From b15c675109f79f86101f827aba1657701d4a5fab Mon Sep 17 00:00:00 2001
From: Marco Matthies <71844+marcom@users.noreply.github.com>
Date: Wed, 15 Nov 2023 19:12:44 +0100
Subject: [PATCH 1/2] [Infernal] Update to v1.1.5

---
 I/Infernal/build_tarballs.jl                  | 33 +++++--------------
 .../patches/rmark-missing-gsl-link.patch      | 13 ++++++++
 2 files changed, 21 insertions(+), 25 deletions(-)
 create mode 100644 I/Infernal/bundled/patches/rmark-missing-gsl-link.patch

diff --git a/I/Infernal/build_tarballs.jl b/I/Infernal/build_tarballs.jl
index c0bee6e7a86..0d4c13648cf 100644
--- a/I/Infernal/build_tarballs.jl
+++ b/I/Infernal/build_tarballs.jl
@@ -1,29 +1,18 @@
-# Note that this script can accept some limited command-line arguments, run
-# `julia build_tarballs.jl --help` to see a usage message.
 using BinaryBuilder, BinaryBuilderBase, Pkg
 
 name = "Infernal"
-version = v"1.1.4"
+version = v"1.1.5"
 
-easel_version = v"0.48"
-hmmer_version = v"3.3.2"
-
-# Collection of sources required to complete build
 sources = [
-    ArchiveSource("https://github.com/EddyRivasLab/infernal/archive/refs/tags/infernal-$(version).tar.gz",
-                  "311163c0a21a216e90862df81cd6c13811032076535e44fed4eabdcf45093fea"),
-    ArchiveSource("https://github.com/EddyRivasLab/easel/archive/refs/tags/easel-$(easel_version.major).$(easel_version.minor).tar.gz",
-                  "c5d055acbe88fa834e81424a15fc5fa54ac787e35f2ea72d4ffd9ea2c1aa29cf"),
-    ArchiveSource("https://github.com/EddyRivasLab/hmmer/archive/refs/tags/hmmer-$(hmmer_version).tar.gz",
-                  "fab109c67fb8077b32f7907bf07efbc071147be0670aee757c9a3ca7e2d485be")
+    ArchiveSource("http://eddylab.org/infernal/infernal-$(version).tar.gz",
+                  "ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f"),
+    DirectorySource("./bundled")
 ]
 
-# Bash recipe for building across all platforms
 script = raw"""
 cd $WORKSPACE/srcdir/infernal-*/
 
-mv ../easel-*/ easel
-mv ../hmmer-*/ hmmer
+atomic_patch -p1 ../patches/rmark-missing-gsl-link.patch
 
 # Update the config.sub from infernal.  Otherwise we get an error when running
 # configure: "Invalid configuration `x86_64-linux-musl'."
@@ -45,17 +34,13 @@ install_license LICENSE.easel
 install_license ../LICENSE
 """
 
-# These are the platforms we will build for by default, unless further
-# platforms are passed in on the command line
 # Notes
-# - Infernal requires SSE or VMX vector instructions,
-#   VMX only on big-endian platforms (ppc64 not ppc64le)
-# - ARM vector instruction support coming soon
+# - Infernal requires SSE, VMX or NEON vector instructions,
+#   VMX only works on big-endian platforms (ppc64 not ppc64le)
 # - build fails on windows
 #   easel.c:39:20: fatal error: syslog.h: No such file or directory
-platforms = supported_platforms(; exclude = p -> Sys.iswindows(p) || proc_family(p) != "intel")
+platforms = supported_platforms(; exclude = p -> Sys.iswindows(p) || proc_family(p) ∉ ("intel", "arm"))
 
-# The products that we will ensure are always built
 products = [
     ExecutableProduct("cmalign", :cmalign),
     ExecutableProduct("cmbuild", :cmbuild),
@@ -93,10 +78,8 @@ products = [
     ExecutableProduct("esl-weight", :esl_weight),
 ]
 
-# Dependencies that must be installed before this package can be built
 dependencies = [
     Dependency(PackageSpec(name="GSL_jll", uuid="1b77fbbe-d8ee-58f0-85f9-836ddc23a7a4"))
 ]
 
-# Build the tarballs, and possibly a `build.jl` as well.
 build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; julia_compat="1.6")
diff --git a/I/Infernal/bundled/patches/rmark-missing-gsl-link.patch b/I/Infernal/bundled/patches/rmark-missing-gsl-link.patch
new file mode 100644
index 00000000000..fbefc7ed498
--- /dev/null
+++ b/I/Infernal/bundled/patches/rmark-missing-gsl-link.patch
@@ -0,0 +1,13 @@
+diff --git a/rmark/Makefile.in b/rmark/Makefile.in
+index 95bed07..060e713 100644
+--- a/rmark/Makefile.in
++++ b/rmark/Makefile.in
+@@ -10,7 +10,7 @@ PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
+ CPPFLAGS       = @CPPFLAGS@
+ LDFLAGS        = @LDFLAGS@
+ DEFS           = @DEFS@
+-LIBS           = -lhmmer -leasel @LIBS@ @PTHREAD_LIBS@ -lm
++LIBS           = -lhmmer -leasel @LIBS@ @PTHREAD_LIBS@ -lm -lgsl -lgslcblas
+ IMPLDIR        = impl_@IMPL_CHOICE@
+ 
+ SRCDIR   = ../src

From 64865b85f8b9431b093907970c88840edde91f66 Mon Sep 17 00:00:00 2001
From: Marco Matthies <71844+marcom@users.noreply.github.com>
Date: Wed, 15 Nov 2023 19:17:59 +0100
Subject: [PATCH 2/2] Update I/Infernal/build_tarballs.jl
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>
---
 I/Infernal/build_tarballs.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/I/Infernal/build_tarballs.jl b/I/Infernal/build_tarballs.jl
index 0d4c13648cf..9099cee23cf 100644
--- a/I/Infernal/build_tarballs.jl
+++ b/I/Infernal/build_tarballs.jl
@@ -79,7 +79,7 @@ products = [
 ]
 
 dependencies = [
-    Dependency(PackageSpec(name="GSL_jll", uuid="1b77fbbe-d8ee-58f0-85f9-836ddc23a7a4"))
+    Dependency(PackageSpec(name="GSL_jll", uuid="1b77fbbe-d8ee-58f0-85f9-836ddc23a7a4"); compat="~2.7.2")
 ]
 
 build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; julia_compat="1.6")