From d13c10810a5bd572ad8beec637ad43181cb4e657 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 +- submodules/alntools | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/submodules/FASTAN b/submodules/FASTAN index d27f8187c..89ea226e8 160000 --- a/submodules/FASTAN +++ b/submodules/FASTAN @@ -1 +1 @@ -Subproject commit d27f8187c40fbb3e0d98502fcd85ba31f1b88630 +Subproject commit 89ea226e8356fdea15a74ac14a8385c46837a9be diff --git a/submodules/FASTGA b/submodules/FASTGA index 26744e1ee..567135715 160000 --- a/submodules/FASTGA +++ b/submodules/FASTGA @@ -1 +1 @@ -Subproject commit 26744e1eee77c81ca2f92b9598a35b1c92ce70a6 +Subproject commit 5671357153851ea67b612d0400ba646947bd647e diff --git a/submodules/alntools b/submodules/alntools index 233bf8bde..aa4333d03 160000 --- a/submodules/alntools +++ b/submodules/alntools @@ -1 +1 @@ -Subproject commit 233bf8bde302d1f7ec91e43170f3af6e35d36161 +Subproject commit aa4333d03c47280e3012d4db6f7d897a79e00051 From c012f79565a6caf3811467d970da3e72db7bde94 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 6d2086fc0..91f8d36d0 100644 --- a/Makefile +++ b/Makefile @@ -314,7 +314,7 @@ 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}