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Replace hardcoded paths #19

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dennishendriksen opened this issue Aug 26, 2020 · 2 comments
Closed

Replace hardcoded paths #19

dennishendriksen opened this issue Aug 26, 2020 · 2 comments
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enhancement New feature or request

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@dennishendriksen
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dennishendriksen commented Aug 26, 2020 •
edited

/apps/data/Ensembl/VEP/100
paths in conf.template
@dennishendriksen dennishendriksen added the enhancement New feature or request label Aug 26, 2020
@dennishendriksen dennishendriksen changed the title Replace hardcoded cache dir Replace hardcoded paths Aug 28, 2020
@svandenhoek
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vip/pipeline_annotate.sh

Line 177 in 5845048

file="/apps/data/VKGL/VKGL_public_consensus_jun2020_normalized.vcf.gz"

vip/pipeline_annotate.sh

Line 183 in 5845048

file="/apps/data/CAPICE/${ASSEMBLY}/capice_v1.0_indels.vcf.gz"

vip/pipeline_annotate.sh

Line 189 in 5845048

file="/apps/data/CAPICE/${ASSEMBLY}/capice_v1.0_snvs.vcf.gz"

vip/pipeline_annotate.sh

Line 299 in 5845048

--offline --cache --dir_cache /apps/data/Ensembl/VEP/100 \

@svandenhoek svandenhoek mentioned this issue Sep 8, 2020
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@dennishendriksen
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Most hardcoded paths have been removed, separate issues exist #167 and #168 for the remaining hardcoded paths.

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