- galaxy-dev - lists.galaxyproject.org

Setting the output label based on input parameters?
by Nikhil Joshi 16 Sep '11

16 Sep '11

Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik.

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redirecting sdterr
by Mikel Egaña Aranguren 16 Sep '11

16 Sep '11

Hi; I'm sure this has been mentioned before but perhaps it has been fixed. I'm writting a wrapper of a Java tool for Galaxy. The tool throws info to stderr even when working properly, and Galaxy interprets it as a bug. Is there any way of redirecting stderr (It seems that normal UNIX redirection to a file does not work) or making Galaxy ignore it? Thanks -- Mikel Egaña Aranguren, PhD http://mikeleganaaranguren.com Marie Curie post-doc at Ontology Engineering Group, UPM http://www.oeg-upm.net/

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optional integer value in tool config
by Sarah Diehl 16 Sep '11

16 Sep '11

Hello, in the config of a tool I want to integrate into Galaxy I would like to have a parameter with the following properties: <param name="var" type="integer" label="Var" value="50" optional="true" min="10" max="100" /> So it should be possible to leave this field empty, but when you choose to enter a number it should be between 10 and 100. The problem now is that Galaxy refuses to accept it when this field is empty. After encountering this problem I tried to solve the issue within Cheetah and tried the following: #if $var.value < 10 or $var.value > 100 #set $var.value = "" #end if Galaxy however throws the following error when loading the tool: galaxy.tools ERROR 2011-07-04 14:04:14,231 error reading tool from path: path/to/tool.xml Traceback (most recent call last): File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/galaxy/galaxy_server/lib/galaxy/util/__init__.py", line 104, in parse_xml tree = ElementTree.parse(fname) File "/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 583, in parse parser.feed(data) File "/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1242, in feed self._parser.Parse(data, 0) ExpatError: not well-formed (invalid token): line 230, column 21 The token it is complaining about is the <. I searched the Cheetah documentation and also Google but was not able to come up with a solution. Could anyone of you knowledgeable guys help me find a solution to this, please? I would be very grateful! Thanks in advance! Best regards, Sarah

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Re: [galaxy-dev] [galaxy-user] galaxy test-data organization
by Jennifer Jackson 16 Sep '11

16 Sep '11

> To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > You will want to choose one or both of these: http://lists.bx.psu.edu/listinfo/galaxy-user http://lists.bx.psu.edu/listinfo/galaxy-dev -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Re: [galaxy-dev] [galaxy-user] galaxy test-data organization
by Jennifer Jackson 16 Sep '11

16 Sep '11

Hello Joe, Functional test-data is located here in the source: http://bitbucket.org/galaxy/galaxy-central/src/07c5fbd618f3/test-data/ The name/comments of each is the best way to understand the link between a test and a tool (could be many-to-many). Next time, a question like this about a local instance would be better directed to the galaxy-dev(a)bx.psu.edu mailing list, so I am going to forward this there. There is an active user community, perhaps someone has organized the functional test data in a different other way for their own purposes and would like to share the method. Thanks for using Galaxy! Best, Jen Galaxy team On 8/27/11 7:17 AM, Joseph Hargitai wrote: > ===> Please use "Reply All" when responding to this email!<=== > > > > > > Hi, > > is there by any chance a per application breakdown of the test-data > structure? > > best, > joe > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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passing environment to pbs runner
by Oleksandr Moskalenko 15 Sep '11

15 Sep '11

I need to get Galaxy to use tools that are not located in the system path. At the command line I can export the PATH either manually or with environment modules 'module load foo'. However, there doesn't seem to be a clear way to pass the $PATH and other environmental variables to the pbs runner. For instance, I use Torque with a dedicated "galaxy" queue. So, I configured the "default_cluster_job_runner = pbs:///galaxy/" in universe_wsgi.ini. The problem is that the pbs runner does not pass the environment to the scheduler. I sort of circumvented this by sourcing an environment setup file from 'pbs_template' in pbs.py, but I keep wondering about a better way to do it. I currently use tools set up using environment modules, so this is what I added the following to pbs_template: . /etc/profile.d/modules.sh module load bio Thanks, Alex

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Re: [galaxy-dev] Contribution of tools to galaxy main server
by Greg Von Kuster 15 Sep '11

15 Sep '11

Hello Dongjun, Thanks very much for your interest in sharing this tool with the Galaxy community. At this time the process for sharing tools is to upload your tool to the Galaxy tool shed at http://toolshed.g2.bx.psu.edu/. Ideally your tool will include functional tests and your tool shed repository will include small input / output datasets for these tests. If your tool uses any 3rd party dependencies, the <requirements> tag set in the tool config should reflect them appropriately. For clarification on tool config syntax, see our wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax. In the past, the process used by the core Galaxy development team to share tools was to include them in the Galaxy distribution, but we are beginning to phase this process out, replacing it with the tool shed. Over time we will be eliminating tools from the distribution, and local Galaxy instances will install them from the Galaxy tool shed. This same process will be used for populating our main Galaxy instance here at Penn State with tools. So for now, please upload your tool to the tool shed. Thanks again, Greg Von Kuster On Sep 9, 2011, at 4:08 PM, Dongjun Chung wrote: > Dear Greg von Kuster, > > Hello, this is Dongjun Chung, a PhD student at the University of Wisconsin-Madison. > > We recently developed a tool for galaxy and hope to contribute our tool to galaxy main server. We have developed a tool for allocation of multi-reads (reads that map to multiple locations on the reference genome) in ChIP-seq. In contrast, basically all the currently available ChIP-seq peak callers utilize only uni-reads (reads the map to a unique location on the reference genome). This tool implements our paper recently published in PLoS computational biology: > > Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E, Dewey C, and Keles S (2011), “Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data,” PLoS Computational Biology, 7(7): e1002111. > > http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.100… > > We believe that our tool could be appropriate for galaxy main server because there is no tool for this purpose in the server yet and this tool should be beneficial to general galaxy users, especially researchers studying eukaryotic genomes. We already completed developing corresponding wrapper and tool definition files for galaxy. Our tool can accept FASTA/FASTQ as input and its output can also work nicely with diverse ChIP-seq peak callers such as MACS peak caller which is already in the galaxy main server. > > If the galaxy development team can accept our tool as a part of galaxy in the main server, please let us know anything you need for us to contribute our tool to galaxy. We can prepare what is needed to meet the requirements. > > Sincerely, > Dongjun Chung > > PhD student > Department of Statistics > University of Wisconsin-Madison > > On 09/09/2011 12:59 PM, Dongjun Chung wrote: >> >> >> >> ---------- Forwarded message ---------- >> From: Greg Von Kuster <greg(a)bx.psu.edu> >> Date: Wed, Aug 31, 2011 at 2:38 PM >> Subject: Re: [galaxy-dev] contribute tools to galaxy? >> To: Dongjun Chung <dongjun.chung(a)gmail.com> >> Cc: galaxy-dev(a)lists.bx.psu.edu >> >> >> Hello Dongjun, see my answers to your question inline. >> >> On Aug 28, 2011, at 10:12 AM, Dongjun Chung wrote: >> >>> Hi All, >>> >>> I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great work. >>> >>> I have a question regarding contribution of software to galaxy. We developed a ChIP-seq peak calling algorithm and software (R package) and hope to contribute it to galaxy. I have read the wiki and prior mailing list about the contribution system but it is still somewhat confusing to me. >>> >>> 1. It seems that I can contribute our software to "tool shed" if I prepare appropriate code & definition files. Then, users can download and use it with their locally installed galaxy. However, these files committed to tool shed will not appear in galaxy main or test servers. Am I correct? >> >> Tools from the Galaxy tool shed may or may not be available in the Galaxy test / main servers hosted at Penn State. >> >>> >>> 2. What is clear relationship between main/test servers & tool shed? >> >> The Galaxy tool shed enables the Galaxy community to share tools. These tools are generally used in local Galaxy installations, but not available on the Penn State instances. >> >>> Can we contribute our software to main or test servers as well? >> >> The tools available on the Penn State servers are generally developed by the Galaxy core development team, and are available in the Galaxy distribution. If your tools complement the tools currently available in the distribution, the Galaxy core development team may agree to include them. However, see my comments 2 answers below regarding upcoming enhancements to Galaxy and the tool shed. >> >>> Or only galaxy core developers can add new tools to galaxy main or test servers? >> >> Yes. >> >>> If so, which software is considered to be added to servers? Are they chosen from tools contributed to tool shed? >> >> Currently, tools available in the distribution and on the Penn State instances are generally developed by the core Galaxy development team. However, upcoming enhancements to Galaxy and the Galaxy tool shed will enable automatic installation of tools from the tool shed into local Galaxy instances, eliminating the necessity to include tools in the distribution. This automation will be available fairly soon. >> >>> >>> 3. If our software is a R package, then users need to download and install it first in their R system before they use our software within their galaxy system even in the case they have appropriate definition files. Am I right? Or is there any better solution for this? >> >> If your tools require R, then those that use your tools will need to install R in the Galaxy environment path so the tools will be functional. Tools that have dependencies like this should include a <requirements> tag set in the tool config. >> >> See http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequiremen… >> >>> >>> Thanks! >>> >>> Best, >>> Dongjun ___________________________________________________________ >>> 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/ >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> >> > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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ProFTPd on Ubuntu system.
by Luobin Yang 14 Sep '11

14 Sep '11

Hi, Has anyone set up ProFTPd successfully on Ubuntu 10.04 to enable FTP upload on Galaxy? I followed the instructions on this link ( http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't work. Thanks, Luobin

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Re: [galaxy-dev] cluster path question
by Ann Black 14 Sep '11

14 Sep '11

Hello everyone - I am also running into this issue trying to get galaxy integrated with our sun grid engine. My galaxy user's .bash_profile does not appear to get sourced when the jobs run. I augmented the sample sam_filter.py tutorial such that it output path and user info so I could see how the jobs were being run: out = open( sys.argv[2], "w" ) out2 = open("/data/galaxy-dist/ann.out", "w") out2.write(socket.gethostname()) out2.write("\n") out2.write(os.environ['PATH']) out2.write("\n") drmaa = os.environ.get('DRMAA_LIBRARY_PATH') if drmaa is None: out2.write("None") else: out2.write(os.environ.get('DRMAA_LIBRARY_PATH')) out2.write("\n") out2.write(str(os.geteuid())) out2.write("\n") out2.write(str(os.getegid())) shutil.copytree("/data/galaxy-dist/database/pbs","/data/galaxy-dist/ann") the job is being dispatched as my galaxy user, however the my augments to PATH and additional env vars that I have exported in our galaxy user's .bash_profile are not present when the script runs (ie, .bash_profile is not sourced). When I use qsub to manually run the galaxy script that gets generated under database/pbs, the output to ann.out reflects my PATH and exported env vars. Was there any other solution to this issue besides the drmaa.py script augment? Thanks much for your help, Ann

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Upgrading postgres version
by James Vincent 13 Sep '11

13 Sep '11

Hello, We'd like to migrate from postgres 8.4 installed system wide through Ubunutu package manager to postres version 9 installed from source. Is there a smooth and easy route for this or is it the manual database dump/migrate pain that I think it will be? Thanks, Jim

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