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SNPhylo - Fix scripts installation path#1759

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boegel merged 2 commits intoeasybuilders:developfrom
vanzod:snphylo_scripts_path
Jun 25, 2019
Merged

SNPhylo - Fix scripts installation path#1759
boegel merged 2 commits intoeasybuilders:developfrom
vanzod:snphylo_scripts_path

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@vanzod vanzod commented Jun 24, 2019

The current easyblock installs the scripts provided by SNPhylo/20160204 in $EBROOTSNPHYLO/scripts while the snphylo.sh main executable in SNPhylo/20160204 looks for them in $EBROOTSNPHYLO/bin/scripts and fails with the following error:

Start to remove low quality data.
/opt/easybuild/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/3.6.3/bin/python: can't open file '/opt/easybuild/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/SNPhylo/20160204-Python-3.6.3-R-3.4.3/bin/scripts/remove_no_genotype_data.py': [Errno 2] No such file or directory

@vanzod vanzod added the bug fix label Jun 24, 2019
@vanzod vanzod added this to the 3.x milestone Jun 24, 2019
@vanzod vanzod requested a review from boegel June 24, 2019 16:10
@vanzod vanzod changed the title Fix scripts installation path SNPhylo - Fix scripts installation path Jun 24, 2019
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boegel commented Jun 24, 2019

@vanzod Can we enhance the sanity check to catch this?

@boegel boegel modified the milestones: 3.x, next release (3.9.3) Jun 24, 2019
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vanzod commented Jun 24, 2019

@boegel Ok, so I tested with the older SNPhylo/20140701 and that one also requires the scripts in $EBROOTSNPHYLO/bin/scripts. This simplifies the issue since both versions should install the scripts in the same path. The last code refactoring now works for both versions and the sanity checks have also been updated.

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boegel commented Jun 24, 2019

@vanzod Is there any way to come up with a sanity check command using snphylo.sh that could help avoid re-introducing this issue?

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vanzod commented Jun 24, 2019

@boegel No, in order to do that you need a dataset and start an actual run.

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boegel approved these changes Jun 25, 2019
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lgtm

re-tested with both SNPhylo-20140701-foss-2016a.eb and SNPhylo-20160204-foss-2017b-Python-2.7.14-R-3.4.3.eb

@boegel boegel merged commit dbb5717 into easybuilders:develop Jun 25, 2019
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