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

Downloading datasets without username/password when login is required
by Sytchev, Ilya 26 Feb '13

26 Feb '13

Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya

2 3

Tabular file metadata - columns names
by Peter 22 Feb '13

22 Feb '13

Hi all, I'd like to know more about Galaxy's column metadata for tabular files. In the workflow editor under "Edit Step Actions" you can pick "Assign Columns", and then give column numbers for five predefined cases: Chrom, Start, End, Strand, Name. Do these "named columns" get shown anywhere in the Galaxy UI? For example, in a column select parameter widget? Is it possible to assign these columns in a tool's wrapper XML file? >From http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax I'm aware of the metadata_source attribute to *copy* the meta data from the input file, but that isn't always relevant. Can I somehow specify that my tool has tabular output where column 1 is "Name"? Is it possible to introduce additional column types? e.g. "evalue" or "Description". Thanks, Peter

3 7

environment variables and paths for toolshed tools
by David Hoover 20 Feb '13

20 Feb '13

Are there any environment variables that are honored by toolshed installed tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or $GALAXY_HOME, then uploaded it the test toolshed, then installed it automatically. Neither of these resolved to what I expected. I don't want to hard-code the path in the xml tool file, but rather have a default location for other executables and jar files. How should this best be done? David Hoover Helix Systems Staff

3 14

changing datasets file_path storage location
by Shantanu Pavgi (Campus) 19 Feb '13

19 Feb '13

We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed? -- Thanks, Shantanu

3 4

run_functional_tests.sh -sid option
by Peter 11 Feb '13

11 Feb '13

Hi, I'm trying to use run_functional_tests.sh to run all the tests for a section (group of tools). I've read the output from: ./run_functional_tests.sh help For example, from the tools_conf.xml.sample we have <section name="ENCODE Tools" id="EncodeTools"> <tool file="encode/gencode_partition.xml" /> <tool file="encode/random_intervals.xml" /> </section> And looking at these tools' XML files, <tool id="gencode_partition1" name="Gencode Partition"> and: <tool id="random_intervals1" name="Random Intervals"> I'd like to run the functional tests for the ENCODE tools, Using the switch for an individual tool id (-id) works, ./run_functional_tests.sh -id gencode_partition1 ... Ran 1 test in 22.302s ... and so does this (well, it say the tool doesn't have any tests which is true in this example): ./run_functional_tests.sh -id random_intervals1 ... Ran 1 test in 0.027s ... However, I also tried using the section id switch (-sid), ./run_functional_tests.sh -sid EncodeTools ... Ran 0 tests in 0.000s ... I also tried using the section name, /run_functional_tests.sh -sid "ENCODE Tools" Is this (-sid not working) a known issue, or am I using it wrong? Thanks, Peter

4 5

deleted_new kills handlers
by Ido Tamir 22 Jan '13

22 Jan '13

Dear galaxy maintainers, we have the problem that killing jobs running on drmaa before they run leading to a deleted_new state, kills our handlers (sometimes?). The job gets sent to the handler, but the handler never acknowledges the jobs (local and drmaa) and all submitted jobs afterwards stay in submitted state. Normally submission works fine, running also. Is such a problem known to anybody else? in my universe_wsgi.ini: enable_job_recovery = False I don't know which other settings could affect this. Could it be an old drmaa library, maybe because the SGE was updated after galaxy installation? Other ideas? thank you very much, ido

2 2

Visualise Galaxy workflows using graphviz
by Peter van Heusden 21 Jan '13

21 Jan '13

Hi there Because my Galaxy workflows tend to sprawl outside the viewable space in my browser, I've written a script that, when given a workflow JSON file as input, writes out a graphviz dot format graph of the workflow. By default the graph treats datasets as nodes and analyses as edges (unlike the Galaxy workflow editor, but quite like the way the history is presented), but you can choose to have analyses as nodes (and thus datasets as edges) too. In case anyone else finds this useful, the code can be downloaded from my bitbucket: https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_… Usage is something like: ./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg >workflow.svg and then you can view your workflow.svg with eog or another viewer. Peter

3 3

Job output not returned from Cluster
by Sascha Kastens 17 Jan '13

17 Jan '13

Hi all, I have exactly the same problem as described here: http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879… All the SGE stuff is administrated in our company and unfortunately they know nothing about Galaxy and so it?s my task to get it running. Everything works fine except the problem mentioned above. I?ve contacted Erick but haven?t received a response yet. If anybody can give me some hints where I can look at to solve the problem or at least what I can tell the admins, I would be really grateful. Thanks in advance. If you need further information let me know! Cheers, Sascha

4 8

Re: [galaxy-dev] [galaxy-bugs] galaxy.genenetwork.org
by Lei Yan 11 Jan '13

11 Jan '13

Dear Dannon and James, On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker <dannonbaker(a)me.com> wrote: > > • I installed a Cloud Galaxy instance one month ago, and a user > reported that it still has some problems. At that time, I found that it can > be upgraded to new version in the administration page, so I did so. But its > log showed that it “has error”, and the service cannot start. I then tried > to reboot the machine, but Galaxy still could not start and the service is > not responding. > > Can you share the cloud log? This would be the best place to look to find > out what the errors are. > For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”. > > > • Then I tried to build a new Cloud Galaxy, but after trying at > least 8 times it still didn’t work. Each time, after I launched the Cloud > Galaxy instance, even its State is "running" and the "Status Checks" is > "2/2 checks passed”, but it would still not respond if I opened “http:// > ******.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on > the cloud". > > Can you share any more information about this? Can you confirm that > you're using the supported AMI, have launched with the correct security > groups, etc? For future reference, just using usegalaxy.org/cloudlaunchis probably the easiest way to make sure you avoid any launch issues. Are > you able to SSH in to the instance? > I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to "Welcome to Galaxy on the cloud". > > > > Could you please give us some suggestions or let us know who we should > contact about this issue? > > Sending email directly to galaxy-bugs, as you have, for stuff you'd rather > not share with the wider community is the best bet. For anything that > isn't sensitive, emailing galaxy-dev is useful if you're working with > customized or local/cloud installs. > > > I cannot find any telephone number on the Galaxy community pages, and it > would be better if I could talk to someone about the problem over the phone. > > Would it be helpful to chat over IRC and debug this? See the "IRC > Channel" information on http://wiki.galaxyproject.org/Get%20Involved. > > -Dannon Thanks so much for your help. Lei Yan leiyan2000(a)gmail.com UTHSC

3 4

Transfer Manager
by Kyle Ellrott 09 Jan '13

09 Jan '13

Is there any documentation on the transfer manager? Is this a mechanism that I could use to synchronize data libraries between two different Galaxy installations? Kyle

3 4