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

Creating R galaxy wrapper where a function checks file extension
by Martin Vickers 02 Oct '15

02 Oct '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, I've been tasked with getting someone's R script working in our galaxy installation and I'm struggling to resolve an issue with an bioconductor function that appears to not like the galaxy naming convention (e.g. dataset_2.dat) for the bam index file. The R script can run from the command line like this; Rscript script.R input1.xls alignment.bam alignment.bai p so I have created a wrapper using planemo that does this, and that's fine. The problem is, when I run the script in galaxy, I get the following error from R; Error in value[[3L]](cond) : failed to open BamFile: failed to load BAM index file: /tmp/tmpdP2eBC/files/000/dataset_3.dat Calls: f_oGRSeparateStrands ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning messages: In doTryCatch(return(expr), name, parentenv, handler) : [bam_index_load] fail to load BAM index. Execution halted The function that reads the bam + bai file in the script is; bam = readGAlignments(file=bam.file, index=bai.file, param=ScanBamParam(which=gr.signal)) http://www.rdocumentation.org/packages/GenomicRanges/html/GAlignments.html In the documentation for this function it states the following; "file, index, The path to the BAM file to read, and to the index file of the BAM file to read, respectively. The latter is given /without/ the '.bai' extension. See |scanBam <http://www.rdocumentation.org/packages/Rsamtools/functions/scanBam.html>| for more information." I've played around with this a little and from the command line I've been successfully able to run the script to completion when the input bam file and bai are completely different names; e.g. Rscript script.R input1.xls something.bam meh.bai p but I can't run it if I change the extension, e.g. Rscript script.R input1.xls something.dat meh.dat p Error in value[[3L]](cond) : failed to open BamFile: failed to load BAM index file: /tmp/tmpdP2eBC/files/000/dataset_3.dat Calls: f_oGRSeparateStrands ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning messages: In doTryCatch(return(expr), name, parentenv, handler) : [bam_index_load] fail to load BAM index. Execution halted Does anyone have any experience of resolving this kind of issue? - -- - -- Dr. Martin Vickers Data Manager/HPC Systems Administrator Institute of Biological, Environmental and Rural Sciences IBERS New Building Aberystwyth University SY23 3FG w: http://www.martin-vickers.co.uk/ e: mjv08(a)aber.ac.uk t: 01970 62 2807 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJWDlUgAAoJEHa0a8GkKQgIpUcIAK9OZ9402FRaROF89b6bO1CY d+KP/X0NCxY+AXEddU3lhXi8O9haaKRA/pmxsGyydP0VQfaCrSSlS9nzhncG6Zav gpXe5NjFkwe8a/qaZTVf0YjlYq0sI81S7QAJnzlKXvYSjcz1xNDE9O4qSHqdhefX oI6GWmR+vHi7CTqNuHwpyY9Qoafd5nls0oQoCYDh9YWrn9GZ8fe1qQ9W7iUli/oT dPMYwWs0OL8NfSCuIcz2Dbr1XMt+o5HpQY/afoGWaq3zz5Ie0NhCLKz34bFps3IW 8K0DEROmCTxsXBa54gnnkhVgCI3zkfFCfa47xp13vT2dJALdzYoT6vDj8aC/mes= =ijgr -----END PGP SIGNATURE-----

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Documentation of Galaxy API metadata objects
by Clare Sloggett 01 Oct '15

01 Oct '15

Hi all, I'm wondering if there is any documentation of the JSON structures returned by particular Galaxy REST API calls. Some aspects of the Galaxy API are effectively documented via bioblend's structure, and others are documented at http://galaxy.readthedocs.org/en/master/api_doc.html . However I don't know where to look to find out the actual JSON structure that should be returned by an API call. Does this exist? For instance, if I call (using bioblend) gi.histories.show_history(..., contents=True, details="all"), I will get back a list of dicts where each dict contains dataset metadata, e.g.: { u'api_type': u'file', u'create_time': u'2015-09-28T06:00:19.850421', u'data_type': u'galaxy.datatypes.sequence.FastqSanger', u'file_name': u'/mnt/galaxy/files/000/dataset_2.dat', .... I'd like to know how to find out what dictionary keys to expect for a particular API call in a particular Galaxy version. In this example, IIRC at some point the key 'file_name' changed to 'file_path', but I don't know how to determine which version of Galaxy uses which convention. I don't think this change would necessarily be reflected in bioblend, because bioblend just returns the entire JSON structure as a Python object without caring much about its contents. I also don't know how to derive this information from the Galaxy source code itself (even though I know where the API code is under webapp), so alternatively any guidance on that would be helpful! Thanks, Clare

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October 2015 News of the Galaxy
by Dave Clements 01 Oct '15

01 Oct '15

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