Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt
Hi everyone,
I just wanted to ask how the extra_file_path is handled in case of job
running as the real user since the file_path is only writable by the
galaxy user. Any clue?
Thanks,
L-A
5 years, 9 months
Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech
Hi,
you specify username, password and email in the body (payload) of the POST
as Key:Value pairs.
Code from the API method: (
https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/...)
username = payload[ 'username' ] email = payload[ 'email' ] password =
payload[ 'password' ]
There are also other conditions that need to be fulfilled (e.g. user
creation has to be turned on in the configuration) - you will find these
when you look at the source code of the method (because the documentation
is not perfect yet, sorry).
M.
On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote:
> hi,
> I still have some confusion.
> post /api/users , when i use postman, it seems like this:
>
>
> No other parameters? How to confirm the new user's information?Such as
> user name, password.
> Can you give me a example please?Thank you!
>
> At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote:
>
> Hello,
>
> to create a user through API you send a POST request to /api/users
>
> More information about User API here:
>
>
> https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galax...
>
> Martin
>
>
> On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote:
>
>> hello,
>> I want to create users through Galaxy API.For example, I can get users
>> information through url like this(use postman):
>> http://localhost:8080/api/users?key=my_key
>> But how to create a user?
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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>> and other Galaxy lists, please use the interface at:
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>>
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>>
>
>
>
>
6 years, 5 months
tabular file displayed without tabs
by Ryan G
Hi - I have a tools that generates a tab-delimited text file as output.
when I click the eye icon to view the data, all the fields are compressed
as if there were no tabs. If I expand the history view, the little preview
window shows the contents as tabbed. I've verified that the spaces are
indeed '\t' tab characters. Why would Galaxy not display this file as a
tab-delimited file?
6 years, 7 months
not sure what I can do about this...
by Fernandez Edgar
Hello Gents,
So someone asked me to install the package Prokka on Galaxy.
I did and everything went well!
However, the following error comes up, when they try to work with Prokka:
Fatal error: Exit code 2 ()
[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.
[20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null
According to a google search, there is very little on this error.
And it has been around for a while but I didn't find a posted solution.
Any suggestions?
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, 8 months
atlas 3.10 IUC error
by Olivier CLAUDE
Hello again,
I am truly sorry to bother everyone again but i still experience problems:
This time with atlas 3.10 owned by iuc
At the beginning without modifying anything, the error log was saying " mkdir : cannot create directory ATLAS/build : No such file or directory"
After that I tried to modify the tool_dependencies.xml :
L48 : "mkdir ATLAS/build &&" changed to "mkdir build &&"
The error is "/bin/sh: 4 : cannot open /host/static_full_blas_lapack.diff: No such file"
I can see it, if I go with a web browser, but I cannot download it manually nor click on it without crashing the web browser.
Any idea?
Thanks again,
M Olivier CLAUDE- PhD Student
INSERM/UPMC UMRS ICAN 1166 – Equipe 2
Faculté de médecine Pitié-Salpêtrière
91, bld de l'Hôpital - 3ème étage - Porte 305
75013 Paris - FRANCE
6 years, 8 months
Data removal after ftp import.
by Zuzanna K. Filutowska
Dear All,
is there any option to not remove files that has been imported to Galaxy
from FTP directory and to not remove files that haven't been imported
since 3 days?
--
Regards,
--
Zuzanna K. Filutowska, HPC Systems Administrator
Poznan Supercomputing and Networking Center
Institute of Bioorganic Chemistry Polish Academy of Sciences
Seize the day boys! Make your lifes extraordinary! --John Keating
6 years, 9 months
error loading files into galaxy
by Hakeem Almabrazi
Hi,
I started getting the following error whenever I try to load a file into Galaxy local.
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in <module>
from galaxy import eggs
ImportError: cannot import name eggs
I will appreciate if someone can tell me what could happen to cause such issue and how to resolve it.
Regards,
6 years, 11 months
Upload issue in local installation
by Batsal Devkota
I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever.
In the terminal window where I start galaxy, I get the following error report:
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
The last line keeps going for ever... writes new line every 4 secs.
I am stuck and don't know where to look. Please help.
Batsal.
7 years
python_mysqldb caused zip_safe flag not set
by Mic
Hello,
I tried to install CEAS from testtoolshed, but I have recieved the below
error from python_mysqldb
(tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f)
The installation directory for this tool dependency had contents but the
database had no record. The installation log may show this tool dependency
to be correctly installed, but due to the missing database record it is now
being set to Error.
I installed MariaDB 10.1 on Ubuntu 14.04 in the following way:
apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80
0xcbcb082a1bb943db
add-apt-repository 'deb [arch=amd64,i386]
http://mirror.aarnet.edu.au/pub/MariaDB/repo/10.1/ubuntu trusty main'
apt-get update
apt-get install mariadb-server libmariadbclient-dev
The INSTALLATION.log shows the following information:
...
byte-compiling build/bdist.linux-x86_64/egg/MySQLdb/cursors.py to
cursors.pyc
creating stub loader for _mysql.so
byte-compiling build/bdist.linux-x86_64/egg/_mysql.py to _mysql.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/SOURCES.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/top_level.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
creating dist
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Creating
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/site.py
Processing MySQL_python-1.2.5-py2.7-linux-x86_64.egg
Copying MySQL_python-1.2.5-py2.7-linux-x86_64.egg to
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
Adding MySQL-python 1.2.5 to easy-install.pth file
Installed
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/MySQL_python-1.2.5-py2.7-linux-x86_64.egg
Processing dependencies for MySQL-python==1.2.5
Finished processing dependencies for MySQL-python==1.2.5
#############################################
#############################################
export
PYTHONPATH=$PYTHONPATH:/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
&&
python setup.py install --install-lib
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
--install-scripts
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/bin
STDERR
zip_safe flag not set; analyzing archive contents...
What did I miss?
Thank you in advance.
Mic
7 years