Hi All, I am installing and testing galaxy-dist locally and I have installed all the rgenetics tools and have them working but there seems to be a one problem. If I upload a lped file, then edit the attributes and convert it to a plink pbed file the tools such as QC reports and Case Control will work. If however I select "(as pbed) RgeneticsData" to run the tool directly I receive the following error: input data 1 is in error state I don't think this error is strictly related to rgenetics but something goes wrong after tools/parameters/basic.py gets called. Thanks for producing a fantastic resource and I would appreciate any help, -- Jason Ellul Bioinformatician Cancer Research Division Peter MacCallum Cancer Centre TEL: +61 3 9656 1512 FAX: +61 3 9656 1411 EMAIL: jason.ellul@petermac.org Address: St Andrew's Place East Melbourne Victoria 3002 Australia Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
Jason, Thanks for pointing this error out - it's now fixed in galaxy-central and appears to be working on test. This fix will be on main after the next scheduled update. On Sun, May 15, 2011 at 8:43 PM, Ellul Jason <Jason.Ellul@petermac.org> wrote:
Hi All,
I am installing and testing galaxy-dist locally and I have installed all the rgenetics tools and have them working but there seems to be a one problem.
If I upload a lped file, then edit the attributes and convert it to a plink pbed file the tools such as QC reports and Case Control will work. If however I select "(as pbed) RgeneticsData" to run the tool directly I receive the following error:
input data 1 is in error state I don't think this error is strictly related to rgenetics but something goes wrong after tools/parameters/basic.py gets called.
Thanks for producing a fantastic resource and I would appreciate any help, --
Jason Ellul Bioinformatician Cancer Research Division
Peter MacCallum Cancer Centre TEL: +61 3 9656 1512 FAX: +61 3 9656 1411 EMAIL: jason.ellul@petermac.org
Address: St Andrew's Place East Melbourne Victoria 3002 Australia Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia
This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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