From a74669585a742ca83e9b976d7f6854a20570460f Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 5 Jul 2024 12:24:01 +0000
Subject: [PATCH 1/3] {2023.06}[GCCcore/12.3.0-GCC/12.3.0-gompi/2023a]
 bio-packages

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml      | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

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 ade226c217..7fc42e2e34 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
@@ -1,2 +1,17 @@
 easyconfigs:
   - BCFtools-1.18-GCC-12.3.0.eb
+  - BWA-0.7.18-GCCcore-12.3.0.eb
+  - CapnProto-1.0.1-GCCcore-12.3.0.eb
+  - DendroPy-4.6.1-GCCcore-12.3.0.eb
+  - DIAMOND-2.1.8-GCC-12.3.0.eb
+  - FastME-2.1.6.3-GCC-12.3.0.eb
+  - fastp-0.23.4-GCC-12.3.0.eb
+  - HMMER-3.4-gompi-2023a.eb
+  - IQ-TREE-2.3.5-gompi-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20955
+        from-commit: 185f88b9a03d65a7fb74edc7acb4221e87e90784      
+  - KronaTools-2.8.1-GCCcore-12.3.0.eb
+  - LSD2-2.4.1-GCCcore-12.3.0.eb
+  - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
+  - ncbi-vdb-3.0.10-gompi-2023a.e

From 4d9390ef015f03abe54ca3f61cd84ca6b1164c07 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Fri, 5 Jul 2024 14:30:32 +0200
Subject: [PATCH 2/3] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 7fc42e2e34..34ec3257e8 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
@@ -14,4 +14,4 @@ easyconfigs:
   - KronaTools-2.8.1-GCCcore-12.3.0.eb
   - LSD2-2.4.1-GCCcore-12.3.0.eb
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
-  - ncbi-vdb-3.0.10-gompi-2023a.e
+  - ncbi-vdb-3.0.10-gompi-2023a.eb

From 49cbcc8de452e9cc51a3969b860932caf109a9bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 22:02:31 +0200
Subject: [PATCH 3/3] implement changes from
 https://github.com/EESSI/software-layer/pull/635 and
 https://github.com/EESSI/software-layer/pull/636

---
 create_tarball.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 0a7669f73f..2dee665060 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -26,7 +26,8 @@ if [ ! -d ${software_dir} ]; then
     exit 2
 fi
 
-overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
+cvmfs_repo_name=${cvmfs_repo#/cvmfs/}
+overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo_name}/overlay-upper"
 
 software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then