Question: cloudmap error on galaxy
1
jianghb • 10 wrote:
Hello Everyone,
I am running cloudmap on Galaxy. Here it reported this problem.
Dataset generation errors
Dataset 82: CloudMap: Variant Discovery Mapping with WGS data on data 70
Tool execution generated the following error message: Traceback (most recent call last): File "/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/gregory-minevich/cloudmap_variant_discovery_mapping/2ce68f42fd3a/cloudmap_variant_discovery_mapping/VDM_Mapping.py", line 10, in <module> from rpy import * ImportError: No module named rpy
===================================================== Anybody has a solution to this?
Thank you very much.
Thanks for reporting the issue. One other user reported the problem and we are investigating. More soon. Jen
The issue has been confirmed to be a rpy dependency issue. This was to be resolved with the latest update today, but more testing is needed to confirm. We will get back to you tomorrow with an update. Jen, Galaxy team
Hello Jennifer,
The cloudmap reported a different error after fixing last one. Please see below:
Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/galaxy/software/linux2.6-x86_64/pkg/r-2.11.0_g2main/lib64/R/library/stats/libs/stats.so': libf77blas.so.3gf: cannot open shared object file: No such file or directory During startup - Warning message: package stats in options("defaultPackages") was not found
Error in lines(loess.smooth(x, y, span = 0.2), lwd = 5, col = "green") :
could not find function "loess.smooth"
There was an error creating the location plot pdf... Please try again
Thank you.
From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Thursday, April 21, 2016 6:34 PM To: Jiang, Hongbing Subject: [galaxy-biostar] cloudmap error on galaxy
Activity on a post you are following on Galaxy Biostarhttp://biostar.usegalaxy.org
User Jennifer Hillman JacksonJennifer Hillman Jackson wrote Comment: cloudmap error on galaxyC: cloudmap error on galaxy:
The issue has been confirmed to be a rpy dependency issue. This was to be resolved with the latest update today, but more testing is needed to confirm. We will get back to you tomorrow with an update. Jen, Galaxy team