From 03385ca71264a4c5051aafdc9a5912c2843fa45a Mon Sep 17 00:00:00 2001
From: Pablo <pablo.aledo@seqera.io>
Date: Mon, 17 Jul 2023 12:37:50 +0200
Subject: [PATCH 1/2] add recipes needed for samtools

Signed-off-by: Pablo <pablo.aledo@seqera.io>
---
 recipes/htslib/1.1/meta.yaml        |  2 +-
 recipes/htslib/1.3.1/meta.yaml      |  2 +-
 recipes/htslib/fix_hwcapasimd.patch | 22 +++++++++++++++
 recipes/htslib/meta.yaml            |  8 +++---
 recipes/samtools/1.17/build.sh      |  9 +++++++
 recipes/samtools/1.17/meta.yaml     | 42 +++++++++++++++++++++++++++++
 6 files changed, 80 insertions(+), 5 deletions(-)
 create mode 100644 recipes/htslib/fix_hwcapasimd.patch
 create mode 100644 recipes/samtools/1.17/build.sh
 create mode 100644 recipes/samtools/1.17/meta.yaml

diff --git a/recipes/htslib/1.1/meta.yaml b/recipes/htslib/1.1/meta.yaml
index c178435..445cb04 100644
--- a/recipes/htslib/1.1/meta.yaml
+++ b/recipes/htslib/1.1/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: "1.1"
 
 build:
-  number: 3
+  number: 5
 
 source:
   url: https://github.com/samtools/htslib/archive/1.1.tar.gz
diff --git a/recipes/htslib/1.3.1/meta.yaml b/recipes/htslib/1.3.1/meta.yaml
index cc82567..095ed52 100644
--- a/recipes/htslib/1.3.1/meta.yaml
+++ b/recipes/htslib/1.3.1/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: "1.3.1"
 
 build:
-  number: 5
+  number: 7
 
 source:
   url: https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2
diff --git a/recipes/htslib/fix_hwcapasimd.patch b/recipes/htslib/fix_hwcapasimd.patch
new file mode 100644
index 0000000..2a5202c
--- /dev/null
+++ b/recipes/htslib/fix_hwcapasimd.patch
@@ -0,0 +1,22 @@
+diff --git a/htscodecs/htscodecs/rANS_static4x16pr.c b/htscodecs/htscodecs/rANS_static4x16pr.c
+index b6d5580..43c7792 100644
+--- a/htscodecs/htscodecs/rANS_static4x16pr.c
++++ b/htscodecs/htscodecs/rANS_static4x16pr.c
+@@ -1018,7 +1018,7 @@ static inline int have_neon() {
+ #if defined(__linux__) && defined(__arm__)
+     return (getauxval(AT_HWCAP) & HWCAP_NEON) != 0;
+ #elif defined(__linux__) && defined(__aarch64__)
+-    return (getauxval(AT_HWCAP) & HWCAP_ASIMD) != 0;
++    return (getauxval(AT_HWCAP) & 2) != 0;
+ #elif defined(__APPLE__)
+     return 1;
+ #elif defined(__FreeBSD__) && defined(__arm__)
+@@ -1028,7 +1028,7 @@ static inline int have_neon() {
+ #elif defined(__FreeBSD__) && defined(__aarch64__)
+     u_long cap;
+     if (elf_aux_info(AT_HWCAP, &cap, sizeof cap) != 0) return 0;
+-    return (cap & HWCAP_ASIMD) != 0;
++    return (cap & 2) != 0;
+ #elif defined(_WIN32)
+     return IsProcessorFeaturePresent(PF_ARM_V8_INSTRUCTIONS_AVAILABLE) != 0;
+ #else
diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml
index e4878d4..a3fa55b 100644
--- a/recipes/htslib/meta.yaml
+++ b/recipes/htslib/meta.yaml
@@ -1,17 +1,19 @@
-{% set version = "1.16" %}
+{% set version = "1.17" %}
 
 package:
   name: htslib
   version: {{ version }}
 
 build:
-  number: 0
+  number: 2
   run_exports:
     - {{ pin_subpackage('htslib', max_pin='x.x') }}
 
 source:
   url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2
-  sha256: 606b7c7aff73734cf033ecd156f40529fa5792f54524952a28938ca0890d7924
+  sha256: 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f
+  patches:
+    - fix_hwcapasimd.patch
 
 requirements:
   build:
diff --git a/recipes/samtools/1.17/build.sh b/recipes/samtools/1.17/build.sh
new file mode 100644
index 0000000..f460625
--- /dev/null
+++ b/recipes/samtools/1.17/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# Ensure we run successfully using either conda-forge or defaults ncurses
+# (unlike other platforms, the latter does not automatically pull in libtinfo)
+CURSES_LIB="-ltinfow -lncursesw"
+
+./configure --prefix=$PREFIX --with-htslib=system CURSES_LIB="$CURSES_LIB"
+make all
+make install
diff --git a/recipes/samtools/1.17/meta.yaml b/recipes/samtools/1.17/meta.yaml
new file mode 100644
index 0000000..8170e44
--- /dev/null
+++ b/recipes/samtools/1.17/meta.yaml
@@ -0,0 +1,42 @@
+{% set version = "1.17" %}
+
+package:
+  name: samtools
+  version: {{ version }}
+
+build:
+  number: 1
+
+source:
+  url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2
+  sha256: 3adf390b628219fd6408f14602a4c4aa90e63e18b395dad722ab519438a2a729
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }} 
+  host:
+    - htslib
+    - ncurses
+    - zlib
+  run:
+    - htslib
+    - ncurses
+    - zlib
+
+about:
+  home: https://github.com/samtools/samtools
+  license: MIT
+  license_file: LICENSE
+  summary: Tools for dealing with SAM, BAM and CRAM files
+
+test:
+  commands:
+    - samtools --help
+    # test if https protocol works, if it doesnt samtools will fail with "Protocol not supported"
+    - samtools view 'https://example.com' 2>&1 | grep 'fail to read the header' -q
+
+extra:
+  identifiers:
+    - biotools:samtools
+    - usegalaxy-eu:samtools_flagstat

From 3d3d06f2bfde7099ef58cc762d06ccb6e8eb82db Mon Sep 17 00:00:00 2001
From: Pablo <pablo.aledo@seqera.io>
Date: Mon, 17 Jul 2023 12:39:11 +0200
Subject: [PATCH 2/2] build samtools [ci build]

Signed-off-by: Pablo <pablo.aledo@seqera.io>
---
 recipes/samtools/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml
index 75b47f9..64ba152 100644
--- a/recipes/samtools/meta.yaml
+++ b/recipes/samtools/meta.yaml
@@ -40,3 +40,4 @@ extra:
   identifiers:
     - biotools:samtools
     - usegalaxy-eu:samtools_flagstat
+