From b605cd0151406b03ab47472a21af65044cc32f75 Mon Sep 17 00:00:00 2001
From: snehring <7978778+snehring@users.noreply.github.com>
Date: Mon, 8 May 2023 10:32:05 -0500
Subject: trinity: adding version 2.15.1 (#37076)

---
 var/spack/repos/builtin/packages/trinity/2.15.1.patch | 11 +++++++++++
 var/spack/repos/builtin/packages/trinity/package.py   |  7 +++++++
 2 files changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/trinity/2.15.1.patch

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/trinity/2.15.1.patch b/var/spack/repos/builtin/packages/trinity/2.15.1.patch
new file mode 100644
index 0000000000..b93de86c90
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trinity/2.15.1.patch
@@ -0,0 +1,11 @@
+--- a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp      2023-02-05 18:46:28.000000000 +0000
++++ b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp      2023-04-20 22:25:49.785300259 +0000
+@@ -2,7 +2,7 @@
+ #include <stdio.h>
+ // #include <unistd.h>
+ #include <stdlib.h>
+-#include <string.h>
++#include <string>
+ #include <cstring>
+ #include <getopt.h>
+ #include <stdint.h>
diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py
index 1c2bf6f03c..a74fcc774a 100644
--- a/var/spack/repos/builtin/packages/trinity/package.py
+++ b/var/spack/repos/builtin/packages/trinity/package.py
@@ -22,6 +22,11 @@ class Trinity(MakefilePackage):
     homepage = "https://trinityrnaseq.github.io/"
     url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz"
 
+    version(
+        "2.15.1.FULL",
+        sha256="ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580",
+        url="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.15.1/trinityrnaseq-v2.15.1.FULL.tar.gz",
+    )
     version(
         "2.15.0.FULL",
         sha256="d67de43e535e1173be75de98dcfbdab0bf67f814c9e465a44dfd056cefeb529d",
@@ -87,6 +92,8 @@ class Trinity(MakefilePackage):
     depends_on("r-argparse", type="run")
     depends_on("r-sm", type="run")
 
+    patch("2.15.1.patch", when="@2.15.1.FULL")
+
     def build(self, spec, prefix):
         make()
         make("trinity_essentials")
-- 
cgit v1.2.3-70-g09d2