Question: self hosted galaxy instance hicexplorer commands not found
1
wei1.guo • 10 wrote:
Hi, We have a self hosted galaxy instance running on release_16.04 (0ba99fe246099cc1827f71f2722d253becee64ba).
I have installed/reinstalled the hicExplorer tool suite 2.1.4 and the installation status are all green. The samtools dependency is met with 1.6.
For example
Tool shed:
toolshed.g2.bx.psu.edu
Name:
hicexplorer_hicplotviewpoint
Description:
Wrapper for HiCExplorer: hicPlotViewpoint
Revision:
67bd57e960a3
Owner:
bgruening
Location:
/project/apps/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/67bd57e960a3/hicexplorer_hicplotviewpoint
Deleted:
False
Name:
hicPlotViewpoint
Description:
plot interactions around a viewpoint
Id
hicexplorer_hicplotviewpoint
Guid:
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/2.1.4.0
Version:
2.1.4.0
Version command string:
hicPlotViewpoint --version
However, I cannot run any of the hicExplorer tools, it always spit out command not found error 127.
Name: hicPlotViewpoint [data 4]: Plot
Created: Tue 23 Oct 2018 09:05:31 PM (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: png
Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/2.1.4.0
Galaxy Tool Version: 2.1.4.0
Tool Version: /project/apps/galaxy/galaxy/database/jobs_directory/022/22300/tool_script.sh: line 9: hicPlotViewpoint: command not found
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 127
History Content API ID: 59f1bc6585fec27a
Job API ID: 037ab7dffab3ebf5
History API ID: 3f00d864a8cefbf4
UUID: a7e04079-af95-4087-a176-c50c94f3fa5d
Full Path: /project/apps/galaxy/galaxy_files/031/dataset_31351.dat
Job Command-Line: ln -s '/project/apps/galaxy/galaxy_files/031/dataset_31343.dat' 0_matrix && hicPlotViewpoint --matrix "0_matrix" --outFileName plot.png --region --referencePoint && mv plot.png plot && ls -lah
Job Runtime (Wall Clock) 4 seconds
Cores Allocated 1
Job Start Time 2018-10-23 16:05:32
Job End Time 2018-10-23 16:05:36
After searching around a bit there is no obvious disclosed solution. Could anyone please help? Thanks a lot.
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modified 4 weeks ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
4 weeks ago by
wei1.guo • 10
Hi,
this looks more like a conda issue. Can you check if your Galaxy already supports conda and that you have enabled it? For me this looks like the dependency on hicexplorer is not properly installed. You could try to install it manually with conda, but I would really recommend to update your Galaxy instance.
Thanks Bjoern. We do not have conda enabled. We are still using virtualenv. samtools 1.6 is installed and is ported to the $PATH of the galaxy user.
Indeed, it shows dependency error, complaining both samtools and hicexplorer. I am not sure why samtools is missing but it is in the $PATH.
Hi - Thanks for reporting the problems. I've asked the tool author for some advice at Gitter. The author may write back here or there, and chats are sometimes a quicker way to address configuration problems so please feel free to join in there: https://gitter.im/galaxy-iuc/iuc?at=5bd1f91cab17df2631ec6f2e
Upgrading your Galaxy version might be the best solution but let's see what the recommendation is.
That author is located in the EU -- and many chats are asynchronous - so your patience is appreciated due to the time difference.
Thanks! Jen, Galaxy team