file as a separate parameter.
Is it possible to do this in Galaxy? And is there a best practice (or
example) for it?
thanks!
-b
--
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
10 years, 6 months
