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Makefile using system tabix and bgzip #372

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JPWerling opened this issue Nov 15, 2024 · 2 comments · Fixed by #378
Closed

Makefile using system tabix and bgzip #372

JPWerling opened this issue Nov 15, 2024 · 2 comments · Fixed by #378
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bug Something isn't working high High priority

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@JPWerling
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jasen/Makefile

Line 803 in 999b2bd

&& bgzip $$(basename $<) |& tee -a $(INSTALL_LOG)

jasen/Makefile

Line 810 in 999b2bd

&& tabix -p bed $$(basename $<) |& tee -a $(INSTALL_LOG)

The Makefile for use with make install as directed by the documentation is assuming both bgzip and tabix are available on the system level.
Attempted fix by using the previously built samtools container but it does not seem to include the htslib package.

Temporarily fixed by creating container using htslib from dockerhub and using it in Makefile.

@JPWerling JPWerling added the bug Something isn't working label Nov 15, 2024
@ryanjameskennedy ryanjameskennedy self-assigned this Jan 9, 2025
@ryanjameskennedy ryanjameskennedy added the high High priority label Jan 9, 2025
@ryanjameskennedy
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ryanjameskennedy commented Jan 14, 2025

You can just pull the htslib image from galaxy project.

@sylvinite
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Resolved in #378

@ryanjameskennedy ryanjameskennedy linked a pull request Jan 21, 2025 that will close this issue
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3 participants