From fc1f7968f61cfb461942137696a38341af6bf5c1 Mon Sep 17 00:00:00 2001
From: James Reynolds <magnusviri@users.noreply.github.com>
Date: Wed, 30 Aug 2023 09:48:29 -0600
Subject: [PATCH] +htslib.org (#3163)

* +htslib.org

* Needs bzip2

* bz2 and lzma as rundeps

* zlib

* libcurl

---------

Co-authored-by: James Reynolds <magnsuviri@me.com>
Co-authored-by: Jacob Heider <jacob@tea.xyz>
---
 projects/htslib.org/package.yml | 36 +++++++++++++++++++++++++++++++++
 projects/htslib.org/test.sam    |  3 +++
 2 files changed, 39 insertions(+)
 create mode 100644 projects/htslib.org/package.yml
 create mode 100644 projects/htslib.org/test.sam

diff --git a/projects/htslib.org/package.yml b/projects/htslib.org/package.yml
new file mode 100644
index 00000000..523cdb1f
--- /dev/null
+++ b/projects/htslib.org/package.yml
@@ -0,0 +1,36 @@
+distributable:
+  url: https://github.com/samtools/htslib/releases/download/{{version.raw}}/htslib-{{version.raw}}.tar.bz2
+  strip-components: 1
+
+versions:
+  github: samtools/htslib
+
+dependencies:
+  sourceware.org/bzip2: '*'
+  tukaani.org/xz: '*'
+  zlib.net: ^1
+  curl.se: '>=5'
+
+build:
+  dependencies:
+    tea.xyz/gx/cc: '*'
+    gnu.org/make: '*'
+    gnu.org/autoconf: '*'
+    gnu.org/automake: ^1
+  script:
+    - autoreconf -i
+    - ./configure $ARGS
+    - make --jobs {{ hw.concurrency }} install
+  env:
+    ARGS:
+      - --prefix="{{prefix}}"
+
+provides:
+  - bin/bgzip
+  - bin/htsfile
+  - bin/tabix
+
+test: |
+  htsfile test.sam
+  bgzip -c test.sam > sam.gz
+  tabix -p sam sam.gz
diff --git a/projects/htslib.org/test.sam b/projects/htslib.org/test.sam
new file mode 100644
index 00000000..21c55631
--- /dev/null
+++ b/projects/htslib.org/test.sam
@@ -0,0 +1,3 @@
+@SQ	SN:chr1	LN:500
+r1	0	chr1	100	0	4M	*	0	0	ATGC	ABCD
+r2	0	chr1	200	0	4M	*	0	0	AATT	EFGH
\ No newline at end of file