galaxy-user January 2011

galaxy-user@lists.galaxyproject.org

47 participants
59 discussions

SNPs identity
by Elena Shumay 21 Jan '11

21 Jan '11

hi, is there a quick way to add an allele directionality (i.e., C->T) to the SNPs in a given region? thank you! best regards, elena

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Galaxy--upload data file
by Nan Deng 21 Jan '11

21 Jan '11

Hi, I installed Galaxy locally, and just start to use it, and I want to use it to align my short reads with fastq format using Tophat. The first thing I need to do is uploading my data file. If the data is small then that's no problem, but my data is about 5G, so when I upload, it took very long time (it is still uploading). Is it normal? and could you let me know how long it will take? I think since both Galaxy and my data are on my local machine, it should be very easy to let Galaxy know where the data is rather than uploading for such a long time. Thanks Nan

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Error with setuptools version in Galaxy installation on Cluster
by Sonali Amonkar 21 Jan '11

21 Jan '11

Hi, First of all I would like to appreciate the clean and neat documentation written for the Galaxy setup for Cluster. I am attempting to install Galaxy on Penguin cluster with Torque PBS manager. While following the steps I came across an error as below: =========================================================================================================================================================== [user@server pbs_python]$ /galaxy/Python-2.4.6/python scramble.py --------------------------------------------------------------------------- This script requires setuptools version 0.6c12 to run (even to display help). I will attempt to download it for you (from http://pypi.python.org/packages/2.4/s/setuptools/), but you may need to enable firewall access for this script first. I will start the download in 8 seconds. (Note: if this machine does not have network access, please obtain the file http://pypi.python.org/packages/2.4/s/setuptools/setuptools-0.6c12-py2.4.egg and place it in this directory before rerunning this script.) --------------------------------------------------------------------------- Downloading http://pypi.python.org/packages/2.4/s/setuptools/setuptools-0.6c12-py2.4.egg Traceback (most recent call last): File "scramble.py", line 14, in ? from scramble_lib import * File "../../../lib/scramble_lib.py", line 150, in ? use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) ) File "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py", line 92, in use_setuptools return do_download() File "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py", line 70, in do_download egg = download_setuptools(version, download_base, to_dir, download_delay) File "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py", line 131, in download_setuptools src = urllib2.urlopen(url) File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 130, in urlopen return _opener.open(url, data) File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 364, in open response = meth(req, response) File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 471, in http_response response = self.parent.error( File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 402, in error return self._call_chain(*args) File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 337, in _call_chain result = func(*args) File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 480, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) urllib2.HTTPError: HTTP Error 404: Not Found =========================================================================================================================================================== The scramble script here is trying to download an egg which does not exist at the location (try opening the link it is trying to download in a browser - you'll get 404, then see the parent directory - http://pypi.python.org/packages/2.4/s/setuptools/ you'll see last version available i.e. 0.6c11). If we try to download the last version of setuptools 0.6c11 and rename it to the latest version (desperate attempt to make it work), that doesn't work either. =========================================================================================================================================================== [user@server pbs_python]$ mv setuptools-0.6c11-py2.4.egg setuptools-0.6c12-py2.4.egg [user@server pbs_python]$ /galaxy/Python-2.4.6/python scramble.py checking for pbs-config... /usr/lib64/../bin/pbs-config Found torque version: 2.4.0-snap.200812091621 checking for python... /galaxy/Python-2.4.6/python checking for python version... 2.4 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.4/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.4/site-packages configure: creating ./config.status config.status: creating Makefile config.status: creating setup.py scramble(): Patching setup.py Traceback (most recent call last): File "scramble.py", line 49, in ? execfile( "setup.py", globals(), locals() ) File "setup.py", line 32, in ? build_version = int(tmp[2]) ValueError: invalid literal for int(): 0-snap =========================================================================================================================================================== Do let me know if anyone else has faced this issue of the scramble script trying to download a wrong version? Greatly appreciate your time. Warm Regards, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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Mark Your Calendars: Galaxy Developers Conference 25-26 May 2011, in the Netherlands
by Dave Clements 20 Jan '11

20 Jan '11

Hello all, This year's Galaxy Developers Conference will be held May 25-26, 2011 in the Netherlands. The meeting will feature two full days of presentations, workshops, and conversations by and for Galaxy community members. Please mark your calendars. We are in the final stages of making arrangements, and a full meeting announcement will be published in the coming weeks. Thanks, Dave C. -- http://usegalaxy.org/

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file uploads
by 望月孝子 20 Jan '11

20 Jan '11

Dear galaxy-user, When we want to use sam files in our local Galaxy server, we can copy the files in our local Galaxy server to "~/galaxy_dist/database/files/000/" to appear in "history" column in Galaxy window by "cp" command written in attempted script. The step, which is recognizing file guess long time. Could you please tell me if you know the methods, which are the data appear in "history" column faster. Best regards, Takako Mochizuki

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Order of input files when creating a workflow.
by Victor Ruotti 18 Jan '11

18 Jan '11

Hi, Just wanted to report this to see if there any way to keep the order of the input files when creating a workflow. When I create a workflow starting with 4 input files. I named then 1,2,3,4 respective in that order from top to bottom. However when try to run the workflow I get a random order of the files. For example the first time I get from bottom to top 3, 1, 4 ,2. And the order changes every time I try to re order them in the workflow. Thank for your feedback. Victor

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"interval" attribute for Input?
by Sonali Amonkar 18 Jan '11

18 Jan '11

Hi, Currently I am building a workflow which splits a file, say File 1 into chunks of files say File1.0, File1.1, File1.2. I used the interval attribute to have multiple outputs and got the chunks created successfully. <data format="interval" name="output" metadata_source="input"/> However, now I want to connect another tool to this, which Reads multiple inputs(interval). I could not find any documentation for Input interval type. Is this supported? If yes then where can I find the syntax? Warm Regards, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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Delete data library manually
by Jean-Baptiste Denis 18 Jan '11

18 Jan '11

Hello everybody, i'm a sysadmin in charge of installing a Galaxy server. I'm a totally beginner regarding this software. I've installed Galaxy using the documentation on the wiki (with Apache as a proxy and postgresql as database) and everything went fine. I've tried to create a new library as a galaxy admin. I've added a dataset using "Upload files from filesystem paths" without copying data into galaxy. To test the behaviour of Galaxy in a weird situation i've added "/" (:D), clicked on "Upload to library" and closed the navigation tab after one minute. As a result, the new data library appears under the "Manage data libraries" page. But, when i click on it, i've got a server error. Here is the traceback : -------------------------- .... File '/home/galaxy/galaxy-dist/database/compiled_templates/library/common/browse_library.mako.py', line 229 in render_render_content if not trans.app.security_agent.library_is_public( library, contents=True ): File '/home/sis/jbdenis/galaxy-dist/lib/galaxy/security/__init__.py', line 541 in library_is_public File '/home/sis/jbdenis/galaxy-dist/lib/galaxy/security/__init__.py', line 559 in folder_is_public File '/home/sis/jbdenis/galaxy-dist/lib/galaxy/security/__init__.py', line 559 in folder_is_public File '/home/sis/jbdenis/galaxy-dist/lib/galaxy/security/__init__.py', line 559 in folder_is_public File '/home/sis/jbdenis/galaxy-dist/lib/galaxy/security/__init__.py', line 562 in folder_is_public AttributeError: 'NoneType' object has no attribute 'dataset' -------------------------- My question is : how can i delete this library without messing with the database consistency? Any hints ?

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FW: Run tools/Workflow from command line
by Sonali Amonkar 17 Jan '11

17 Jan '11

Hi Jen, I agree what you mentioned on Tools. Does Galaxy have any provision for executing Workflows from command line too? Also about the API, I went through the Central version of readme link given by Roman. At initial glance I was unable to figure out what the scripts are for(am basically not familiar with Python). Until I try to figure that out, can you just let me know whether, in the first place, if Galaxy does provide (or has a Beta version planned of) some API library (say Galaxy.tar) which I can pick up and put in my Java project and then create workflows & tools? I am at a very initial stage of understanding Galaxy so do let me know if any question of mine sounds unclear. Thanks for your time. Warm Regards, Sonali Amonkar ________________________________________ From: Jennifer Jackson [jen(a)bx.psu.edu] Sent: Friday, January 14, 2011 9:23 PM To: Sonali Amonkar Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] Run tools/Workflow from command line Hi Sonali, Roman sent you the info for the API (thanks!) and here is some information about the command line usage. Basically, any of the tools can be run from the command line. Example: python <tool> <input file> < output file> All of the tool dependencies would need to be in place: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies Sort of related to this question, but also to a prior question: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax I don't know if you have this already, but this is a google search link for the Galaxy wiki at bitbucket. Add in your own search terms to locate documents - these will cover in detail most of these sort of topics. http://www.google.com/search?q=site%3Ahttp%3A%2F%2Fbitbucket.org%2Fgalaxy%2… You can also search prior mailing list posts, using google or Nabble at GMOD (GMOD only has most recent posts). http://www.google.com/search?q=site%3Ahttp%3A%2F%2Flists.bx.psu.edu%2Fpiper… http://gmod.org/wiki/Galaxy#Mailing_Lists Best, Jen Galaxy team On 1/14/11 1:50 AM, Sonali Amonkar wrote: > Hi, > > 1.Does Galaxy provide command line execution of Workflows / tools? > > 2.Does Galaxy provide API of its own, which can be imported as a library > in another program and used for executing certain workflows? > > Thanks for your time. > > Regards, > > Sonali Amonkar > > DISCLAIMER ========== This e-mail may contain privileged and > confidential information which is the property of Persistent Systems > Ltd. It is intended only for the use of the individual or entity to > which it is addressed. If you are not the intended recipient, you are > not authorized to read, retain, copy, print, distribute or use this > message. If you have received this communication in error, please notify > the sender and delete all copies of this message. Persistent Systems > Ltd. does not accept any liability for virus infected mails. > > > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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commercial support
by Attila Berces 16 Jan '11

16 Jan '11

Happy new year to all Galaxy users! Most of you are expert users and do not need commercial support. This email is to those who may benefit from support for using, customizing Galaxy pipelines or tailoring it and tuning it to their particular needs. If this is an interest to you please fill out our survey about commercial support http://www.surveymonkey.com/s/S3NW72Q thank you for your participation, Attila Berces Omixon

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galaxy-user January 2011