From 448f0ab05440c4904a64cf5b83d9f340f349f54c Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 5 Aug 2024 06:52:05 +0000
Subject: [PATCH] {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml          |  1 +
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml          |  1 +
 eb_hooks.py                                           | 11 +++++++++++
 3 files changed, 13 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
index 7a04eaa9d3..27a79d8c80 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - BLAST+-2.14.0-gompi-2022b.eb
+  - BioPerl-1.7.8-GCCcore-12.2.0.eb 
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 90dda5236b..e60cd83909 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -30,3 +30,4 @@ easyconfigs:
   - librosa-0.10.1-foss-2023a.eb
   - xarray-2023.9.0-gfbf-2023a.eb
   - SciTools-Iris-3.9.0-foss-2023a.eb
+  - BioPerl-1.7.8-GCCcore-12.3.0.eb
diff --git a/eb_hooks.py b/eb_hooks.py
index 7f7e4e57bd..eafcb5b417 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -647,6 +647,16 @@ def post_sanitycheck_hook(self, *args, **kwargs):
         POST_SANITYCHECK_HOOKS[self.name](self, *args, **kwargs)
 
 
+def post_sanitycheck_bioperl(self, *args, **kwargs):
+    """
+    Allow the copy of easyblock perlmodule.py to /tmp/eb... after sanity check by changing directory permissions 
+    """
+    if self.name == 'BioPerl':
+        print_msg("Adding user write permission for EasyBuild directories under /tmp/eb*...")
+        bioperlcmd = "chmod u+w -R /tmp/eb*"
+        run_cmd(bioperlcmd)
+
+
 def post_sanitycheck_cuda(self, *args, **kwargs):
     """
     Remove files from CUDA installation that we are not allowed to ship,
@@ -791,5 +801,6 @@ def inject_gpu_property(ec):
 }
 
 POST_SANITYCHECK_HOOKS = {
+    'BioPerl': post_sanitycheck_bioperl,
     'CUDA': post_sanitycheck_cuda,
 }