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Updating GRIDSS to a newer version #69

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lsantuari opened this issue Jul 22, 2021 · 4 comments
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Updating GRIDSS to a newer version #69

lsantuari opened this issue Jul 22, 2021 · 4 comments
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@lsantuari
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Modify the file environment.yaml to update GRIDSS version.
@arnikz
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arnikz commented Jul 22, 2021

This issue is related to #35.

@arnikz arnikz removed their assignment Jul 22, 2021
lsantuari added a commit that referenced this issue Aug 20, 2021
@lsantuari
update gridss version #69
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@arnikz arnikz changed the title Updating GRIDSS to version v2.12.0 Updating GRIDSS to a newer version Aug 23, 2021
lsantuari added a commit that referenced this issue Aug 23, 2021
@lsantuari
Update env file for all callers #35 #69
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@lsantuari lsantuari mentioned this issue Aug 23, 2021
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lsantuari added a commit that referenced this issue Sep 3, 2021
@lsantuari
gridss2 works #35 #69
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@lsantuari
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TODO: apparently GRIDSS2 needs one reference (FASTA) symlink for each running instance.

lsantuari added a commit that referenced this issue Jan 13, 2022
@lsantuari
use github actions #35 #69
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@lsantuari
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@arnikz GitHub Actions fails because with GRIDSS2 I am using a reduced version of ENCFF001TDO.bed with only chr22 entries: ENCFF001TDO.bed. If I remember well, GRIDSS2 complains if I use the full ENCFF001TDO.bed file. Would you suggest to update the test function?

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arnikz commented Jan 14, 2022

Another option is to use the reduced file while keeping the org. filename.

@arnikz arnikz closed this as completed Sep 5, 2023
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