March 2012 - galaxy-dev - lists.galaxyproject.org

How to configure "Get Data | get microbial data"
by JIE CHEN 09 Mar '12

09 Mar '12

Dear all, I have spent several days trying to make "get microbial data" to work in my local Galaxy instance, but failed. What i did is: 1. cd /galaxy-dist/tool-data/ 2. nano microbial_data 3. uncomment the lines starting with "ORG", "CHR" or "DATA" After that, i restarted Galaxy and can see the options on the web. However, it cannot work yet. I am pretty sure that is because the URLs are not properly specified and i don't have a local mirror of all the related files yet. Can anyone help and tell me where and how to download the files? And how can i continue to make it work? (In addition, i find some information under the link http://gmod.827538.n3.nabble.com/Setting-up-microbial-data-loc-given-a-mirr…. But still cannot figure out how to do it) THANKS A LOT!!! Cheers, Tyler

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postgres
by christin weinberg 09 Mar '12

09 Mar '12

Dear all, I would like to clarify whether we have understood something about the database correctly. Is is right that all calculations with galaxy are stored as a link in the database. And the data are stored somewhereelse? Is it possible to store the data only in the database? For some advice, I am very grateful. Best regards, Christin -- Christin Weinberg Institute for Applied Computer Science (IACS) FH Stralsund - University of Applied Sciences Phone: +49 3831 456948 E-Mail : Christin.Weinberg(a)fh-stralsund.de

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Display galaxy variable
by Sarah Maman 09 Mar '12

09 Mar '12

Hello, In a Galaxy tool, I would like to display a pre-completed path in the xml inputbox, inside the tool.xml file. Consequently, I would like to add a variable in an <param value="" /> tag , like this : <tool id="test" name="test" version=""> <command interpreter="sh">test.sh $in $out</command> <inputs> <param name="filepath" type="text" size="100" value="/work/$out" /> </inputs> ... and in test.sh : $out is defined to be ${trans.user.username} Do you have any idea to display ${trans.user.username} variable in order to be shown in galaxy interface (gui) thanks to xml file ? I achieve to display ${trans.user.username} in /templates/root/tool_menu.mako but not in the xml file. Thanks in advance, Sarah

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Tool and dynamic <options>
by Yuri D'Elia 09 Mar '12

09 Mar '12

Hi everyone. I'm writing a tool that can take a parameter with a dynamic list of values. The tool XML file looks like this: <conditional ...> <param name="outer" .... type="select"> <option value="1">XYZ</option> <option value="2">ZYX</option> <option value="3">ZXY</option> </param> <when value="1"> <param name="inner" .... type="select"> ... </param> </when> </conditional> I would like to generate the inner <option> elements dynamically by calling an external utility in response to the first parameter ("outer"), or at least some piece of python code. I know I can use <options> to load this from an external file, but that's not enough. I tried to use <code>, but I'm afraid I wasn't able to generate the list of options dynamically (by using the first conditional when selected). I couldn't find a tool that uses <code> to this end. Does anybody have any suggestion? I was thinking of adding a new attribute to <options>, like <options load_from_command="....">. Would you accept such a patch to galaxy? Thanks.

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Re: [galaxy-dev] Welcome.html page
by Hans-Rudolf Hotz 09 Mar '12

09 Mar '12

On 03/09/2012 01:04 AM, Huayan Gao wrote: > Dear Hans, > > I emptied cache and it is not showing up the changes. I changed a computer and tried again. No luck. > > Yes, I killed the process and restart the server, no luck. > > It should be pretty straight forward but it just did not come out as I expected. > > Any ideas? > first (wild) guess: you have two galaxy servers (ie galaxy directories). you change the file in one, but in the web browser, you are looking at a different installation. so just double checking: what happens when you delete (ie re-name or move to a different location): ~/galaxy_dist/static/welcome.html ~/galaxy_dist/tool_conf.xml ~/galaxy_dist/tool_conf.xml.sample and restart the server? the missing "tool_conf.xml" should cause the start-up to fail Regards, Hans > Best, > Huayan > > > On 8 Mar, 2012, at 10:52 PM, Hans-Rudolf Hotz wrote: > >> Hi Huayan >> >>> I got a silly question for you. My galaxy is running now but I'd like >>> to customize it. >>> I've changed the welcome.html page but the galaxy mirror site is >>> showing the old one. Do I need to change some other files or other >>> configurations? >> >> Are you sure the page is not cached locally? >> >>> Also, I add<lable> in tool_conf.xml file but it does not show up >>> either. Is there another file I need to change too? >>> >> >> I assume you mean "label", have you restarted your galaxy server? >> >> >> I hope this helps >> Regards, Hans >> >> >> >> >> >>> Best, >>> Huayan >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >

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Re: [galaxy-dev] [galaxy-user] Problem using Galaxy on the cloud
by Brad Chapman 08 Mar '12

08 Mar '12

Jan; No problem, sorry I don't have a nicer immediate solution for you. I appreciate the problem report and hopefully we'll figure out a clean fix for this. CloudBioLinux does have Velvet included by default, so you should be able to use it without needing to compile. Were you having trouble building, or running it? Velvet and other assemblers are memory hungry, so the issue you were seeing may be due to running out of memory. 'top' is a useful way to monitor memory usage from the console. If it is a memory issue, AWS does have some high-memory instances you could try: http://aws.amazon.com/ec2/instance-types/ I don't have a lot of experience doing assembly so unfortunately don't have good estimates for memory usage. It might be worth asking on the Velvet mailing list if you are still running into issues. Hope this helps, Brad > Thanks Brad, > > I will see if I can do what you suggest-even if you are talking > Klingon now:) . I really just want to use Velvet, so I may try to > install it through CloudBioLinux-although last time I tried that I > seemed to crash everything. I really need to get better at this > stuff-or move to a place with bioinformatics support. > > Many Many Thanks, > Jan > > On Mar 7, 2012, at 9:22 PM, Brad Chapman wrote: > > > Jan; > Thanks for getting back with all the detailed information. I dug into > this further and understand what is happening: > > - tools/data_source/upload.py calls > lib/galaxy/datatypes/sniff.py:stream_to_file > - stream_to_file uses pythons tempfile module > - tempfile defaults to using /tmp > - As large files stream in the temporary space fills up, causing the > issue you are seeing. > > The best way to work around this is to have the galaxy user on Amazon > export TMPDIR to point at a temporary directory on /mnt/galaxyData > instead of the root filesystem. > > I'm hoping that Enis or Dannon might be able to help out with the best > place to set this in CloudMan to avoid the issue, I've cc'ed them in. > > If you want to manually fix it to get some work done, you could create a > directory /mnt/galaxyData/tmp and then symlink /tmp there: > > ln -s /mnt/galaxyData/tmp /tmp > > Hope this helps and we can come up with a more permanent fix. Thanks > again, > Brad > > > Thanks Brad, > Sorry it has taken me so long to respond. I had a meeting sort of day. I started another instance to recreate what is happening to me in more detail. I hope this helps. I tried to color code things so you could follow everything more easily. > > This is what I have when I start up Galaxy through BioCloudCentral before I import any files... > > Get cloud support with Ubuntu Advantage Cloud Guest > http://www.ubuntu.com/business/services/cloud > ubuntu@ip-10-44-78-218:~$ df -h > Filesystem Size Used Avail Use% Mounted on > /dev/xvda1 20G 13G 6.1G 68% / > udev 8.4G 4.0K 8.4G 1% /dev > tmpfs 3.4G 644K 3.4G 1% /run > none 5.0M 0 5.0M 0% /run/lock > none 8.4G 0 8.4G 0% /run/shm > /dev/xvdb 404G 201M 383G 1% /mnt > > After starting to import data (pasted https://s3.amazonaws.com/thunnus/BluefinAQ30_shuffled.fastq) it starts filling up immediately > > Filesystem Size Used Avail Use% Mounted on > /dev/xvda1 20G 19G 0 100% / > udev 8.4G 4.0K 8.4G 1% /dev > tmpfs 3.4G 660K 3.4G 1% /run > none 5.0M 0 5.0M 0% /run/lock > none 8.4G 0 8.4G 0% /run/shm > /dev/xvdb 404G 201M 383G 1% /mnt > /dev/xvdg1 700G 654G 47G 94% /mnt/galaxyIndices > /dev/xvdg2 10G 1.7G 8.4G 17% /mnt/galaxyTools > /dev/xvdg3 500G 81M 500G 1% /mnt/galaxyData > > > Jan McDowell > The Virginia Institute of Marine Science > The College of William and Mary > Department of Fisheries Science > Phone: 804-684-7263 > Fax: 804-684-7157 > mcdowell(a)vims.edu<mailto:mcdowell@vims.edu> > Non-text part: text/html

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local performance
by Charles Gawad 08 Mar '12

08 Mar '12

Hello, I am new to galaxy and bioinformatics in general. I have installed galaxy (and supporting software) on my mac pro with 8 cores and 24 Gb of memory. The main issue is that it runs really slow. When I look at CPU and memory allocation to python, less than 10% of each are being used. Is there an easy fix? thanks, Chuck

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unable to add tools in tool_conf.xml
by Sivasangari NANDY 08 Mar '12

08 Mar '12

Hi friends, I've got a problem, i'm not able to add a tool in ttol_conf.xml. Actually i can see one tool that i've added but when i put the second Galaxy doesn't take it into account : <section name="My_tools" id="mtools"> <tool file="mytools/tool_countGC.xml" />  <tool file="mytools/rec_expression.xml" />  </section> My paster.log gives that : galaxy.tools ERROR 2012-03-08 16:07:57,849 error reading tool from path: mytools/rec_expression.xmlTraceback (most recent call last): File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 446, in parse self.parse_inputs( root ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 528, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 708, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 801, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 813, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/parameters/basic.py", line 159, in build raise ValueError( "Unknown tool parameter type '%s'" % param_type )ValueError: Unknown tool parameter type 'string' Have you got aany idea ?advance thanks,

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refresh loc files without restart
by Bossers, Alex 08 Mar '12

08 Mar '12

Early 2011 there was a discussion and feature request to be able to refresh loc files on a running galaxy instance. This is not only convenient for updating loc files for blast, bowtie, bwa and such, but also opens possibilities to update and dynamically populate such files to be used in other custom tools. Is there any progress on this? Or has anyone hacked the system to be able to? Like the tool_refresh option? Alex

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uploads stuck in history
by Jorrit Boekel 08 Mar '12

08 Mar '12

Dear list, I have stumbled on some strange behaviour when uploading files to galaxy via the upload.py tool. At times, the upload seems to be stalled in history and is never actually performed, followed by a seemingly infinite history update (see log below). My system is Ubuntu 11.10 and runs Python 2.7.2. I find the behaviour in both my own modified galaxy install (based on galaxy-dist), and in a fresh clone from galaxy-central. I have tried to upload different files, and all seem to sometimes trigger the behaviour, but not all the time. A restart of galaxy sometimes sorts things out. Common for the debug messages is that it seems there is never a job id generated as in "galaxy.tools.actions.upload_common INFO 2012-02-22 10:06:36,186 tool upload1 created job id 2". Has anyone seen similar things or can it be a problem with my system? cheers, jorrit --------------Debug messa: galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request returned None from get_history(): http://localhost:8080/ 127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST /root/user_get_usage HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /root/user_get_usage HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:23 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:27 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:31 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:35 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:39 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:43 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 127.0.0.1 - - [22/Feb/2012:09:48:47 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"

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