Galaxy start problem
by Junchen Diao
Hi,
I am trying to install galaxy on my computer, after I run ' sh
run.sh', I got an error message as follows:
[Errno 1] Operation not permitted: '/Users/junchendiao/.python-eggs'
The Python egg cache directory is currently set to:
/Users/junchendiao/.python-eggs
Perhaps your account does not have write access to this directory? You can
change the cache directory by setting the PYTHON_EGG_CACHE environment
variable to point to an accessible directory.
I searched how to fix the python eggs problem, but none of which
succeeded. I wonder if you can help me to address this problem.
Thank you,
Junchen
--
Junchen Diao
Ph.D Candidate
Department of Systems Biology
UT MD Anderson Cancer Center
Houston, TX
USA
6 years, 11 months
discover_datasets
by srodriguez
Hi,
I am developing a tool with unknown output dataset number;
so, I am trying to use discover_datasets tag.
I have tested the following code as explained in the galaxy project
documentation:
https://bitbucket.org/galaxy/galaxy-central/raw/d1f51ff3c495b52b621ea6562...
But, when I look at he result, I only obtain a single dataset corresponding
to the "report".
When I check in the job_working_directory, no "subdir(1,2 and 3)" folders
have been created and no datasets displayed on galaxy as results.
Can someone help me understand how discover_datasets work and why all the
supposed multi datasets are not displayed in the galaxy interface?
Thanks in advance.
Best regards,
Sabrina
Sabrina LEGOUEIX RODRIGUEZ
Responsable Plateau Bioinformatique
TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue
Ariane • 31520 Ramonville Saint-Agne
Tél. : +33 (0) 5 61 28 57 92
sabrina.rodriguez(a)toulouse.inra.fr
www.toulouse-white-biotechnology.com
6 years, 11 months
planemo and tool dependencies
by Steve Cassidy
Hi all,
I'm trying to test some tools under planemo and can't find out how to
have it install tool dependencies while setting up the environment.
The dependency is on a particular python module and we have a
tool_dependencies.xml file to describe it. I can't see a way to tell
planemo serve etc to refer to that file to get the dependencies.
Any help appreciated.
Steve
--
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/
6 years, 11 months
Account Disabled
by Teshome Dagne Mulugeta
Hi,
One of our galaxy user is not able to login and gets "Account Disabled" message. It says "Your account is no longer valid, contact your Galaxy administrator to activate your account."
No one disabled the user and we couldn't find where to activate his account again.
Thanks for the help.
Cheers,
Teshome
6 years, 11 months
SFTP configuration with ProFTPD
by Jose Juan Almagro Armenteros
Hello everyone,
I am a bit stuck trying to set up a SFTP on my local Galaxy. I already have
an FTP server as described in the Galaxy wiki and in this post "
http://galacticengineer.blogspot.co.uk/2015/02/ftp-upload-to-galaxy-using...",
which works correctly with the user authentication.
The problem is that when I switched to SFTP (using some posts that
described how to do this on ProFTPD with mod_sftp.c), the user
authentication stopped working. I don't really know what specific
modifications should I do to the proftpd.conf file, which is the same as
the one in the wiki, to make it works.
I would really appreciate if you have any idea about how to change from FTP
to SFTP in Galaxy or if any of you have a config file working for SFTP.
Thank you and best regards,
Jose
6 years, 11 months
loading with Auto detect and fastqsanger options issue!
by Hakeem Almabrazi
Hi,
I have installed Galaxy as cluster in my local env. I have few fastq.gz files in my file system that I want to link them to galaxy instead of loading them. When I select "Auto Detect" during the loading I noticed two things.
First, it is taking way longer to link the files with the AutoDetect option compared to when I chose Fastqsanger as my file type. It takes less than a second if I specify the type, i.e Fastqsanger. Any reason why is that? Is there a way to speed up the first option (Auto Detect)?
Second, when it finish linking for AutoDetect option, it shows the DataType for these files as "data" rather than fastq files.
Does this mean my fastq.gz files are not recognize as fastq files?
To validate my fastq files, I tried to use FastqValidator tool I get an error saying "BGZF EOF marker is missing". How can I fix these files?
I appreciate any kind of help,
Regards,
Hak
Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.
6 years, 11 months
docker-galaxy image with custom tools as new container?
by Piotr Grabowski
Dear Galaxy-Devs,
I am currently developing a tool/workflow based on KNIME platform for data
analysis. The plan is for my group to publish this tool at some point and
we decided that Galaxy might be a very good platform to base it on. Galaxy
could simply run KNIME on a server (along with R script inside the KNIME
workflow) and serve the output files to the user.
However, I am quite new to the Docker concept and I am not sure if I get it
right. Do you think I could take the Galaxy Docker image (
https://github.com/bgruening/docker-galaxy-stable) and edit the container
so it would also contain KNIME and R with our workflow ?
This way I would like to obtain a Docker container that would have both
this Galaxy version plus our tools and that could be simply moved to
another machine to show, say, to my boss or deploy on a server for testing ?
>From the webpage I got the feeling that those docker images an
non-editable, is that right ?
I would be very thankful for helping me with the first steps!
All the best,
Piotr
6 years, 11 months
Torque 5.0.1 pbs_python
by michael buren
Hi,
I am following a previous posting
#47 (Torque 5.0.x Support) – pbs_python
| |
| | | | | |
| #47 (Torque 5.0.x Support) – pbs_pythonWe are using torque 5.0.0, so I downloaded the latest stable pbs_python version (4.4.0). I am having problems with the make portion of pbs_python (4.4.0) with torque (5.0.0). |
| |
| View on oss.trac.surfsara.nl | Preview by Yahoo |
| |
| |
Has ps_python egg-4.6.0 been released? Only the pbs_python-4.4.0 seems to be showing in the archives.Scrambling with pbs_python-4.4 and torque-5.0.1 doesn't seem to work:
[galaxy@system galaxy]$ LIBTORQUE_DIR=/opt/torque/5.0.1/lib/libtorque.so python scripts/scramble.py -e pbs_pythonfetch_one(): Using existing source, remove to download again: /nv/hp16/galaxy/galaxy/scripts/scramble/archives/pbs_python-4.4.0.tar.gzunpack_source(): Removing old build directory at: /nv/hp16/galaxy/galaxy/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_pythonunpack_source(): Unpacked to: /nv/hp16/galaxy/galaxy/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_pythoncopy_build_script(): Using build script /nv/hp16/galaxy/galaxy/scripts/scramble/scripts/pbs_python.pyrun_scramble_script(): Beginning buildrun_scramble_script(): Executing in /nv/hp16/galaxy/galaxy/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python: /usr/bin/python scramble.pyTraceback (most recent call last): File "scramble.py", line 14, in <module> from scramble_lib import * File "../../../lib/scramble_lib.py", line 146, in <module> from setuptools import * File "/usr/lib/python2.6/site-packages/setuptools-18.2-py2.6.egg/setuptools/__init__.py", line 11, in <module> from setuptools.extension import Extension File "/usr/lib/python2.6/site-packages/setuptools-18.2-py2.6.egg/setuptools/extension.py", line 8, in <module> from .dist import _get_unpatched File "/usr/lib/python2.6/site-packages/setuptools-18.2-py2.6.egg/setuptools/dist.py", line 21, in <module> packaging = pkg_resources.packagingAttributeError: 'module' object has no attribute 'packaging'Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/nv/hp16/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/nv/hp16/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) )galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0[galaxy@system galaxy]$ LIBTORQUE_DIR=/opt/torque/5.0.1/lib/libtorque.so python scripts/scramble.py -e pbs_python
6 years, 11 months
July 2015 Galaxy Release (v 15.07)
by Martin Čech
The very-slightly-delayed July 2015 Galaxy Release is out!
Full release notes:
http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html
Highlights
* *Interactive Environments* - The interactive environments (IE) framework
features several updates this release and Galaxy is now distributed with a
new IE for RStudio implemented by Eric Rasche.
* *Workflow Editor Enhancements* - The workflow editor has been
significantly revamped - it now uses newer tool form components and allow
construction of workflows with tools explicitly producing output
collections.
* *Policies for Committers and Pull Requests* - The process for adding
committers to the project and fielding pull requests has been formalized
and documented in the source code. Three new committers have been added to
the project - Björn Grüning, Nicola Soranzo, and Eric Rasche.
*Thank you for using Galaxy! *
The Galaxy Team
https://wiki.galaxyproject.org/GalaxyTeam
6 years, 11 months
