Question: self hosted galaxy instance hicexplorer commands not found
1
gravatar for wei1.guo
4 weeks ago by
wei1.guo10
wei1.guo10 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.

ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson25k • written 4 weeks ago by wei1.guo10
1

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.

ADD REPLYlink written 4 weeks ago by Bjoern Gruening5.1k

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.

galaxy.jobs DEBUG 2018-10-26 13:39:48,187 (22306) Working directory for job is: /project/apps/galaxy/galaxy/database/jobs_directory/022/22306
galaxy.jobs.handler DEBUG 2018-10-26 13:39:48,276 (22306) Dispatching to local runner
galaxy.jobs DEBUG 2018-10-26 13:39:48,304 (22306) Persisting job destination (destination id: local)
galaxy.jobs.runners DEBUG 2018-10-26 13:39:48,318 Job [22306] queued (42.224 ms)
galaxy.jobs.handler INFO 2018-10-26 13:39:48,329 (22306) Job dispatched
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,463 Building dependency shell command for dependency 'hicexplorer'
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,463 Find dependency hicexplorer version 2.1.4
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,463 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,464 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,464 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,464 Resolver conda returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,464 Resolver conda returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps WARNING 2018-10-26 13:39:48,464 Failed to resolve dependency on 'hicexplorer', ignoring
galaxy.jobs.command_factory INFO 2018-10-26 13:39:48,515 Built script [/project/apps/galaxy/galaxy/database/jobs_directory/022/22306/tool_script.sh] for tool command[hicPlotViewpoint --version > /project/apps/galaxy/galaxy_tmp/GALAXY_VERSION_STRING_22306 2>&1; 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]
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,764 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,764 Find dependency samtools version None
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,764 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,764 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,765 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,765 Resolver conda returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps DEBUG 2018-10-26 13:39:48,765 Resolver conda returned <galaxy.tools.deps.resolvers.nulldependency object="" at="" 0x7fb831796450=""> (isnull? True)
galaxy.tools.deps WARNING 2018-10-26 13:39:48,765 Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.runners DEBUG 2018-10-26 13:39:48,768 (22306) command is:    ......abridged due to comment characters limit ....... 
galaxy.jobs.runners.local DEBUG 2018-10-26 13:39:48,861 (22306) executing job script: /project/apps/galaxy/galaxy/database/jobs_directory/022/22306/galaxy_22306.sh
galaxy.jobs DEBUG 2018-10-26 13:39:48,878 (22306) Persisting job destination (destination id: local)
galaxy.jobs.runners.local DEBUG 2018-10-26 13:40:08,126 execution finished: /project/apps/galaxy/galaxy/database/jobs_directory/022/22306/galaxy_22306.sh
galaxy.jobs.output_checker INFO 2018-10-26 13:40:08,134 Job 22306: Fatal error: Exit code 127 ()
galaxy.jobs.output_checker DEBUG 2018-10-26 13:40:08,135 Tool exit code indicates an error, failing job.
galaxy.jobs DEBUG 2018-10-26 13:40:08,213 (22306) setting dataset 31357 state to ERROR
galaxy.jobs INFO 2018-10-26 13:40:08,383 Collecting metrics for Job 22306
galaxy.jobs DEBUG 2018-10-26 13:40:08,396 job 22306 ended (finish() executed in (269.351 ms))

Upgrading the instance is in plan. But I have to solve this problem. Thanks again. Bjoern and Jennifer.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by wei1.guo10

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

ADD REPLYlink written 4 weeks ago by Jennifer Hillman Jackson25k
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