Question: cloudmap error on galaxy
1
gravatar for jianghb
2.3 years ago by
jianghb10
jianghb10 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.

galaxy cloudmap • 652 views
ADD COMMENTlink written 2.3 years ago by jianghb10

Thanks for reporting the issue. One other user reported the problem and we are investigating. More soon. Jen

ADD REPLYlink written 2.3 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 2.2 years ago by jianghb10
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