From ed76ecc2c2941cca000677342282aac07d2170e3 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 27 Feb 2024 19:09:52 +0000
Subject: [PATCH 1/2] {2023.06}[GCC/12.3.0] Tools

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml    | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 9758969c1c..e0111ce479 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -41,3 +41,6 @@ easyconfigs:
       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19646
       options:
         from-pr: 19646
+  - SAMtools-1.18-GCC-12.3.0.eb
+  - VCFtools-0.1.16-GCC-12.3.0.eb
+  - BEDTools-2.31.0-GCC-12.3.0.eb

From a7e0560df6f301983b04c6c3fbd8bdeaf8d1bb07 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Wed, 28 Feb 2024 07:29:23 +0000
Subject: [PATCH 2/2] {2023.06}[GCC/12.3.0] Tools

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml        |  1 +
 eb_hooks.py                                         | 13 +++++++++++++
 2 files changed, 14 insertions(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index e0111ce479..1db0363415 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -41,6 +41,7 @@ easyconfigs:
       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19646
       options:
         from-pr: 19646
+  - dask-2023.9.2-foss-2023a.eb
   - SAMtools-1.18-GCC-12.3.0.eb
   - VCFtools-0.1.16-GCC-12.3.0.eb
   - BEDTools-2.31.0-GCC-12.3.0.eb
diff --git a/eb_hooks.py b/eb_hooks.py
index 1e7501a194..585b70a899 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -209,6 +209,18 @@ def parse_hook_openblas_relax_lapack_tests_num_errors(ec, eprefix):
         raise EasyBuildError("OpenBLAS-specific hook triggered for non-OpenBLAS easyconfig?!")
 
 
+def parse_hook_Pillow_SIMD_harcoded_paths(ec, eprefix):
+    # patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template
+    # (which will be empty if EasyBuild is not configured to use an alternate sysroot);
+    # see also https://gitlab.com/eessi/support/-/issues/9
+    if ec.name == 'Pillow-SIMD':
+        ec.update('preinstallopts', """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """)
+        ec.update('preinstallopts', """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """)
+        print_msg("Using custom configure options for %s: %s", ec.name, ec['preinstallopts'])
+    else:
+        raise EasyBuildError("Pillow-SIMD-specific hook triggered for non-Pillow-SIMD easyconfig?!")
+
+
 def parse_hook_pybind11_replace_catch2(ec, eprefix):
     """
     Replace Catch2 build dependency in pybind11 easyconfigs with one that doesn't use system toolchain.
@@ -578,6 +590,7 @@ def inject_gpu_property(ec):
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
+    'Pillow-SIMD' : parse_hook_Pillow_SIMD_harcoded_paths,
     'pybind11': parse_hook_pybind11_replace_catch2,
     'Qt5': parse_hook_qt5_check_qtwebengine_disable,
     'UCX': parse_hook_ucx_eprefix,