May 2015 - galaxy-dev - lists.galaxyproject.org

History/Dataset UUID instead of integer ID?
by Ben Bimber 06 May '15

06 May '15

Hello, I am working with blend4j and bioblend to interact with galaxy. In general, the API seems to require the UUID of a dataset/history, etc. I may be missing something obvious, but I am not finding great ways to obtain this from cheetah substitutions. For example, I can use ${history.id} or ${ output.id} to get the integer ID of that dataset/history. ${output.uuid} is not recognized. I am looking here as a reference: https://github.com/galaxyproject/galaxy/blob/e73d90c94edc63d181c30bd1942918… https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/model/__init__.… and would have expected UUID to get exposed in some manner. Is there a standard way to obtain the UUID? Thanks, Ben

2 2

bam split and gatk calling
by Roberto Alonso CIPF 06 May '15

06 May '15

Hello, I have been working in the Galaxy parallelization module and I would like to ask you some questions that I have about how to face one problem. I have done one pull request about splitting bams: https://github.com/galaxyproject/galaxy/pull/184 Regarding this, I think it is useful but it could be more while accessing somehow the interval. I better explain it with an example: If I define a simple tool like this, with the parallelism tag "actived": <tool id="gatk" name="call with gatk"> <description>gatk</description> * <parallelism method="multi" split_mode="by_interval" split_size="100000000" merge_outputs="output" split_inputs="input" ></parallelism>* <command> ## by_rname ln -s $input input.bam; samtools index input.bam; UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/hg19_ucsc.fa -I input.bam -o $output -L *REGION* ; </command> <inputs> <param format="bam" name="input" type="data" label="bam"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs> <help> bwa </help> </tool> The region is based on the field split_size, it is better explained in the PR. How does the code from the PR work? It goes through the bam file and does something like "samtools view *REGION *-o bam_splitted.bam", so then GATK does the calling for this small bam, but what is the problem? As you know, in the software GATK if you don't pass the region as an argument in the command line it goes through all the genome, so it is very slow. So, what would you recommend to me to be able to pass this information to GATK? I was thinking to create, at the same time the bam is splitted, a file region.bed and use it in the tool definition xml, so the command would be like this: <command> ... UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/hg19_ucsc.fa -I input.bam -o $output -L *region.bed*; </command> This solution does not convince me too much because it is a bit intrusive in the tool definition and also because you have to trust that the *region.bed* file exists. Do you have any opinion, suggestion...? Thanks a lot! Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso(a)cipf.es

3 6

Re: [galaxy-dev] find UUID of current history in tool XML wrapper?
by Dooley, Damion 05 May '15

05 May '15

About 1. find UUID of current history in tool XML wrapper? (Ben Bimber) 2. Re: find UUID of current history in tool XML wrapper? (John Chilton) I think this will work for you, I've simplified the code. I was able to do this somewhat circuitously (=bonfire of time) for my upcoming Versioned Data tool. In your tool XML definition file: <param name="history_id" display="radio" type="drill_down" dynamic_options="vdb_init_tool_user(__trans__)" /> ... <code file="versioned_data_form.py" /> Not sure if making history_id a hidden field would work (I seemed to recall __trans__ variable only exposed to select param). And in a script named versioned_data_form.py we have: def vdb_init_tool_user(trans): """ ... ALSO: squeezing history_id in this way since no other way to pass it. "trans" is provided only by tool form presentation via <code file="..."> ... """ history_id = str(trans.security.encode_id(trans.history.id)) items = [ { 'name': 'think of something to say here', 'value': history_id, 'options':[], 'selected': True } ] return items

4 8

Galaxy on CentOS?
by Carlos Lijeron 05 May '15

05 May '15

Hello everyone, We are soon acquiring our cluster which has CentOS on the master node along with Bright Cluster Manager and workload manager. We are wondering if there is a guideline on how to install and support Galaxy on CentOS. Does anyone have any info on this? Thanks ! Carlos.

5 8

Re. find UUID of current history in tool XML wrapper? (Ben Bimber)
by Dooley, Damion 05 May '15

05 May '15

I wanted to add that I have a niche justification for having UUID available in tool interface. My tool needed to scan user's current history in order to determine if user already had generated relevant datasets. If they didn't exist, my tool triggered the generation of them, and loaded them into user's current history. In other words, a caching system. Without the UUID, I'd theoretically have to scan a User's entire list of histories, looking for the cacheable data, and that is error prone too. (A history dataset caching mechanism also becomes a step towards workflows that have checkpoints, that can be restarted at a checkpoint). Damion

1 0

Problem adding system build for visualization
by Fourie Joubert 05 May '15

05 May '15

Hi Folks I am trying to add a custom genome so that all users can choose it as reference in trackster (and others). When I go to " Show loaded, system-installed builds <javascript:void(0);>" the build is listed, but it does not appear in the trackster reference build drop-down list. I have provided the fasta file and 2bit file. I have built the necessary indices for bowtie, bwa, etc. using the data managers... builds.txt is: #Egrandis Eucalyptus grandis 297v2 (Egrandis) (Egrandis) I have provided the lengths file as: tool-data/shared/ucsc/chrom/Egrandis.len twobit.loc is #Egrandis tool-data/shared/Eucalyptus/2bit/Egrandis.2bit Have I missed a step to make it show up in the trackster reference build drop-down? Any help would be sincerely appreciated. Best regards! Fourie -- -------------- Prof Fourie Joubert Centre for Bioinformatics and Computational Biology Genomics Research Institute University of Pretoria fourie.joubert(a)up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.

1 0

Job submission failed
by Vipin TS 04 May '15

04 May '15

Hi dev-team, I am experiencing an issue with my production instance in dispatching the jobs. When I click on execute button, each tool page shows the popup error message as here: [image: Inline image 1] I am not sure what is happening, not getting any single line of error message in log file. Here is the version I am using: changeset: 17051:28113eeee212 branch: stable date: Mon Mar 16 22:38:27 2015 -0400 summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 any suggestions, Thank you! Vipin | Rätsch Lab

4 8

find UUID of current history in tool XML wrapper?
by Ben Bimber 04 May '15

04 May '15

Hello, I am trying to pass the UUID or name of the current history to a script as part of a tool XML wrapper. I was hoping some substitution like ${output.hid}, ${history_id} or similar would give this, but have not had luck. Is there an approach to do this? On a related note: does anyone have debugging tips or pointers to code that would help me figure out which substitutions galaxy will support? The tool wrapper docs list some; however, this isnt complete. Thanks in advance, Ben

2 1

use of copied history while original user account deleled (and purged)
by Olivia Doppelt-Azeroual 04 May '15

04 May '15

Dear Developers, We manage a Galaxy instance at Institut Pasteur where there are more than a hundred users. Among them there are postdocs that are meant to leave the institute. Our Galaxy instance is configured with LDAP authentication. The LDAP entry is suppressed shortly after the end of contracts. We are facing the following problem: A user left a few month ago, 1/ before leaving, she shared interesting histories with another colleague of the lab. 2/ before leaving, the colleague created a copy of every shared history in her own Galaxy account. 3/ The colleague made a few tests to check that the data were really transfered, by displaying them or downloading them and everything was ok. 4/ The time passed and the ldap user account of the user who left was suppressed. We deleted then purged her Galaxy account. 5/ The colleague has tried to relaunch some analysis using the copied histories. The data are there as her colleague is able to download the files or display them, but the jobs haven't been launched. They have remained grey in the copied history. The problem is that there are no logs at all on the galaxy side. No command line is generated either. On the reporting side of Galaxy, we see that the jobs have been created but their status remains "NEW' We know that this will be a recurrent problem if we can't resolve it. Have someone already complained about something like that? Best regards, -- Olivia Doppelt-Azeroual, PhD Fabien Mareuil, PhD Bioinformatics Engineer Galaxy Team - CIB/C3BI Institut Pasteur, Paris

2 1

Possible to pass hostName to a tool?
by Ben Bimber 01 May '15

01 May '15

Hello, I apologize for the second email as this is related to a question from two days ago. I am writing a galaxy tool that runs code that will query the galaxy server. Within the tool wrapper XML, is there a way to write the API URL of the current server? I dont see anything along these lines documented. Thanks in advance for any help, Ben

2 1