September 2015 - galaxy-dev - lists.galaxyproject.org

Galaxy start problem
by Junchen Diao 09 Sep '15

09 Sep '15

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

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discover_datasets
by srodriguez 09 Sep '15

09 Sep '15

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/d1f51ff3c495b52b621ea6562ef… 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

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planemo and tool dependencies
by Steve Cassidy 09 Sep '15

09 Sep '15

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/

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Account Disabled
by Teshome Dagne Mulugeta 09 Sep '15

09 Sep '15

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

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SFTP configuration with ProFTPD
by Jose Juan Almagro Armenteros 09 Sep '15

09 Sep '15

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-p…", 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

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loading with Auto detect and fastqsanger options issue!
by Hakeem Almabrazi 07 Sep '15

07 Sep '15

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.

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docker-galaxy image with custom tools as new container?
by Piotr Grabowski 05 Sep '15

05 Sep '15

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

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Torque 5.0.1 pbs_python
by michael buren 04 Sep '15

04 Sep '15

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

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Mid 2015 Galaxy CloudMan release
by Dave Clements 03 Sep '15

03 Sep '15

*We just released an update to Galaxy CloudMan.* CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration or imposed quotas. Once running, you have complete control over Galaxy, including the ability to install new tools. This is the most complete update of the Galaxy on the Cloud platform to date with all the cloud components being built from the ground up. The following is a summary of the major changes: - *Galaxy on the Cloud*: all new galaxy and indices file systems, with Galaxy 15.07 release, ~200 preinstalled Galaxy tools, and nearly half a terabyte of updated reference genome data. - *Galaxy on the Cloud*: switched to a different Cloud Launch application, available athttps://launch.usegalaxy.org/ - *Galaxy on the Cloud*: Integrated Galaxy IPython Interactive Environments - *CloudMan*: Creating cluster shares is now fast (~30 seconds vs. hours) - Created a wealth of new documentation, including a description of the all new automated method for building private/custom instances https://wiki.galaxyproject.org/CloudMan/Building See the CHANGELOG <https://github.com/galaxyproject/cloudman/blob/master/CHANGELOG.md> for a more complete set of changes or just give it a try: see the all new Getting Started <https://wiki.galaxyproject.org/CloudMan/GettingStarted> documentation. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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July 2015 Galaxy Release (v 15.07)
by Martin Čech 03 Sep '15

03 Sep '15

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

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