May 2011 - galaxy-dev - lists.galaxyproject.org

new galaxy-dist fixes multiple IE UI bugs
by Leandro Hermida 25 May '11

25 May '11

Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE, for e.g. the workflow editor works now works and the history expand/collapse works! :)

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galaxy download
by jasmine jacob 24 May '11

24 May '11

Hi, I am a new linux user, would like to use galaxy directly on my computer could you instruct me how to download galaxy? thanks Jasmine Jacob-Hirsch Functional Genomics Cancer Research Center Sheba Medical Center 972-3-5302147 972-523790500

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Fwd: Your message to galaxy-dev awaits moderator approval
by shashi shekhar 24 May '11

24 May '11

---------- Forwarded message ---------- From: <galaxy-dev-bounces(a)lists.bx.psu.edu> Date: Mon, May 23, 2011 at 11:42 AM Subject: Your message to galaxy-dev awaits moderator approval To: meshashi29(a)gmail.com Your mail to 'galaxy-dev' with the subject requirement of complete command in code file Is being held until the list moderator can review it for approval. The reason it is being held: Post by non-member to a members-only list Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://lists.bx.psu.edu/confirm/galaxy-dev/32ca9fa0742b2f4b3a3e5ad2f9c57f06…

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nice quality Galaxy logo and name
by Leandro Hermida 24 May '11

24 May '11

Hi there, Would anyone have a nice quality Galaxy logo and name image for presentations and posters? I've been using the one in the left hand corner of the server which ok but wondering if there is a better official one or something regards, leandro

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Load balanced configuration unable to access Admin -> Manage jobs?
by Olen Vance Sluder Jr 24 May '11

24 May '11

I have had good success in setting up a load balanced configuration with nginx except that I get the following error when accessing Admin -> Manage jobs: "This Galaxy instance is not configured to run jobs. If using multiple servers, please directly access the job running instance to manage jobs." When I access the runner instance directly at <http://localhost:8079/admin/jobs>, the browser just hangs with no response. A quick search of the wiki and the dev mailing list archive didn't turn up a solution, so any help would be appreciated. Thanks, Olen

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Re: [galaxy-dev] egg install failure: docutils, GeneTrack
by Spunde, Alex 24 May '11

24 May '11

Same thing: [aspunde@ilmnhw-biolin10 galaxy-dist]$ python ./scripts/fetch_eggs.py Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-li nux-x86_64-ucs2.egg Fetched http://eggs.g2.bx.psu.edu/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998 f0caf01c5be731e926f4b0481f658f0-py2.6.egg One or more of the python eggs necessary to run Galaxy couldn't be downloaded automatically. You can try building them by hand (all at once) with: python scripts/scramble.py Or individually: python scripts/scramble.py Babel python scripts/scramble.py docutils python scripts/scramble.py GeneTrack From: Spunde, Alex Sent: Monday, May 16, 2011 10:56 AM To: 'galaxy-dev(a)bx.psu.edu' Subject: egg install failure: docutils, GeneTrack Hi Trying to install Galaxy on local machine, using hg: hg clone http://bitbucket.org/galaxy/galaxy-dist Get error messages for two eggs: Scrambling the following eggs failed: docutils GeneTrack Here is more details for docutils (practically same for GeneTrack): [aspunde@ilmnhw-biolin10 galaxy-dist]$ python scripts/scramble.py docutils fetch_one(): Using existing source, remove to download again: /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/archive s/docutils-0.7.tar.gz unpack_source(): Removing old build directory at: /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/build/p y2.6/docutils unpack_source(): Unpacked to: /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/build/p y2.6/docutils copy_build_script(): Using build script /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/scripts /generic.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/build/p y2.6/docutils: /escher/bioinfoHW/opensource/lib/bin/python scramble.py Traceback (most recent call last): File "scramble.py", line 29, in <module> execfile( "setup.py", globals(), locals() ) IOError: [Errno 2] No such file or directory: 'setup.py' Traceback (most recent call last): File "scripts/scramble.py", line 44, in <module> egg.scramble() File "/escher/bioinfoHW/opensource/Galaxy/galaxy-dist/lib/galaxy/eggs/scrambl e.py", line 57, in scramble self.run_scramble_script() File "/escher/bioinfoHW/opensource/Galaxy/galaxy-dist/lib/galaxy/eggs/scrambl e.py", line 206, 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 docutils 0.7 Here is basic info about system: [aspunde@ilmnhw-biolin10 galaxy-dist]$ python --version Python 2.6 $ hg --version Mercurial Distributed SCM (version 1.8.3) $ uname -a Linux ilmnhw-biolin10.hwus.illumina.com 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Thanks Alex Spunde

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Re: [galaxy-dev] Uploading Binary Files into Galaxy
by Darren.Cullerne＠csiro.au 24 May '11

24 May '11

Hi All, Sorry for the delay, I have had a couple of other projects on the go. Still no good. I have made the data type unsniffable and added what I thought was the correct information. I have also added the extension (sfx) to the list of unsniffable binary formats in binary.py but it does not make a difference. Code is as follows: ./datatypes_conf.xml <datatype extension="sfx" type="galaxy.datatypes.binary:Sfx" display_in_upload="true"/> ./lib/galaxy/datatypes/binary.py class Sfx( Binary ): """ Kanga and uAssembler Suffix Array """ file_ext = "sfx" def __init__( self, **kwd ): Binary.__init__( self, **kwd ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Suffix Array sfx' dataset.blurb = 'binary data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' My gut feeling is that this is related to the fact that Galaxy wants to look in the file, but as soon as its opened, it can't recognise the characters and it reports "The uploaded binary file contains inappropriate content". I thought the set_peek method I have above would override the one described in the Class Binary. I have tried adding a sniffer tag into datatypes_conf.xml, but I get the same result whether the sniffer tag is there or not. I am sure I have missed a step or piece of content but I have no idea what I am missing... Thanks again for your time, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.cullerne(a)csiro.au<mailto:darren.cullerne@csiro.au>

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Follow the 2011 Galaxy Community Conference on Twitter
by Dave Clements 24 May '11

24 May '11

Hello all, The 2011 Galaxy Community Conference starts in about 10 hours with the sold out Introduction to Galaxy session, and then gets fully rolling Wednesday morning with the main meeting. See the schedule ( http://galaxy.psu.edu/gcc2011/Programme.html) for full details. If you want to follow the meeting on Twitter, we are encouraging copious tweeting by participants using the #usegalaxy hashtag. You can follow at https://twitter.com/#!/search/%23usegalaxy or http://galaxy.psu.edu/gcc2011/Home.html In addition, NBIC, the conference host, is also sponsoring the videotaping of all 23 talks. These will be placed online after the conference and will be open to anyone. We have 148 registered attendees (about twice as many as last year) form 19 countries (6 continents!) Well over 100 different organizations will have representatives at the meeting. I'm expecting great things. Thanks, Dave C -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Problem fore getting tool Command in code file
by shashi shekhar 24 May '11

24 May '11

Hi All, I need the tool command in code file and want to change the command . is there any way to change the command which is given under command tag . Reagrds shashi shekhar

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Uploading Binary Files into Galaxy
by Darren.Cullerne＠csiro.au 24 May '11

24 May '11

Hi All, Sorry for the delay, I have had a couple of other projects on the go. Still no good. I have made the data type unsniffable and added what I thought was the correct information. I have also added the extension (sfx) to the list of unsniffable binary formats in binary.py but it does not make a difference. Code is as follows: ./datatypes_conf.xml <datatype extension="sfx" type="galaxy.datatypes.binary:Sfx" display_in_upload="true"/> ./lib/galaxy/datatypes/binary.py class Sfx( Binary ): """ Kanga and uAssembler Suffix Array """ file_ext = "sfx" def __init__( self, **kwd ): Binary.__init__( self, **kwd ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Suffix Array sfx' dataset.blurb = 'binary data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' My gut feeling is that this is related to the fact that Galaxy wants to look in the file, but as soon as its opened, it can't recognise the characters and it reports "The uploaded binary file contains inappropriate content". I thought the set_peek method I have above would override the one described in the Class Binary. I have tried adding a sniffer tag into datatypes_conf.xml, but I get the same result whether the sniffer tag is there or not. I am sure I have missed a step or piece of content but I have no idea what I am missing... Thanks again for your time, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.cullerne(a)csiro.au<mailto:darren.cullerne@csiro.au>

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