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tseemann / VelvetOptimiser

:chart_with_upwards_trend: Automatically optimise three of Velvet's assembly parameters.
GNU General Public License v2.0
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Fix crash when filename contains dash #20

Closed abretaud closed 6 years ago

abretaud commented 7 years ago

Hi,

I'm trying to use the https://galaxyproject.github.io/training-material/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html tutorial (preparing for a training session at the end of the month)

I had a crash of velvetoptimiser because our galaxy server is installed in a path with a dash (/opt/galaxy-dist):

Fatal error: Exit code 2 ()

****************************************************
           VelvetOptimiser.pl Version 2.2.5
****************************************************
Number of CPUs available: 10
Current free RAM: 47.052GB
Velvet OMP compiler setting: 2
Oct  2 17:06:13 Starting to check input parameters.
*** 1 files specified for -separate option in block: -fastq   -shortPaired  -separate /opt/galaxy. Require exactly 2.
 at /opt/galaxy-dist/conda/envs/mulled-v1-6487bd322a704c25a7d7ff8eed84db64d562929ef48f39b2bd4c32f5535f3181/bin/VelvetOptimiser.pl line 490.
*** File /opt/galaxy doesn't exist or is unreadable.
 at /opt/galaxy-dist/conda/envs/mulled-v1-6487bd322a704c25a7d7ff8eed84db64d562929ef48f39b2bd4c32f5535f3181/bin/VelvetOptimiser.pl line 490.
Block -fastq   -shortPaired  -separate /opt/galaxy FAILED!
*** Unknown option used: -dist/database/files/002/058/dataset_2058865.dat in file block: -dist/database/files/002/058/dataset_2058865.dat /opt/galaxy
 at /opt/galaxy-dist/conda/envs/mulled-v1-6487bd322a704c25a7d7ff8eed84db64d562929ef48f39b2bd4c32f5535f3181/bin/VelvetOptimiser.pl line 490.
*** File /opt/galaxy doesn't exist or is unreadable.
 at /opt/galaxy-dist/conda/envs/mulled-v1-6487bd322a704c25a7d7ff8eed84db64d562929ef48f39b2bd4c32f5535f3181/bin/VelvetOptimiser.pl line 490.
Block -dist/database/files/002/058/dataset_2058865.dat /opt/galaxy FAILED!
*** Unknown option used: -dist/database/files/002/058/dataset_2058866.dat in file block: -dist/database/files/002/058/dataset_2058866.dat
 at /opt/galaxy-dist/conda/envs/mulled-v1-6487bd322a704c25a7d7ff8eed84db64d562929ef48f39b2bd4c32f5535f3181/bin/VelvetOptimiser.pl line 490.
Block -dist/database/files/002/058/dataset_2058866.dat FAILED!
Please re-start with a corrected velveth parameter string. at /opt/galaxy-dist/conda/envs/mulled-v1-6487bd322a704c25a7d7ff8eed84db64d562929ef48f39b2bd4c32f5535f3181/bin/VelvetOptimiser.pl line 492.

Here's a patch which fixes the problem (I just hope it doesn't break anything else)

By the way, I saw this old PR for galaxy tools: https://github.com/galaxyproject/tools-iuc/pull/862 Do you still have plans to work on it? Now that we can get rid of tool_dependencies.xml I think it would be easier to finish. I can help if it's needed

Cheers

Slugger70 commented 6 years ago

Thanks Anthony!