-----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@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-----