- galaxy-dev - lists.galaxyproject.org

upload from local filesysem
by J. Greenbaum 23 May '12

23 May '12

It seems that this topic has been covered at least several times and I've found this thread to be helpful: http://user.list.galaxyproject.org/Speed-up-uploading-into-local-Galaxy-ter… However, as far as I understand, this will only allow the Admin to do the upload from a local disk. Has anyone had success allowing a regular user to upload from a local disk? This seems like a common issue, particularly with large sequencing files. It would be great to be able to add this as the first step in a workflow. Any info would be appreciated. Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgbaum(a)liai.org La Jolla Institute for Allergy and Immunology

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Create Trackster visualizations via API
by Ayton Meintjes 23 May '12

23 May '12

Is it possible to create visualizations via the API yet? Can't seem to find an example. Ayton

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specifying nodes/processors with PBS
by J. Greenbaum 23 May '12

23 May '12

Hi, I've successfully configured a local galaxy instance to submit jobs to our local cluster, but have a question regarding setting PBS options such as the number of nodes and processors to use. I've followed the guide here: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster?highlight=%28pbs… Is there any way to do this in a tool-specific manner. For example, for running tophat to do a mapping run, I would want it to use 24 CPUs, but for simply converting a file type I would want only 1 CPU requested. Is there a way to specify this somewhere? Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgbaum(a)liai.org La Jolla Institute for Allergy and Immunology

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cannot access conditional parameter in command
by Anne Pajon 23 May '12

23 May '12

Hi, I'm writing a galaxy tool xml file for an in house existing R script. I have a conditional parameter set for selecting the dataset to work with but I would like to access the path of the file from the data table I've created: <table name="cri_datasets" comment_char="#"> <columns>value, name, path</columns> <file path="tool-data/cri/datasets.loc" /> </table> Here is the beginning of the xml file: <command interpreter="R --vanilla --slave -f"> rp.R --args $dataset.name.fields.name $dataset.name.fields.path $input $column $output_txt $output_html $output_html.files_path $dataset.outcome $dataset.receptor $dataset.treatment $dataset.er $dataset.age $dataset.grade $dataset.signature $dataset.margins $dataset.groups $dataset.gleason $dataset.tstage 2>stderr || cat stderr 1>&2 </command> <inputs> <param name="input" type="data" format="tabular,txt" label="Source file" help="File containing a list of gene symbols"/> <param name="column" type="data_column" data_ref="input" numerical="False" label="Column" help="Column containing gene symbols (only available for tabular input file)" /> <conditional name="dataset"> <param name="name" type="select" label="Dataset"> <options from_data_table="cri_datasets" /> </param> ... but when running the tool, here is the error message I get: Traceback (most recent call last): File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/runners/local.py", line 59, in run_job job_wrapper.prepare() File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/__init__.py", line 429, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py", line 1971, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/opt/local/home/webapp/galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'fields' while searching for 'dataset.name.fields.name' Is it possible to access the other columns of a loc file? It seems possible based of what I read on the wiki http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coptions.3E… using from_data_table and syntax of ${param.fields.path} but I could not manage to make it work. Any help would be very much appreciated. Thanks! Kind regards, Anne. -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon(a)cancer.org.uk | +44 (0)1223 404 334 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

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Pushing changes upstream to Galaxy
by Peter van Heusden 23 May '12

23 May '12

Hi there As I adapt Galaxy to the needs of the particular workflows I'm implementing, I invariably end up "tweaking" the existing code, especially the tool definitions and the datatypes config file. These tweaks are often minor - e.g. adding an extra parameter to Ross Lazarus' ClustalW's code, changing the way the binary is called (e.g. clustalw2 on ubuntu is installed as clustalw, BLAST+ is installed single threaded so the -num_threads option in the ncbi_blastn_wrapper.xml doesn't work), but a) Sometimes they make sense to share with the rest of the Galaxy community b) local changes make it more tricky to keep in sync with upstream changes to Galaxy What's the best procedure for proposing changes up upstream galaxy? Posting patches to galaxy-dev? Is there some mercurial magic that can help? Thanks, Peter

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LateValidationError in Extract features
by Peter van Heusden 23 May '12

23 May '12

Hi there I've got a workflow that uses BioPerl's bp_genbank2gff3 to convert Genbank to GFF3, then hands the GFF3 to Extract features to filter to only genes, before moving on. The workflow JSON is at http://pastebin.com/zHWsC6YT. Step 4 - the Genbank2GFF runs fine, and if I view the output in the history I can see the resulting GFF, but step 8 - the Extract features, fails with a LateValidationError, as follows: Traceback (most recent call last): File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 144, in queue_job job_wrapper.prepare() File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/jobs/__init__.py", line 130, in prepare self.tool.handle_unvalidated_param_values( incoming, self.app ) File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1872, in handle_unvalidated_param_values self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1890, in handle_unvalidated_param_values_helper self.handle_unvalidated_param_values_helper( input.cases[current].inputs, values, app, context, prefix ) File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1912, in handle_unvalidated_param_values_helper raise LateValidationError( message ) LateValidationError This Galaxy is Postgres and SGE, with galaxy-dist as of last night. Another strange thing is that while I select that the output of step 4 should be visible, it is, in fact, hidden in the new history. How to debug this? How can I see which input is not validating? Thanks, Peter

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Uploading problem
by julie dubois 23 May '12

23 May '12

Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor. Thank you Julie

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Load Files in local instance Ubuntu 12.04 LTS /tmp as /tmpfs
by Luciano Cosme 22 May '12

22 May '12

Hi, I decided to format my PC and reinstall everything. I have Ubuntu 12.04LTS installed in one 1TB hard drive (/ and swap) and the /home folder installed in a 3TB hard drive. I created a /tmp partition of 110GB and a /tmp partion of 110GB, both in the 1TB HD. Then I mounted /tmp as /tmpfs using fstab. Here is the df -h output: Filesystem Size Used Avail Use% Mounted on /dev/sda2 817G 3.9G 771G 1% / udev 12G 4.0K 12G 1% /dev tmpfs 100G 16K 100G 1% /tmp tmpfs 4.8G 992K 4.8G 1% /run none 5.0M 0 5.0M 0% /run/lock none 12G 148K 12G 1% /run/shm /dev/sdb2 2.6T 99G 2.4T 4% /home /dev/sdc1 1.9T 1.6T 301G 84% /media/My Book Then I try to upload files as administrator on my local instance of galaxy and it fails. Since I even have a swap partition with 100GB and using the /tmp partition I don't know why it is not working. What I notice is that it is using the /tmpfs mounted on /run, which is only 4.8GB. I also tried to change universe.ini to use /tmp as temporary files storage: # Temporary files are stored in this directory. new_file_path = /tmp I can upload files that are smaller than 4.8GB, but not bigger than it. Previously it was working fine on the other Ubuntu version. I was using /tmp as tmpfs, but I don't know how to configure the Galaxy to use the the tmpfs mounted at /tmp and not the tmpfs mounted at /run. I asked similar question before and I was able to fix it on Ubuntu 10.04 LTS, but now Ubuntu have this tmpfs mounted on /run, which is not in fstab. Thank you. Luciano -- *Luciano Cosme* --------------------------------------------- PhD Candidate Texas A&M Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 cosme(a)tamu.edu ---------------------------------------------

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param.dynamic_options: How can I disable escaping HTML tags?
by Tim te Beek 22 May '12

22 May '12

Hi all, Up until today I was happily using the following to produce the options for a Galaxy tool of mine based on a daily updated remote resource: """ <code file="select_taxa.py"/> ... <param name="genomes" type="select" display="checkboxes" multiple="true" optional="true" force_select="false" label="Choose Genomes" dynamic_options="get_complete_genomes()"> """ The get_complete_genomes() call returns and iterator with tuples of ("Label", "Value", False), which are shown to the user. Previously, any HTML tags I added in "Label" were correctly rendered in the browser. However, since updating Galaxy to the latest distribution this morning, my HTML tags now are escaped which shows the tags to the user rather than changing the rendering. Rendering the HTML tags was crucial to retain readability in a tree with over 2000 options, so I would like to enable it again (disable escaping) in my local installation. How can I disable escaping HTML tags in my param.dynamic_options? Thanks in advance, Tim

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Newbie question, adding a custom perl script
by Ciara Ledero 22 May '12

22 May '12

> > Hi there! > Recently, I modified a Galaxy-intended velvet script so that the user would be able to put in his/her desired output directory ( the original script does not allow this). I just used a text box so as to ask for the output directory path (e.g. /home/galaxy/outputFolder). Then I just let Perl do the rest. Maybe in your case, you could just ask for the input and output directory paths. Then maybe you could just generate a text file that logs the end status of the process (i.e. whether it has been successful or not). This text file would be the one that shows up in your history. Cheers, CL Hi, > > A co-worker has a perl script that takes a directory path, and then > interates over a the file in that directory and processes them into an > output directory. > I want to integrate that into galaxy. I've figured out that I'll need > to create a tool XML conf with the inputs , outputs etc. > > My question is what param type should I use for a directory, in the > input and output ? Or maybe what I'm looking for a is an input, output > type that is a set of file (rather than tying it to a filesystem) > > Sorry for my beginners questions ! > > Thanks > > Mac > >

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