From 4eaf3570ce532f026440a2041124655e455ef8f1 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Wed, 14 Jan 2026 10:00:09 -0500 Subject: [PATCH 1/2] update FASTGA and FASTAN to latest commits --- submodules/FASTAN | 2 +- submodules/FASTGA | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/submodules/FASTAN b/submodules/FASTAN index d27f8187c..2395ad457 160000 --- a/submodules/FASTAN +++ b/submodules/FASTAN @@ -1 +1 @@ -Subproject commit d27f8187c40fbb3e0d98502fcd85ba31f1b88630 +Subproject commit 2395ad4572acb040cd4dc1308a2d973a6d794738 diff --git a/submodules/FASTGA b/submodules/FASTGA index 26744e1ee..6c5b8b610 160000 --- a/submodules/FASTGA +++ b/submodules/FASTGA @@ -1 +1 @@ -Subproject commit 26744e1eee77c81ca2f92b9598a35b1c92ce70a6 +Subproject commit 6c5b8b610dd6cdfc0b898536cd9384927e031423 From 5a3d0f511971298f60ed80ba141095a7697dccd2 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Wed, 14 Jan 2026 11:38:53 -0500 Subject: [PATCH 2/2] hack fastga build to use pthread --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 9fabeb0a4..b1ef2defb 100644 --- a/Makefile +++ b/Makefile @@ -313,7 +313,7 @@ suball.collapse-bubble: chmod +x submodules/collapse-bubble/scripts/merge_duplicates.py ln -f submodules/collapse-bubble/scripts/merge_duplicates.py ${BINDIR} suball.FASTGA: - cd submodules/FASTGA && ${MAKE} + cd submodules/FASTGA && sed -i '/-lpthread/!s/-lm -lz/-lpthread -lm -lz/g' Makefile && ${MAKE} ln -f submodules/FASTGA/FastGA ${BINDIR} ln -f submodules/FASTGA/ALNtoPAF ${BINDIR} ln -f submodules/FASTGA/FAtoGDB ${BINDIR}